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Gowda SA, Bourland FM, Kaur B, Jones DC, Kuraparthy V. Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.). Theor Appl Genet 2023; 136:230. [PMID: 37875695 DOI: 10.1007/s00122-023-04477-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
KEY MESSAGE Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton. Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of Gossypium hirsutum L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (FST) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest FST values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including Transcription factor Vascular Plant One-Zinc Finger 1 (VOZ1) and Protein Photoperiod-Independent Early Flowering 1 (PIE1) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.
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Affiliation(s)
- S Anjan Gowda
- Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Fred M Bourland
- NE Research and Extension Center, Crop, Soil, and Environmental Sciences, University of Arkansas, Keiser, AR, 72351, USA
| | - Baljinder Kaur
- Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Don C Jones
- Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA
| | - Vasu Kuraparthy
- Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA.
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Andriamirado M, Balantekin AB, Bass CD, Bergeron DE, Bernard EP, Bowden NS, Bryan CD, Carr R, Classen T, Conant AJ, Deichert G, Delgado A, Diwan MV, Dolinski MJ, Erickson A, Foust BT, Gaison JK, Galindo-Uribari A, Gilbert CE, Gokhale S, Grant C, Hans S, Hansell AB, Heeger KM, Heffron B, Jaffe DE, Jayakumar S, Ji X, Jones DC, Koblanski J, Kunkle P, Kyzylova O, LaBelle D, Lane CE, Langford TJ, LaRosa J, Littlejohn BR, Lu X, Maricic J, Mendenhall MP, Meyer AM, Milincic R, Mueller PE, Mumm HP, Napolitano J, Neilson R, Nikkel JA, Nour S, Palomino Gallo JL, Pushin DA, Qian X, Roca C, Rosero R, Searles M, Surukuchi PT, Sutanto F, Tyra MA, Venegas-Vargas D, Weatherly PB, Wilhelmi J, Woolverton A, Yeh M, Zhang C, Zhang X. Final Measurement of the ^{235}U Antineutrino Energy Spectrum with the PROSPECT-I Detector at HFIR. Phys Rev Lett 2023; 131:021802. [PMID: 37505961 DOI: 10.1103/physrevlett.131.021802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/14/2023] [Accepted: 05/11/2023] [Indexed: 07/30/2023]
Abstract
This Letter reports one of the most precise measurements to date of the antineutrino spectrum from a purely ^{235}U-fueled reactor, made with the final dataset from the PROSPECT-I detector at the High Flux Isotope Reactor. By extracting information from previously unused detector segments, this analysis effectively doubles the statistics of the previous PROSPECT measurement. The reconstructed energy spectrum is unfolded into antineutrino energy and compared with both the Huber-Mueller model and a spectrum from a commercial reactor burning multiple fuel isotopes. A local excess over the model is observed in the 5-7 MeV energy region. Comparison of the PROSPECT results with those from commercial reactors provides new constraints on the origin of this excess, disfavoring at 2.0 and 3.7 standard deviations the hypotheses that antineutrinos from ^{235}U are solely responsible and noncontributors to the excess observed at commercial reactors, respectively.
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Affiliation(s)
- M Andriamirado
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - A B Balantekin
- Department of Physics, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - C D Bass
- Department of Physics, Le Moyne College, Syracuse, New York 13214, USA
| | - D E Bergeron
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - E P Bernard
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - N S Bowden
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - C D Bryan
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - R Carr
- Department of Physics, United States Naval Academy, Annapolis, Maryland 21402, USA
| | - T Classen
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - A J Conant
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - G Deichert
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - A Delgado
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M V Diwan
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - M J Dolinski
- Department of Physics, Drexel University, Philadelphia PA 19104-2875, Pennsylvania, USA
| | - A Erickson
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - B T Foust
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - J K Gaison
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - A Galindo-Uribari
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - C E Gilbert
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - S Gokhale
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C Grant
- Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| | - S Hans
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - A B Hansell
- Department of Physics, Susquehanna University, Selinsgrove, Pennsylvania 17870, USA
| | - K M Heeger
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - B Heffron
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - S Jayakumar
- Department of Physics, Drexel University, Philadelphia PA 19104-2875, Pennsylvania, USA
| | - X Ji
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - D C Jones
- Department of Physics (035-08), Temple University, 1925 N 12th Street, Philadelphia, Pennsylvania 19122-1801, USA
| | - J Koblanski
- Department of Physics and Astronomy, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - P Kunkle
- Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| | - O Kyzylova
- Department of Physics, Drexel University, Philadelphia PA 19104-2875, Pennsylvania, USA
| | - D LaBelle
- Department of Physics, Drexel University, Philadelphia PA 19104-2875, Pennsylvania, USA
| | - C E Lane
- Department of Physics, Drexel University, Philadelphia PA 19104-2875, Pennsylvania, USA
| | - T J Langford
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - J LaRosa
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - B R Littlejohn
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - X Lu
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - J Maricic
- Department of Physics and Astronomy, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - M P Mendenhall
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - A M Meyer
- Department of Physics and Astronomy, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - R Milincic
- Department of Physics and Astronomy, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - P E Mueller
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - H P Mumm
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - J Napolitano
- Department of Physics (035-08), Temple University, 1925 N 12th Street, Philadelphia, Pennsylvania 19122-1801, USA
| | - R Neilson
- Department of Physics, Drexel University, Philadelphia PA 19104-2875, Pennsylvania, USA
| | - J A Nikkel
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - S Nour
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - J L Palomino Gallo
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - D A Pushin
- Institute for Quantum Computing and Department of Physics, University of Waterloo, Waterloo, ON N2L 3G1 Ontario, Canada
| | - X Qian
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C Roca
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - R Rosero
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - M Searles
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - P T Surukuchi
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - F Sutanto
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - M A Tyra
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - D Venegas-Vargas
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - P B Weatherly
- Department of Physics, Drexel University, Philadelphia PA 19104-2875, Pennsylvania, USA
| | - J Wilhelmi
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - A Woolverton
- Institute for Quantum Computing and Department of Physics, University of Waterloo, Waterloo, ON N2L 3G1 Ontario, Canada
| | - M Yeh
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C Zhang
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - X Zhang
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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Fang DD, Thyssen GN, Wang M, Jenkins JN, McCarty JC, Jones DC. Genomic confirmation of Gossypium barbadense introgression into G. hirsutum and a subsequent MAGIC population. Mol Genet Genomics 2023; 298:143-152. [PMID: 36346467 DOI: 10.1007/s00438-022-01974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
Introgression of superior fiber traits from Pima cotton (Gossypium barbadense, GB) into high yield Upland cotton (G. hirsutum) has been a breeding objective for many years in a few breeding programs in the world. However, progress has been very slow due to introgression barriers resulting from whole genome hybridization between the two species. To minimize such barriers, chromosome substitution lines (CS-B) from Pima cotton 3-79 in an Upland cotton cultivar TM-1 were developed. A multiparent advanced generation inter-cross (MAGIC) population consisting of 180 recombinant inbred lines (RILs) was subsequently made using the 18 CS-B lines and three Upland cotton cultivars as parents. In this research, we sequenced the whole genomes of the 21 parents and 180 RILs to examine the G. barbadense introgression. Of the 18 CS-B lines, 11 contained the target GB chromosome or chromosome segment, two contained more than two GB chromosomes, and five did not have the expected introgression. Residual introgression in non-target chromosomes was prevalent in all CS-B lines. A clear structure existed in the MAGIC population and the 180 RILs were distributed into three groups, i.e., high, moderate, and low GB introgression. Large blocks of GB chromosome introgression were still present in some RILs after five cycles of random-mating, an indication of recombination suppression or other unknown reasons present in the population. Identity by descent analysis revealed that the MAGIC RILs contained less introgression than expected. This research presents an insight on understanding the complex problems of introgression between cotton species.
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Affiliation(s)
- David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA.
| | - Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Johnie N Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Jack C McCarty
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
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4
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Adhikari D, Albataineh H, Androic D, Aniol KA, Armstrong DS, Averett T, Ayerbe Gayoso C, Barcus SK, Bellini V, Beminiwattha RS, Benesch JF, Bhatt H, Bhatta Pathak D, Bhetuwal D, Blaikie B, Boyd J, Campagna Q, Camsonne A, Cates GD, Chen Y, Clarke C, Cornejo JC, Covrig Dusa S, Dalton MM, Datta P, Deshpande A, Dutta D, Feldman C, Fuchey E, Gal C, Gaskell D, Gautam T, Gericke M, Ghosh C, Halilovic I, Hansen JO, Hassan O, Hauenstein F, Henry W, Horowitz CJ, Jantzi C, Jian S, Johnston S, Jones DC, Kakkar S, Katugampola S, Keppel C, King PM, King DE, Kumar KS, Kutz T, Lashley-Colthirst N, Leverick G, Liu H, Liyanage N, Mammei J, Mammei R, McCaughan M, McNulty D, Meekins D, Metts C, Michaels R, Mihovilovic M, Mondal MM, Napolitano J, Narayan A, Nikolaev D, Owen V, Palatchi C, Pan J, Pandey B, Park S, Paschke KD, Petrusky M, Pitt ML, Premathilake S, Quinn B, Radloff R, Rahman S, Rashad MNH, Rathnayake A, Reed BT, Reimer PE, Richards R, Riordan S, Roblin YR, Seeds S, Shahinyan A, Souder P, Thiel M, Tian Y, Urciuoli GM, Wertz EW, Wojtsekhowski B, Yale B, Ye T, Yoon A, Xiong W, Zec A, Zhang W, Zhang J, Zheng X. Precision Determination of the Neutral Weak Form Factor of ^{48}Ca. Phys Rev Lett 2022; 129:042501. [PMID: 35939025 DOI: 10.1103/physrevlett.129.042501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
We report a precise measurement of the parity-violating (PV) asymmetry A_{PV} in the elastic scattering of longitudinally polarized electrons from ^{48}Ca. We measure A_{PV}=2668±106(stat)±40(syst) parts per billion, leading to an extraction of the neutral weak form factor F_{W}(q=0.8733 fm^{-1})=0.1304±0.0052(stat)±0.0020(syst) and the charge minus the weak form factor F_{ch}-F_{W}=0.0277±0.0055. The resulting neutron skin thickness R_{n}-R_{p}=0.121±0.026(exp)±0.024(model) fm is relatively thin yet consistent with many model calculations. The combined CREX and PREX results will have implications for future energy density functional calculations and on the density dependence of the symmetry energy of nuclear matter.
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Affiliation(s)
- D Adhikari
- Idaho State University, Pocatello, Idaho 83209, USA
| | - H Albataineh
- Texas A & M University-Kingsville, Kingsville, Texas 78363, USA
| | - D Androic
- University of Zagreb, Faculty of Science, Zagreb, HR 10002, Croatia
| | - K A Aniol
- California State University, Los Angeles, Los Angeles, California 90032, USA
| | | | - T Averett
- William and Mary, Williamsburg, Virginia 23185, USA
| | | | - S K Barcus
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - V Bellini
- Istituto Nazionale di Fisica Nucleare, Sezione di Catania, 95123 Catania, Italy
| | | | - J F Benesch
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - H Bhatt
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | | | - D Bhetuwal
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - B Blaikie
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Boyd
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - Q Campagna
- William and Mary, Williamsburg, Virginia 23185, USA
| | - A Camsonne
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - G D Cates
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - Y Chen
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - C Clarke
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - J C Cornejo
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - S Covrig Dusa
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M M Dalton
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P Datta
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - A Deshpande
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - D Dutta
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - C Feldman
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook, New York 11794, USA
| | - E Fuchey
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - C Gal
- Mississippi State University, Mississippi State, Mississippi 39762, USA
- University of Virginia, Charlottesville, Virginia 22904, USA
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
| | - D Gaskell
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - T Gautam
- Hampton University, Hampton, Virginia 23668, USA
| | - M Gericke
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - C Ghosh
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - I Halilovic
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J-O Hansen
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - O Hassan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - F Hauenstein
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - W Henry
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - C J Horowitz
- Indiana University, Bloomington, Indiana 47405, USA
| | - C Jantzi
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - S Jian
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - S Johnston
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - D C Jones
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - S Kakkar
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - S Katugampola
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - C Keppel
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P M King
- Ohio University, Athens, Ohio 45701, USA
| | - D E King
- Temple University, Philadelphia, Pennsylvania 19122, USA
- Syracuse University, Syracuse, New York 13244, USA
| | - K S Kumar
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - T Kutz
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | | | - G Leverick
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - H Liu
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - N Liyanage
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - J Mammei
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - R Mammei
- University of Winnipeg, Winnipeg, Manitoba R3B2E9, Canada
| | - M McCaughan
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - D McNulty
- Idaho State University, Pocatello, Idaho 83209, USA
| | - D Meekins
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - C Metts
- William and Mary, Williamsburg, Virginia 23185, USA
| | - R Michaels
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M Mihovilovic
- Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - M M Mondal
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
| | - J Napolitano
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - A Narayan
- Veer Kunwar Singh University, Ara, Bihar 802301, India
| | - D Nikolaev
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - V Owen
- William and Mary, Williamsburg, Virginia 23185, USA
| | - C Palatchi
- University of Virginia, Charlottesville, Virginia 22904, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
| | - J Pan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - B Pandey
- Hampton University, Hampton, Virginia 23668, USA
| | - S Park
- Mississippi State University, Mississippi State, Mississippi 39762, USA
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - K D Paschke
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - M Petrusky
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - M L Pitt
- Virginia Tech, Blacksburg, Virginia 24061, USA
| | - S Premathilake
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - B Quinn
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - R Radloff
- Ohio University, Athens, Ohio 45701, USA
| | - S Rahman
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - M N H Rashad
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - A Rathnayake
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - B T Reed
- Indiana University, Bloomington, Indiana 47405, USA
| | - P E Reimer
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - R Richards
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - S Riordan
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Y R Roblin
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Seeds
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - A Shahinyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - P Souder
- Syracuse University, Syracuse, New York 13244, USA
| | - M Thiel
- Institut für Kernphysik, Johannes Gutenberg-Universität, Mainz 55122, Germany
| | - Y Tian
- Syracuse University, Syracuse, New York 13244, USA
| | | | - E W Wertz
- William and Mary, Williamsburg, Virginia 23185, USA
| | - B Wojtsekhowski
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - B Yale
- William and Mary, Williamsburg, Virginia 23185, USA
| | - T Ye
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - A Yoon
- Christopher Newport University, Newport News, Virginia 23606, USA
| | - W Xiong
- Syracuse University, Syracuse, New York 13244, USA
- Shandong University, Qingdao, Shandong 266237, China
| | - A Zec
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - W Zhang
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - J Zhang
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
- Shandong University, Qingdao, Shandong 266237, China
| | - X Zheng
- University of Virginia, Charlottesville, Virginia 22904, USA
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5
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Restrepo-Montoya D, Hulse-Kemp AM, Scheffler JA, Haigler CH, Hinze LL, Love J, Percy RG, Jones DC, Frelichowski J. Leveraging National Germplasm Collections to Determine Significantly Associated Categorical Traits in Crops: Upland and Pima Cotton as a Case Study. Front Plant Sci 2022; 13:837038. [PMID: 35557715 PMCID: PMC9087864 DOI: 10.3389/fpls.2022.837038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
Observable qualitative traits are relatively stable across environments and are commonly used to evaluate crop genetic diversity. Recently, molecular markers have largely superseded describing phenotypes in diversity surveys. However, qualitative descriptors are useful in cataloging germplasm collections and for describing new germplasm in patents, publications, and/or the Plant Variety Protection (PVP) system. This research focused on the comparative analysis of standardized cotton traits as represented within the National Cotton Germplasm Collection (NCGC). The cotton traits are named by 'descriptors' that have non-numerical sub-categories (descriptor states) reflecting the details of how each trait manifests or is absent in the plant. We statistically assessed selected accessions from three major groups of Gossypium as defined by the NCGC curator: (1) "Stoneville accessions (SA)," containing mainly Upland cotton (Gossypium hirsutum) cultivars; (2) "Texas accessions (TEX)," containing mainly G. hirsutum landraces; and (3) Gossypium barbadense (Gb), containing cultivars or landraces of Pima cotton (Gossypium barbadense). For 33 cotton descriptors we: (a) revealed distributions of character states for each descriptor within each group; (b) analyzed bivariate associations between paired descriptors; and (c) clustered accessions based on their descriptors. The fewest significant associations between descriptors occurred in the SA dataset, likely reflecting extensive breeding for cultivar development. In contrast, the TEX and Gb datasets showed a higher number of significant associations between descriptors, likely correlating with less impact from breeding efforts. Three significant bivariate associations were identified for all three groups, bract nectaries:boll nectaries, leaf hair:stem hair, and lint color:seed fuzz color. Unsupervised clustering analysis recapitulated the species labels for about 97% of the accessions. Unexpected clustering results indicated accessions that may benefit from potential further investigation. In the future, the significant associations between standardized descriptors can be used by curators to determine whether new exotic/unusual accessions most closely resemble Upland or Pima cotton. In addition, the study shows how existing descriptors for large germplasm datasets can be useful to inform downstream goals in breeding and research, such as identifying rare individuals with specific trait combinations and targeting breakdown of remaining trait associations through breeding, thus demonstrating the utility of the analytical methods employed in categorizing germplasm diversity within the collection.
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Affiliation(s)
- Daniel Restrepo-Montoya
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Amanda M. Hulse-Kemp
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Raleigh, NC, United States
| | - Jodi A. Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Stoneville, MS, United States
| | - Candace H. Haigler
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Lori L. Hinze
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | - Janna Love
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | - Richard G. Percy
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | | | - James Frelichowski
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
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6
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Patel JD, Khanal S, Chandnani R, Adhikari J, Brown N, Chee PW, Jones DC, Paterson AH. Improved Upland Cotton Germplasm for Multiple Fiber Traits Mediated by Transferring and Pyramiding Novel Alleles From Ethyl Methanesulfonate-Generated Mutant Lines Into Elite Genotypes. Front Plant Sci 2022; 13:842741. [PMID: 35498694 PMCID: PMC9044065 DOI: 10.3389/fpls.2022.842741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Ethyl methanesulfonate (EMS) mutagenesis offers important advantages for improving crops, such as cotton, with limited diversity in elite gene pools. EMS-induced point mutations are less frequently associated with deleterious traits than alleles from wild or exotic germplasm. From 157 mutant lines that have significantly improved fiber properties, we focused on nine mutant lines here. A total of eight populations were developed by crossing mutant lines in different combinations into GA230 (GA2004230) background. Multiple lines in each population were significantly improved for the fiber trait that distinguished the donor parent(s), demonstrating that an elite breeding line (GA230) could be improved for fiber qualities using the mutant lines. Genotypes improved for multiple fiber traits of interest suggesting that allele pyramiding is possible. Compared to midparent values, individual progeny in the population conferred fiber quality improvements of as much as 31.7% (in population O) for micronaire (MIC), 16.1% (in population P) for length, 22.4% (in population K) for strength, 4.1% (in population Q) for uniformity, 45.8% (in population N) for elongation, and 13.9% (in population O) for lint percentage (lint%). While further testing for stability of the phenotype and estimation of yield potential is necessary, mutation breeding shows promise as an approach to reduce the problem of the genetic bottleneck of upland cotton. The populations developed here may also contribute to identifying candidate genes and causal mutations for fiber quality improvement.
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Affiliation(s)
- Jinesh D. Patel
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Sameer Khanal
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Rahul Chandnani
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
| | - Nino Brown
- Department of Crop and Soil Sciences, The University of Georgia, Tifton, GA, United States
- NESPAL Molecular Cotton Breeding Laboratory, The University of Georgia, Tifton, GA, United States
| | - Peng W. Chee
- Department of Crop and Soil Sciences, The University of Georgia, Tifton, GA, United States
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC, United States
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, United States
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7
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Adhikari D, Albataineh H, Androic D, Aniol K, Armstrong DS, Averett T, Ayerbe Gayoso C, Barcus S, Bellini V, Beminiwattha RS, Benesch JF, Bhatt H, Bhatta Pathak D, Bhetuwal D, Blaikie B, Boyd J, Campagna Q, Camsonne A, Cates GD, Chen Y, Clarke C, Cornejo JC, Covrig Dusa S, Dalton MM, Datta P, Deshpande A, Dutta D, Feldman C, Fuchey E, Gal C, Gaskell D, Gautam T, Gericke M, Ghosh C, Halilovic I, Hansen JO, Hauenstein F, Henry W, Horowitz CJ, Jantzi C, Jian S, Johnston S, Jones DC, Karki B, Kakkar S, Katugampola S, Keppel CE, King PM, King DE, Knauss M, Kumar KS, Kutz T, Lashley-Colthirst N, Leverick G, Liu H, Liyange N, Malace S, Mammei J, Mammei R, McCaughan M, McNulty D, Meekins D, Metts C, Michaels R, Mihovilovic M, Mondal MM, Napolitano J, Nikolaev D, Rashad MNH, Owen V, Palatchi C, Pan J, Pandey B, Park S, Paschke KD, Petrusky M, Pitt ML, Premathilake S, Puckett AJR, Quinn B, Radloff R, Rahman S, Rathnayake A, Reed BT, Reimer PE, Richards R, Riordan S, Roblin Y, Seeds S, Shahinyan A, Souder PA, Tang L, Thiel M, Tian Y, Urciuoli GM, Wertz EW, Wojtsekhowski B, Xiong W, Yale B, Ye T, Zec A, Zhang W, Zhang J, Zheng X. New Measurements of the Beam-Normal Single Spin Asymmetry in Elastic Electron Scattering over a Range of Spin-0 Nuclei. Phys Rev Lett 2022; 128:142501. [PMID: 35476486 DOI: 10.1103/physrevlett.128.142501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
We report precision determinations of the beam-normal single spin asymmetries (A_{n}) in the elastic scattering of 0.95 and 2.18 GeV electrons off ^{12}C, ^{40}Ca, ^{48}Ca, and ^{208}Pb at very forward angles where the most detailed theoretical calculations have been performed. The first measurements of A_{n} for ^{40}Ca and ^{48}Ca are found to be similar to that of ^{12}C, consistent with expectations and thus demonstrating the validity of theoretical calculations for nuclei with Z≤20. We also report A_{n} for ^{208}Pb at two new momentum transfers (Q^{2}) extending the previous measurement. Our new data confirm the surprising result previously reported, with all three data points showing significant disagreement with the results from the Z≤20 nuclei. These data confirm our basic understanding of the underlying dynamics that govern A_{n} for nuclei containing ≲50 nucleons, but point to the need for further investigation to understand the unusual A_{n} behavior discovered for scattering off ^{208}Pb.
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Affiliation(s)
- D Adhikari
- Idaho State University, Pocatello, Idaho 83209, USA
| | - H Albataineh
- Texas A & M University - Kingsville, Kingsville, Texas 78363, USA
| | - D Androic
- University of Zagreb, Faculty of Science, Zagreb HR 10002, Croatia
| | - K Aniol
- California State University, Los Angeles, Los Angeles, California 90032, USA
| | | | - T Averett
- William & Mary, Williamsburg, Virginia 23185, USA
| | | | - S Barcus
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - V Bellini
- Istituto Nazionale di Fisica Nucleare, Sezione di Catania, 95123 Catania, Italy
| | | | - J F Benesch
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - H Bhatt
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | | | - D Bhetuwal
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - B Blaikie
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Boyd
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - Q Campagna
- William & Mary, Williamsburg, Virginia 23185, USA
| | - A Camsonne
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - G D Cates
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - Y Chen
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - C Clarke
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - J C Cornejo
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - S Covrig Dusa
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M M Dalton
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P Datta
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - A Deshpande
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - D Dutta
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - C Feldman
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook, New York 11794, USA
| | - E Fuchey
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - C Gal
- Mississippi State University, Mississippi State, Mississippi 39762, USA
- University of Virginia, Charlottesville, Virginia 22904, USA
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
| | - D Gaskell
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - T Gautam
- Hampton University, Hampton, Virginia 23668, USA
| | - M Gericke
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - C Ghosh
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - I Halilovic
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J-O Hansen
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - F Hauenstein
- Old Dominion University, Norfolk, Virginia 23529, USA
| | - W Henry
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - C J Horowitz
- Indiana University, Bloomington, Indiana 47405, USA
| | - C Jantzi
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - S Jian
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - S Johnston
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - D C Jones
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - B Karki
- Ohio University, Athens, Ohio 45701, USA
| | - S Kakkar
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - S Katugampola
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - C E Keppel
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P M King
- Ohio University, Athens, Ohio 45701, USA
| | - D E King
- Syracuse University, Syracuse, New York 13244, USA
| | - M Knauss
- Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA
| | - K S Kumar
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - T Kutz
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | | | - G Leverick
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - H Liu
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - N Liyange
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - S Malace
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J Mammei
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - R Mammei
- University of Winnipeg, Winnipeg, Manitoba R3B2E9, Canada
| | - M McCaughan
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - D McNulty
- Idaho State University, Pocatello, Idaho 83209, USA
| | - D Meekins
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - C Metts
- William & Mary, Williamsburg, Virginia 23185, USA
| | - R Michaels
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M Mihovilovic
- Jôzef Stefan Institute, Ljubljana 1000, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana 1000, Slovenia
| | - M M Mondal
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
| | - J Napolitano
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - D Nikolaev
- Temple University, Philadelphia, Pennsylvania 19122, USA
| | - M N H Rashad
- Old Dominion University, Norfolk, Virginia 23529, USA
| | - V Owen
- William & Mary, Williamsburg, Virginia 23185, USA
| | - C Palatchi
- University of Virginia, Charlottesville, Virginia 22904, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
| | - J Pan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - B Pandey
- Hampton University, Hampton, Virginia 23668, USA
| | - S Park
- Mississippi State University, Mississippi State, Mississippi 39762, USA
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - K D Paschke
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - M Petrusky
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - M L Pitt
- Virginia Tech, Blacksburg, Virginia 24061, USA
| | - S Premathilake
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - A J R Puckett
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - B Quinn
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - R Radloff
- Ohio University, Athens, Ohio 45701, USA
| | - S Rahman
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - A Rathnayake
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - B T Reed
- Indiana University, Bloomington, Indiana 47405, USA
| | - P E Reimer
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - R Richards
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - S Riordan
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Y Roblin
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Seeds
- University of Connecticut, Storrs, Connecticut 06269, USA
| | - A Shahinyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - P A Souder
- Syracuse University, Syracuse, New York 13244, USA
| | - L Tang
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
- Hampton University, Hampton, Virginia 23668, USA
| | - M Thiel
- Institut für Kernphysik, Johannes Gutenberg-Universität, Mainz 55099, Germany
| | - Y Tian
- Syracuse University, Syracuse, New York 13244, USA
| | | | - E W Wertz
- William & Mary, Williamsburg, Virginia 23185, USA
| | - B Wojtsekhowski
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - W Xiong
- Syracuse University, Syracuse, New York 13244, USA
| | - B Yale
- William & Mary, Williamsburg, Virginia 23185, USA
| | - T Ye
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - A Zec
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - W Zhang
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
| | - J Zhang
- Stony Brook, State University of New York, Stony Brook, New York 11794, USA
- Center for Frontiers in Nuclear Science, Stony Brook, New York 11794, USA
- Shandong University, Qingdao, Shandong 266237, China
| | - X Zheng
- University of Virginia, Charlottesville, Virginia 22904, USA
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8
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Androić D, Armstrong DS, Bartlett K, Beminiwattha RS, Benesch J, Benmokhtar F, Birchall J, Carlini RD, Cornejo JC, Covrig Dusa S, Dalton MM, Davis CA, Deconinck W, Dowd JF, Dunne JA, Dutta D, Duvall WS, Elaasar M, Falk WR, Finn JM, Forest T, Gal C, Gaskell D, Gericke MTW, Gray VM, Grimm K, Guo F, Hoskins JR, Jones DC, Jones MK, Kargiantoulakis M, King PM, Korkmaz E, Kowalski S, Leacock J, Leckey J, Lee AR, Lee JH, Lee L, MacEwan S, Mack D, Magee JA, Mahurin R, Mammei J, Martin JW, McHugh MJ, Meekins D, Mesick KE, Michaels R, Micherdzinska A, Mkrtchyan A, Mkrtchyan H, Narayan A, Ndukum LZ, Nelyubin V, van Oers WTH, Owen VF, Page SA, Pan J, Paschke KD, Phillips SK, Pitt ML, Radloff RW, Rajotte JF, Ramsay WD, Roche J, Sawatzky B, Seva T, Shabestari MH, Silwal R, Simicevic N, Smith GR, Solvignon P, Spayde DT, Subedi A, Suleiman R, Tadevosyan V, Tobias WA, Tvaskis V, Waidyawansa B, Wang P, Wells SP, Wood SA, Yang S, Zang P, Zhamkochyan S, Christy ME, Horowitz CJ, Fattoyev FJ, Lin Z. Determination of the ^{27}Al Neutron Distribution Radius from a Parity-Violating Electron Scattering Measurement. Phys Rev Lett 2022; 128:132501. [PMID: 35426696 DOI: 10.1103/physrevlett.128.132501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
We report the first measurement of the parity-violating elastic electron scattering asymmetry on ^{27}Al. The ^{27}Al elastic asymmetry is A_{PV}=2.16±0.11(stat)±0.16(syst) ppm, and was measured at ⟨Q^{2}⟩=0.02357±0.00010 GeV^{2}, ⟨θ_{lab}⟩=7.61°±0.02°, and ⟨E_{lab}⟩=1.157 GeV with the Q_{weak} apparatus at Jefferson Lab. Predictions using a simple Born approximation as well as more sophisticated distorted-wave calculations are in good agreement with this result. From this asymmetry the ^{27}Al neutron radius R_{n}=2.89±0.12 fm was determined using a many-models correlation technique. The corresponding neutron skin thickness R_{n}-R_{p}=-0.04±0.12 fm is small, as expected for a light nucleus with a neutron excess of only 1. This result thus serves as a successful benchmark for electroweak determinations of neutron radii on heavier nuclei. A tree-level approach was used to extract the ^{27}Al weak radius R_{w}=3.00±0.15 fm, and the weak skin thickness R_{wk}-R_{ch}=-0.04±0.15 fm. The weak form factor at this Q^{2} is F_{wk}=0.39±0.04.
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Affiliation(s)
- D Androić
- University of Zagreb, Zagreb, HR 10002, Croatia
| | | | - K Bartlett
- William & Mary, Williamsburg, Virginia 23185, USA
| | | | - J Benesch
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - F Benmokhtar
- Christopher Newport University, Newport News, Virginia 23606, USA
| | - J Birchall
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - R D Carlini
- William & Mary, Williamsburg, Virginia 23185, USA
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J C Cornejo
- William & Mary, Williamsburg, Virginia 23185, USA
| | - S Covrig Dusa
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M M Dalton
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - C A Davis
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - W Deconinck
- William & Mary, Williamsburg, Virginia 23185, USA
| | - J F Dowd
- William & Mary, Williamsburg, Virginia 23185, USA
| | - J A Dunne
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - D Dutta
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - W S Duvall
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - M Elaasar
- Southern University at New Orleans, New Orleans, Louisiana 70126, USA
| | - W R Falk
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J M Finn
- William & Mary, Williamsburg, Virginia 23185, USA
| | - T Forest
- Idaho State University, Pocatello, Idaho 83209, USA
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - C Gal
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - D Gaskell
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M T W Gericke
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - V M Gray
- William & Mary, Williamsburg, Virginia 23185, USA
| | - K Grimm
- William & Mary, Williamsburg, Virginia 23185, USA
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - F Guo
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - J R Hoskins
- William & Mary, Williamsburg, Virginia 23185, USA
| | - D C Jones
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - M K Jones
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | | | - P M King
- Ohio University, Athens, Ohio 45701, USA
| | - E Korkmaz
- University of Northern British Columbia, Prince George, British Columbia V2N4Z9, Canada
| | - S Kowalski
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - J Leacock
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - J Leckey
- William & Mary, Williamsburg, Virginia 23185, USA
| | - A R Lee
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - J H Lee
- William & Mary, Williamsburg, Virginia 23185, USA
- Ohio University, Athens, Ohio 45701, USA
| | - L Lee
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - S MacEwan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - D Mack
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - J A Magee
- William & Mary, Williamsburg, Virginia 23185, USA
| | - R Mahurin
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Mammei
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - J W Martin
- University of Winnipeg, Winnipeg, Manitoba R3B2E9, Canada
| | - M J McHugh
- George Washington University, Washington, DC 20052, USA
| | - D Meekins
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - K E Mesick
- George Washington University, Washington, DC 20052, USA
- Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - R Michaels
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | | | - A Mkrtchyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - H Mkrtchyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - A Narayan
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - L Z Ndukum
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - V Nelyubin
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - W T H van Oers
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - V F Owen
- William & Mary, Williamsburg, Virginia 23185, USA
| | - S A Page
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - J Pan
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - K D Paschke
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - S K Phillips
- University of New Hampshire, Durham, New Hampshire 03824, USA
| | - M L Pitt
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | | | - J F Rajotte
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - W D Ramsay
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- TRIUMF, Vancouver, British Columbia V6T2A3, Canada
| | - J Roche
- Ohio University, Athens, Ohio 45701, USA
| | - B Sawatzky
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - T Seva
- University of Zagreb, Zagreb, HR 10002, Croatia
| | - M H Shabestari
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - R Silwal
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - N Simicevic
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - G R Smith
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P Solvignon
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - D T Spayde
- Hendrix College, Conway, Arkansas 72032, USA
| | - A Subedi
- Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - R Suleiman
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - V Tadevosyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - W A Tobias
- University of Virginia, Charlottesville, Virginia 22903, USA
| | - V Tvaskis
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
- University of Winnipeg, Winnipeg, Manitoba R3B2E9, Canada
| | | | - P Wang
- University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
| | - S P Wells
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - S A Wood
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Yang
- William & Mary, Williamsburg, Virginia 23185, USA
| | - P Zang
- Syracuse University, Syracuse, New York 13244, USA
| | - S Zhamkochyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - M E Christy
- Hampton University, Hampton, Virginia 23668, USA
| | - C J Horowitz
- Indiana University, Bloomington, Indiana 47405, USA
| | - F J Fattoyev
- Indiana University, Bloomington, Indiana 47405, USA
| | - Z Lin
- Indiana University, Bloomington, Indiana 47405, USA
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9
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Parris SM, Jeffers SN, Olvey JM, Olvey JM, Adelberg JW, Wen L, Udall JA, Coleman JJ, Jones DC, Saski CA. An In Vitro Co-Culture System for Rapid Differential Response to Fusarium oxysporum f. sp. vasinfectum Race 4 in Three Cotton Cultivars. Plant Dis 2022; 106:990-995. [PMID: 34705484 DOI: 10.1094/pdis-08-21-1743-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) is a devastating fungus pathogen that causes Fusarium wilt in both domesticated cotton species, Gossypium hirsutum (Upland) and G. barbadense (Pima). Greenhouse and field-based pathogenicity assays can be a challenge because of nonuniform inoculum levels, the presence of endophytes, and varying environmental factors. Therefore, an in vitro coculture system was designed to support the growth of both domesticated cotton species and FOV4 via an inert polyphenolic foam substrate with a liquid medium. A Fusarium wilt-susceptible Pima cotton cultivar, G. barbadense 'GB1031'; a highly resistant Pima cotton cultivar, G. barbadense 'DP348RF'; and a susceptible Upland cotton cultivar, G. hirsutum 'TM-1', were evaluated for 30 days during coculture with FOV4 in this foam-based system. Thirty days after inoculation, disease symptoms were more severe in both susceptible cultivars, which displayed higher percentages of foliar damage, and greater plant mortality than observed in 'DP348RF', the resistant Pima cotton cultivar. This foam-based in vitro system may be useful for screening cotton germplasm for resistance to a variety of fungus pathogens and may facilitate the study of biotic interactions in domesticated cotton species under controlled environmental conditions.
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Affiliation(s)
- Stephen M Parris
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
| | - Steven N Jeffers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
| | | | | | - Jeffrey W Adelberg
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
| | - Li Wen
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
| | - Joshua A Udall
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | | | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
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10
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An FP, Andriamirado M, Balantekin AB, Band HR, Bass CD, Bergeron DE, Berish D, Bishai M, Blyth S, Bowden NS, Bryan CD, Cao GF, Cao J, Chang JF, Chang Y, Chen HS, Chen SM, Chen Y, Chen YX, Cheng J, Cheng ZK, Cherwinka JJ, Chu MC, Classen T, Conant AJ, Cummings JP, Dalager O, Deichert G, Delgado A, Deng FS, Ding YY, Diwan MV, Dohnal T, Dolinski MJ, Dolzhikov D, Dove J, Dvořák M, Dwyer DA, Erickson A, Foust BT, Gaison JK, Galindo-Uribarri A, Gallo JP, Gilbert CE, Gonchar M, Gong GH, Gong H, Grassi M, Gu WQ, Guo JY, Guo L, Guo XH, Guo YH, Guo Z, Hackenburg RW, Hans S, Hansell AB, He M, Heeger KM, Heffron B, Heng YK, Hor YK, Hsiung YB, Hu BZ, Hu JR, Hu T, Hu ZJ, Huang HX, Huang JH, Huang XT, Huang YB, Huber P, Koblanski J, Jaffe DE, Jayakumar S, Jen KL, Ji XL, Ji XP, Johnson RA, Jones DC, Kang L, Kettell SH, Kohn S, Kramer M, Kyzylova O, Lane CE, Langford TJ, LaRosa J, Lee J, Lee JHC, Lei RT, Leitner R, Leung JKC, Li F, Li HL, Li JJ, Li QJ, Li RH, Li S, Li SC, Li WD, Li XN, Li XQ, Li YF, Li ZB, Liang H, Lin CJ, Lin GL, Lin S, Ling JJ, Link JM, Littenberg L, Littlejohn BR, Liu JC, Liu JL, Liu JX, Lu C, Lu HQ, Lu X, Luk KB, Ma BZ, Ma XB, Ma XY, Ma YQ, Mandujano RC, Maricic J, Marshall C, McDonald KT, McKeown RD, Mendenhall MP, Meng Y, Meyer AM, Milincic R, Mueller PE, Mumm HP, Napolitano J, Naumov D, Naumova E, Neilson R, Nguyen TMT, Nikkel JA, Nour S, Ochoa-Ricoux JP, Olshevskiy A, Palomino JL, Pan HR, Park J, Patton S, Peng JC, Pun CSJ, Pushin DA, Qi FZ, Qi M, Qian X, Raper N, Ren J, Morales Reveco C, Rosero R, Roskovec B, Ruan XC, Searles M, Steiner H, Sun JL, Surukuchi PT, Tmej T, Treskov K, Tse WH, Tull CE, Tyra MA, Varner RL, Venegas-Vargas D, Viren B, Vorobel V, Wang CH, Wang J, Wang M, Wang NY, Wang RG, Wang W, Wang W, Wang X, Wang Y, Wang YF, Wang Z, Wang Z, Wang ZM, Weatherly PB, Wei HY, Wei LH, Wen LJ, Whisnant K, White C, Wilhelmi J, Wong HLH, Woolverton A, Worcester E, Wu DR, Wu FL, Wu Q, Wu WJ, Xia DM, Xie ZQ, Xing ZZ, Xu HK, Xu JL, Xu T, Xue T, Yang CG, Yang L, Yang YZ, Yao HF, Ye M, Yeh M, Young BL, Yu HZ, Yu ZY, Yue BB, Zavadskyi V, Zeng S, Zeng Y, Zhan L, Zhang C, Zhang FY, Zhang HH, Zhang JW, Zhang QM, Zhang SQ, Zhang X, Zhang XT, Zhang YM, Zhang YX, Zhang YY, Zhang ZJ, Zhang ZP, Zhang ZY, Zhao J, Zhao RZ, Zhou L, Zhuang HL, Zou JH. Joint Determination of Reactor Antineutrino Spectra from ^{235}U and ^{239}Pu Fission by Daya Bay and PROSPECT. Phys Rev Lett 2022; 128:081801. [PMID: 35275656 DOI: 10.1103/physrevlett.128.081801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/17/2021] [Accepted: 10/26/2021] [Indexed: 06/14/2023]
Abstract
A joint determination of the reactor antineutrino spectra resulting from the fission of ^{235}U and ^{239}Pu has been carried out by the Daya Bay and PROSPECT Collaborations. This Letter reports the level of consistency of ^{235}U spectrum measurements from the two experiments and presents new results from a joint analysis of both data sets. The measurements are found to be consistent. The combined analysis reduces the degeneracy between the dominant ^{235}U and ^{239}Pu isotopes and improves the uncertainty of the ^{235}U spectral shape to about 3%. The ^{235}U and ^{239}Pu antineutrino energy spectra are unfolded from the jointly deconvolved reactor spectra using the Wiener-SVD unfolding method, providing a data-based reference for other reactor antineutrino experiments and other applications. This is the first measurement of the ^{235}U and ^{239}Pu spectra based on the combination of experiments at low- and highly enriched uranium reactors.
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Affiliation(s)
- F P An
- Institute of Modern Physics, East China University of Science and Technology, Shanghai
| | - M Andriamirado
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - A B Balantekin
- Department of Physics, University of Wisconsin, Madison, Madison, Wisconsin
| | - H R Band
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut
| | - C D Bass
- Department of Physics, Le Moyne College, Syracuse, New York
| | - D E Bergeron
- National Institute of Standards and Technology, Gaithersburg, Maryland
| | - D Berish
- Department of Physics, Temple University, Philadelphia, Pennsylvania
| | - M Bishai
- Brookhaven National Laboratory, Upton, New York
| | - S Blyth
- Department of Physics, National Taiwan University, Taipei
| | - N S Bowden
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California
| | - C D Bryan
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - G F Cao
- Institute of High Energy Physics, Beijing
| | - J Cao
- Institute of High Energy Physics, Beijing
| | - J F Chang
- Institute of High Energy Physics, Beijing
| | - Y Chang
- National United University, Miao-Li
| | - H S Chen
- Institute of High Energy Physics, Beijing
| | - S M Chen
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Y Chen
- Shenzhen University, Shenzhen
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - Y X Chen
- North China Electric Power University, Beijing
| | - J Cheng
- Institute of High Energy Physics, Beijing
| | - Z K Cheng
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - J J Cherwinka
- Department of Physics, University of Wisconsin, Madison, Madison, Wisconsin
| | - M C Chu
- Chinese University of Hong Kong, Hong Kong
| | - T Classen
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California
| | - A J Conant
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | | | - O Dalager
- Department of Physics and Astronomy, University of California, Irvine, California 92697
| | - G Deichert
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - A Delgado
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - F S Deng
- University of Science and Technology of China, Hefei
| | - Y Y Ding
- Institute of High Energy Physics, Beijing
| | - M V Diwan
- Brookhaven National Laboratory, Upton, New York
| | - T Dohnal
- Charles University, Faculty of Mathematics and Physics, Prague, Czech Republic
| | - M J Dolinski
- Department of Physics, Drexel University, Philadelphia, Pennsylvania
| | - D Dolzhikov
- Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia
| | - J Dove
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - M Dvořák
- Institute of High Energy Physics, Beijing
| | - D A Dwyer
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - A Erickson
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - B T Foust
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut
| | - J K Gaison
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut
| | - A Galindo-Uribarri
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - J P Gallo
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - C E Gilbert
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - M Gonchar
- Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia
| | - G H Gong
- Department of Engineering Physics, Tsinghua University, Beijing
| | - H Gong
- Department of Engineering Physics, Tsinghua University, Beijing
| | - M Grassi
- Department of Physics and Astronomy, University of California, Irvine, California 92697
| | - W Q Gu
- Brookhaven National Laboratory, Upton, New York
| | - J Y Guo
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - L Guo
- Department of Engineering Physics, Tsinghua University, Beijing
| | - X H Guo
- Beijing Normal University, Beijing
| | - Y H Guo
- Department of Nuclear Science and Technology, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an
| | - Z Guo
- Department of Engineering Physics, Tsinghua University, Beijing
| | | | - S Hans
- Brookhaven National Laboratory, Upton, New York
| | - A B Hansell
- Department of Physics, Temple University, Philadelphia, Pennsylvania
| | - M He
- Institute of High Energy Physics, Beijing
| | - K M Heeger
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut
| | - B Heffron
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - Y K Heng
- Institute of High Energy Physics, Beijing
| | - Y K Hor
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - Y B Hsiung
- Department of Physics, National Taiwan University, Taipei
| | - B Z Hu
- Department of Physics, National Taiwan University, Taipei
| | - J R Hu
- Institute of High Energy Physics, Beijing
| | - T Hu
- Institute of High Energy Physics, Beijing
| | - Z J Hu
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - H X Huang
- China Institute of Atomic Energy, Beijing
| | - J H Huang
- Institute of High Energy Physics, Beijing
| | | | - Y B Huang
- Guangxi University, No.100 Daxue East Road, Nanning
| | - P Huber
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia 24061
| | - J Koblanski
- Department of Physics & Astronomy, University of Hawaii, Honolulu, Hawaii
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, New York
| | - S Jayakumar
- Department of Physics, Drexel University, Philadelphia, Pennsylvania
| | - K L Jen
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - X L Ji
- Institute of High Energy Physics, Beijing
| | - X P Ji
- Brookhaven National Laboratory, Upton, New York
| | - R A Johnson
- Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221
| | - D C Jones
- Department of Physics, Temple University, Philadelphia, Pennsylvania
| | - L Kang
- Dongguan University of Technology, Dongguan
| | - S H Kettell
- Brookhaven National Laboratory, Upton, New York
| | - S Kohn
- Department of Physics, University of California, Berkeley, California 94720
| | - M Kramer
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Physics, University of California, Berkeley, California 94720
| | - O Kyzylova
- Department of Physics, Drexel University, Philadelphia, Pennsylvania
| | - C E Lane
- Department of Physics, Drexel University, Philadelphia, Pennsylvania
| | - T J Langford
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut
| | - J LaRosa
- National Institute of Standards and Technology, Gaithersburg, Maryland
| | - J Lee
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - J H C Lee
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - R T Lei
- Dongguan University of Technology, Dongguan
| | - R Leitner
- Charles University, Faculty of Mathematics and Physics, Prague, Czech Republic
| | - J K C Leung
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - F Li
- Institute of High Energy Physics, Beijing
| | - H L Li
- Institute of High Energy Physics, Beijing
| | - J J Li
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Q J Li
- Institute of High Energy Physics, Beijing
| | - R H Li
- Institute of High Energy Physics, Beijing
| | - S Li
- Dongguan University of Technology, Dongguan
| | - S C Li
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia 24061
| | - W D Li
- Institute of High Energy Physics, Beijing
| | - X N Li
- Institute of High Energy Physics, Beijing
| | - X Q Li
- School of Physics, Nankai University, Tianjin
| | - Y F Li
- Institute of High Energy Physics, Beijing
| | - Z B Li
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - H Liang
- University of Science and Technology of China, Hefei
| | - C J Lin
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - G L Lin
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - S Lin
- Dongguan University of Technology, Dongguan
| | - J J Ling
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - J M Link
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia 24061
| | | | - B R Littlejohn
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - J C Liu
- Institute of High Energy Physics, Beijing
| | - J L Liu
- Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai Laboratory for Particle Physics and Cosmology, Shanghai
| | - J X Liu
- Institute of High Energy Physics, Beijing
| | - C Lu
- Joseph Henry Laboratories, Princeton University, Princeton, New Jersey 08544
| | - H Q Lu
- Institute of High Energy Physics, Beijing
| | - X Lu
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - K B Luk
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Physics, University of California, Berkeley, California 94720
| | - B Z Ma
- Shandong University, Jinan
| | - X B Ma
- North China Electric Power University, Beijing
| | - X Y Ma
- Institute of High Energy Physics, Beijing
| | - Y Q Ma
- Institute of High Energy Physics, Beijing
| | - R C Mandujano
- Department of Physics and Astronomy, University of California, Irvine, California 92697
| | - J Maricic
- Department of Physics & Astronomy, University of Hawaii, Honolulu, Hawaii
| | - C Marshall
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - K T McDonald
- Joseph Henry Laboratories, Princeton University, Princeton, New Jersey 08544
| | - R D McKeown
- California Institute of Technology, Pasadena, California 91125
- College of William and Mary, Williamsburg, Virginia 23187
| | - M P Mendenhall
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California
| | - Y Meng
- Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai Laboratory for Particle Physics and Cosmology, Shanghai
| | - A M Meyer
- Department of Physics & Astronomy, University of Hawaii, Honolulu, Hawaii
| | - R Milincic
- Department of Physics & Astronomy, University of Hawaii, Honolulu, Hawaii
| | - P E Mueller
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - H P Mumm
- National Institute of Standards and Technology, Gaithersburg, Maryland
| | - J Napolitano
- Department of Physics, Temple University, Philadelphia, Pennsylvania
| | - D Naumov
- Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia
| | - E Naumova
- Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia
| | - R Neilson
- Department of Physics, Drexel University, Philadelphia, Pennsylvania
| | - T M T Nguyen
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - J A Nikkel
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut
| | - S Nour
- National Institute of Standards and Technology, Gaithersburg, Maryland
| | - J P Ochoa-Ricoux
- Department of Physics and Astronomy, University of California, Irvine, California 92697
| | - A Olshevskiy
- Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia
| | - J L Palomino
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - H-R Pan
- Department of Physics, National Taiwan University, Taipei
| | - J Park
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia 24061
| | - S Patton
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - J C Peng
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - C S J Pun
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - D A Pushin
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario
| | - F Z Qi
- Institute of High Energy Physics, Beijing
| | - M Qi
- Nanjing University, Nanjing
| | - X Qian
- Brookhaven National Laboratory, Upton, New York
| | - N Raper
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - J Ren
- China Institute of Atomic Energy, Beijing
| | - C Morales Reveco
- Department of Physics and Astronomy, University of California, Irvine, California 92697
| | - R Rosero
- Brookhaven National Laboratory, Upton, New York
| | - B Roskovec
- Department of Physics and Astronomy, University of California, Irvine, California 92697
| | - X C Ruan
- China Institute of Atomic Energy, Beijing
| | - M Searles
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - H Steiner
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Physics, University of California, Berkeley, California 94720
| | - J L Sun
- China General Nuclear Power Group, Shenzhen
| | - P T Surukuchi
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut
| | - T Tmej
- Charles University, Faculty of Mathematics and Physics, Prague, Czech Republic
| | - K Treskov
- Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia
| | - W-H Tse
- Chinese University of Hong Kong, Hong Kong
| | - C E Tull
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - M A Tyra
- National Institute of Standards and Technology, Gaithersburg, Maryland
| | - R L Varner
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - D Venegas-Vargas
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - B Viren
- Brookhaven National Laboratory, Upton, New York
| | - V Vorobel
- Charles University, Faculty of Mathematics and Physics, Prague, Czech Republic
| | - C H Wang
- National United University, Miao-Li
| | - J Wang
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - M Wang
- Shandong University, Jinan
| | - N Y Wang
- Beijing Normal University, Beijing
| | - R G Wang
- Institute of High Energy Physics, Beijing
| | - W Wang
- Sun Yat-Sen (Zhongshan) University, Guangzhou
- College of William and Mary, Williamsburg, Virginia 23187
| | - W Wang
- Nanjing University, Nanjing
| | - X Wang
- College of Electronic Science and Engineering, National University of Defense Technology, Changsha
| | - Y Wang
- Nanjing University, Nanjing
| | - Y F Wang
- Institute of High Energy Physics, Beijing
| | - Z Wang
- Institute of High Energy Physics, Beijing
| | - Z Wang
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Z M Wang
- Institute of High Energy Physics, Beijing
| | - P B Weatherly
- Department of Physics, Drexel University, Philadelphia, Pennsylvania
| | - H Y Wei
- Brookhaven National Laboratory, Upton, New York
| | - L H Wei
- Institute of High Energy Physics, Beijing
| | - L J Wen
- Institute of High Energy Physics, Beijing
| | | | - C White
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - J Wilhelmi
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut
| | - H L H Wong
- Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Physics, University of California, Berkeley, California 94720
| | - A Woolverton
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario
| | - E Worcester
- Brookhaven National Laboratory, Upton, New York
| | - D R Wu
- Institute of High Energy Physics, Beijing
| | - F L Wu
- Nanjing University, Nanjing
| | - Q Wu
- Shandong University, Jinan
| | - W J Wu
- Institute of High Energy Physics, Beijing
| | - D M Xia
- Chongqing University, Chongqing
| | - Z Q Xie
- Institute of High Energy Physics, Beijing
| | - Z Z Xing
- Institute of High Energy Physics, Beijing
| | - H K Xu
- Institute of High Energy Physics, Beijing
| | - J L Xu
- Institute of High Energy Physics, Beijing
| | - T Xu
- Department of Engineering Physics, Tsinghua University, Beijing
| | - T Xue
- Department of Engineering Physics, Tsinghua University, Beijing
| | - C G Yang
- Institute of High Energy Physics, Beijing
| | - L Yang
- Dongguan University of Technology, Dongguan
| | - Y Z Yang
- Department of Engineering Physics, Tsinghua University, Beijing
| | - H F Yao
- Institute of High Energy Physics, Beijing
| | - M Ye
- Institute of High Energy Physics, Beijing
| | - M Yeh
- Brookhaven National Laboratory, Upton, New York
| | - B L Young
- Iowa State University, Ames, Iowa 50011
| | - H Z Yu
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - Z Y Yu
- Institute of High Energy Physics, Beijing
| | - B B Yue
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - V Zavadskyi
- Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia
| | - S Zeng
- Institute of High Energy Physics, Beijing
| | - Y Zeng
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - L Zhan
- Institute of High Energy Physics, Beijing
| | - C Zhang
- Brookhaven National Laboratory, Upton, New York
| | - F Y Zhang
- Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai Laboratory for Particle Physics and Cosmology, Shanghai
| | - H H Zhang
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - J W Zhang
- Institute of High Energy Physics, Beijing
| | - Q M Zhang
- Department of Nuclear Science and Technology, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an
| | - S Q Zhang
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - X Zhang
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California
| | - X T Zhang
- Institute of High Energy Physics, Beijing
| | - Y M Zhang
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - Y X Zhang
- China General Nuclear Power Group, Shenzhen
| | - Y Y Zhang
- Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai Laboratory for Particle Physics and Cosmology, Shanghai
| | - Z J Zhang
- Dongguan University of Technology, Dongguan
| | - Z P Zhang
- University of Science and Technology of China, Hefei
| | - Z Y Zhang
- Institute of High Energy Physics, Beijing
| | - J Zhao
- Institute of High Energy Physics, Beijing
| | - R Z Zhao
- Institute of High Energy Physics, Beijing
| | - L Zhou
- Institute of High Energy Physics, Beijing
| | - H L Zhuang
- Institute of High Energy Physics, Beijing
| | - J H Zou
- Institute of High Energy Physics, Beijing
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11
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Almazán H, Andriamirado M, Balantekin AB, Band HR, Bass CD, Bergeron DE, Bernard L, Blanchet A, Bonhomme A, Bowden NS, Bryan CD, Buck C, Classen T, Conant AJ, Deichert G, Del Amo Sanchez P, Delgado A, Diwan MV, Dolinski MJ, El Atmani I, Erickson A, Foust BT, Gaison JK, Galindo-Uribarri A, Gilbert CE, Hans S, Hansell AB, Heeger KM, Heffron B, Jaffe DE, Jayakumar S, Ji X, Jones DC, Koblanski J, Kyzylova O, Labit L, Lamblin J, Lane CE, Langford TJ, LaRosa J, Letourneau A, Lhuillier D, Licciardi M, Lindner M, Littlejohn BR, Lu X, Maricic J, Materna T, Mendenhall MP, Meyer AM, Milincic R, Mueller PE, Mumm HP, Napolitano J, Neilson R, Nikkel JA, Nour S, Palomino JL, Pessard H, Pushin DA, Qian X, Réal JS, Ricol JS, Roca C, Rogly R, Rosero R, Salagnac T, Savu V, Schoppmann S, Searles M, Sergeyeva V, Soldner T, Stutz A, Surukuchi PT, Tyra MA, Varner RL, Venegas-Vargas D, Vialat M, Weatherly PB, White C, Wilhelmi J, Woolverton A, Yeh M, Zhang C, Zhang X. Joint Measurement of the ^{235}U Antineutrino Spectrum by PROSPECT and STEREO. Phys Rev Lett 2022; 128:081802. [PMID: 35275665 DOI: 10.1103/physrevlett.128.081802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The PROSPECT and STEREO collaborations present a combined measurement of the pure ^{235}U antineutrino spectrum, without site specific corrections or detector-dependent effects. The spectral measurements of the two highest precision experiments at research reactors are found to be compatible with χ^{2}/ndf=24.1/21, allowing a joint unfolding of the prompt energy measurements into antineutrino energy. This ν[over ¯]_{e} energy spectrum is provided to the community, and an excess of events relative to the Huber model is found in the 5-6 MeV region. When a Gaussian bump is fitted to the excess, the data-model χ^{2} value is improved, corresponding to a 2.4σ significance.
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Affiliation(s)
- H Almazán
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - M Andriamirado
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - A B Balantekin
- Department of Physics, University of Wisconsin, Madison, Wisconsin, USA
| | - H R Band
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut, USA
| | - C D Bass
- Department of Physics, Le Moyne College, Syracuse, New York, USA
| | - D E Bergeron
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - L Bernard
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - A Blanchet
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - A Bonhomme
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - N S Bowden
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - C D Bryan
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - C Buck
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - T Classen
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - A J Conant
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - G Deichert
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - A Delgado
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, USA
| | - M V Diwan
- Brookhaven National Laboratory, Upton, New York, USA
| | - M J Dolinski
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA
| | - I El Atmani
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - A Erickson
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia USA
| | - B T Foust
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut, USA
| | - J K Gaison
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut, USA
| | - A Galindo-Uribarri
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, USA
| | - C E Gilbert
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, USA
| | - S Hans
- Brookhaven National Laboratory, Upton, New York, USA
| | - A B Hansell
- Department of Physics, Temple University, Philadelphia, Pennsylvania, USA
| | - K M Heeger
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut, USA
| | - B Heffron
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, USA
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, New York, USA
| | - S Jayakumar
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA
| | - X Ji
- Brookhaven National Laboratory, Upton, New York, USA
| | - D C Jones
- Department of Physics, Temple University, Philadelphia, Pennsylvania, USA
| | - J Koblanski
- Department of Physics and Astronomy, University of Hawaii, Honolulu, Hawaii, USA
| | - O Kyzylova
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA
| | - L Labit
- Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - J Lamblin
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - C E Lane
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA
| | - T J Langford
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut, USA
| | - J LaRosa
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - A Letourneau
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - D Lhuillier
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - M Licciardi
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - M Lindner
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - B R Littlejohn
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - X Lu
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, USA
| | - J Maricic
- Department of Physics and Astronomy, University of Hawaii, Honolulu, Hawaii, USA
| | - T Materna
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - M P Mendenhall
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - A M Meyer
- Department of Physics and Astronomy, University of Hawaii, Honolulu, Hawaii, USA
| | - R Milincic
- Department of Physics and Astronomy, University of Hawaii, Honolulu, Hawaii, USA
| | - P E Mueller
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - H P Mumm
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - J Napolitano
- Department of Physics, Temple University, Philadelphia, Pennsylvania, USA
| | - R Neilson
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA
| | - J A Nikkel
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut, USA
| | - S Nour
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - J L Palomino
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - H Pessard
- Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - D A Pushin
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada
| | - X Qian
- Brookhaven National Laboratory, Upton, New York, USA
| | - J-S Réal
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - J-S Ricol
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - C Roca
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - R Rogly
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - R Rosero
- Brookhaven National Laboratory, Upton, New York, USA
| | - T Salagnac
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - V Savu
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - S Schoppmann
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - M Searles
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - V Sergeyeva
- Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - T Soldner
- Institut Laue-Langevin, CS 20156, 38042 Grenoble Cedex 9, France
| | - A Stutz
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - P T Surukuchi
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut, USA
| | - M A Tyra
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - R L Varner
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - D Venegas-Vargas
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, USA
| | - M Vialat
- Institut Laue-Langevin, CS 20156, 38042 Grenoble Cedex 9, France
| | - P B Weatherly
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA
| | - C White
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - J Wilhelmi
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut, USA
| | - A Woolverton
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada
| | - M Yeh
- Brookhaven National Laboratory, Upton, New York, USA
| | - C Zhang
- Brookhaven National Laboratory, Upton, New York, USA
| | - X Zhang
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
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12
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Kim HJ, Kato N, Ndathe R, Thyssen GN, Jones DC, Ratnayaka HH. Evidence for thermosensitivity of the cotton (Gossypium hirsutum L.) immature fiber (im) mutant via hypersensitive stomatal activity. PLoS One 2021; 16:e0259562. [PMID: 34898615 PMCID: PMC8668099 DOI: 10.1371/journal.pone.0259562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Thickness of cotton fiber, referred to as fiber maturity, is a key determinant of fiber quality, lint yield, and textile performance. The cotton immature fiber (im) mutant has been used to study fiber maturity since its fiber is thinner than the wild type near isogeneic line (NIL), Texas Marker-1 (TM-1). The im phenotype is caused by a single recessive mutation of a pentatricopeptide repeat (PPR) gene that reduces the activity of mitochondrial complex I and up-regulates stress responsive genes. However, the mechanisms altering the stress responses in im mutant are not well understood. Thus, we characterized growth and gas exchange in im and TM-1 under no stress and also investigated their stress responses by comparing gas exchange and transcriptomic profiles under high temperature. Phenotypic differences were detected between the NILs in non-fiber tissues although less pronounced than the variation in fibers. At near optimum temperature (28±3°C), im maintained the same photosynthetic performance as TM-1 by means of greater stomatal conductance. In contrast, under high temperature stress (>34°C), im leaves reduced photosynthesis by decreasing the stomatal conductance disproportionately more than TM-1. Transcriptomic analyses showed that the genes involved in heat stress responses were differentially expressed between the NIL leaves. These results indicate that the im mutant previously reported to have low activity of mitochondrial complex I displays increased thermosensitivity by impacting stomatal conductance. They also support a notion that mitochondrial complex I activity is required for maintenance of optimal photosynthetic performance and acclimation of plants to high temperature stress. These findings may be useful in the future efforts to understand how physiological mechanisms play a role in determining cotton fiber maturity and may influence stress responses in other crops.
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Affiliation(s)
- Hee Jin Kim
- USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA, United States of America
- * E-mail: (HJK); (HHR)
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Ruth Ndathe
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Gregory N. Thyssen
- USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA, United States of America
| | - Don C. Jones
- Cotton Incorporated, Cary, NC, United States of America
| | - Harish H. Ratnayaka
- Department of Biology, Xavier University of Louisiana, New Orleans, LA, United States of America
- * E-mail: (HJK); (HHR)
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13
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Adhikari D, Albataineh H, Androic D, Aniol K, Armstrong DS, Averett T, Ayerbe Gayoso C, Barcus S, Bellini V, Beminiwattha RS, Benesch JF, Bhatt H, Bhatta Pathak D, Bhetuwal D, Blaikie B, Campagna Q, Camsonne A, Cates GD, Chen Y, Clarke C, Cornejo JC, Covrig Dusa S, Datta P, Deshpande A, Dutta D, Feldman C, Fuchey E, Gal C, Gaskell D, Gautam T, Gericke M, Ghosh C, Halilovic I, Hansen JO, Hauenstein F, Henry W, Horowitz CJ, Jantzi C, Jian S, Johnston S, Jones DC, Karki B, Katugampola S, Keppel C, King PM, King DE, Knauss M, Kumar KS, Kutz T, Lashley-Colthirst N, Leverick G, Liu H, Liyange N, Malace S, Mammei R, Mammei J, McCaughan M, McNulty D, Meekins D, Metts C, Michaels R, Mondal MM, Napolitano J, Narayan A, Nikolaev D, Rashad MNH, Owen V, Palatchi C, Pan J, Pandey B, Park S, Paschke KD, Petrusky M, Pitt ML, Premathilake S, Puckett AJR, Quinn B, Radloff R, Rahman S, Rathnayake A, Reed BT, Reimer PE, Richards R, Riordan S, Roblin Y, Seeds S, Shahinyan A, Souder P, Tang L, Thiel M, Tian Y, Urciuoli GM, Wertz EW, Wojtsekhowski B, Yale B, Ye T, Yoon A, Zec A, Zhang W, Zhang J, Zheng X. Accurate Determination of the Neutron Skin Thickness of ^{208}Pb through Parity-Violation in Electron Scattering. Phys Rev Lett 2021; 126:172502. [PMID: 33988387 DOI: 10.1103/physrevlett.126.172502] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
We report a precision measurement of the parity-violating asymmetry A_{PV} in the elastic scattering of longitudinally polarized electrons from ^{208}Pb. We measure A_{PV}=550±16(stat)±8(syst) parts per billion, leading to an extraction of the neutral weak form factor F_{W}(Q^{2}=0.00616 GeV^{2})=0.368±0.013. Combined with our previous measurement, the extracted neutron skin thickness is R_{n}-R_{p}=0.283±0.071 fm. The result also yields the first significant direct measurement of the interior weak density of ^{208}Pb: ρ_{W}^{0}=-0.0796±0.0036(exp)±0.0013(theo) fm^{-3} leading to the interior baryon density ρ_{b}^{0}=0.1480±0.0036(exp)±0.0013(theo) fm^{-3}. The measurement accurately constrains the density dependence of the symmetry energy of nuclear matter near saturation density, with implications for the size and composition of neutron stars.
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Affiliation(s)
- D Adhikari
- Idaho State University, Pocatello, ID 83209, USA
| | - H Albataineh
- Texas A & M University-Kingsville, Kingsville, TX 78363, USA
| | - D Androic
- University of Zagreb, Faculty of Science
| | - K Aniol
- California State University, Los Angeles, Los Angeles, California 90032, USA
| | | | - T Averett
- William & Mary, Williamsburg, Virginia 23185, USA
| | | | - S Barcus
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - V Bellini
- Istituto Nazionale di Fisica Nucleare, Sezione di Catania, 95123 Catania, Italy
| | | | - J F Benesch
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - H Bhatt
- Mississippi State University, Mississippi State, MS 39762, USA
| | | | - D Bhetuwal
- Mississippi State University, Mississippi State, MS 39762, USA
| | - B Blaikie
- University of Manitoba, Winnipeg, MB R3T2N2 Canada
| | - Q Campagna
- William & Mary, Williamsburg, Virginia 23185, USA
| | - A Camsonne
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - G D Cates
- University of Virginia, Charlottesville, VA 22904, USA
| | - Y Chen
- Louisiana Tech University, Ruston, LA 71272 USA
| | - C Clarke
- Stony Brook, State University of New York, NY 11794, USA
| | - J C Cornejo
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - S Covrig Dusa
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P Datta
- University of Connecticut, Storrs, CT 06269, USA
| | - A Deshpande
- Stony Brook, State University of New York, NY 11794, USA
- Center for Frontiers in Nuclear Science, NY 11794, USA
| | - D Dutta
- Mississippi State University, Mississippi State, MS 39762, USA
| | - C Feldman
- Stony Brook, State University of New York, NY 11794, USA
| | - E Fuchey
- University of Connecticut, Storrs, CT 06269, USA
| | - C Gal
- University of Virginia, Charlottesville, VA 22904, USA
- Stony Brook, State University of New York, NY 11794, USA
- Center for Frontiers in Nuclear Science, NY 11794, USA
| | - D Gaskell
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - T Gautam
- Hampton University, Hampton, Virginia 23668, USA
| | - M Gericke
- University of Manitoba, Winnipeg, MB R3T2N2 Canada
| | - C Ghosh
- Stony Brook, State University of New York, NY 11794, USA
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - I Halilovic
- University of Manitoba, Winnipeg, MB R3T2N2 Canada
| | - J-O Hansen
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - F Hauenstein
- Old Dominion University, Norfolk, Virginia 23529, USA
| | - W Henry
- Temple University, Philadelphia, PA 19122, USA
| | - C J Horowitz
- Indiana University, Bloomington, Indiana 47405, USA
| | - C Jantzi
- University of Virginia, Charlottesville, VA 22904, USA
| | - S Jian
- University of Virginia, Charlottesville, VA 22904, USA
| | - S Johnston
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - D C Jones
- Temple University, Philadelphia, PA 19122, USA
| | - B Karki
- Ohio University, Athens, Ohio 45701, USA
| | - S Katugampola
- University of Virginia, Charlottesville, VA 22904, USA
| | - C Keppel
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - P M King
- Ohio University, Athens, Ohio 45701, USA
| | - D E King
- Syracuse University, Syracuse, New York 13244, USA
| | - M Knauss
- Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, USA
| | - K S Kumar
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - T Kutz
- Stony Brook, State University of New York, NY 11794, USA
| | | | - G Leverick
- University of Manitoba, Winnipeg, MB R3T2N2 Canada
| | - H Liu
- University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - N Liyange
- University of Virginia, Charlottesville, VA 22904, USA
| | - S Malace
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - R Mammei
- University of Winnipeg, Winnipeg, MB R3B2E9 Canada
| | - J Mammei
- University of Manitoba, Winnipeg, MB R3T2N2 Canada
| | - M McCaughan
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - D McNulty
- Idaho State University, Pocatello, ID 83209, USA
| | - D Meekins
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - C Metts
- William & Mary, Williamsburg, Virginia 23185, USA
| | - R Michaels
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - M M Mondal
- Stony Brook, State University of New York, NY 11794, USA
- Center for Frontiers in Nuclear Science, NY 11794, USA
| | | | | | - D Nikolaev
- Temple University, Philadelphia, PA 19122, USA
| | - M N H Rashad
- Old Dominion University, Norfolk, Virginia 23529, USA
| | - V Owen
- William & Mary, Williamsburg, Virginia 23185, USA
| | - C Palatchi
- University of Virginia, Charlottesville, VA 22904, USA
- Center for Frontiers in Nuclear Science, NY 11794, USA
| | - J Pan
- University of Manitoba, Winnipeg, MB R3T2N2 Canada
| | - B Pandey
- Hampton University, Hampton, Virginia 23668, USA
| | - S Park
- Stony Brook, State University of New York, NY 11794, USA
| | - K D Paschke
- University of Virginia, Charlottesville, VA 22904, USA
| | - M Petrusky
- Stony Brook, State University of New York, NY 11794, USA
| | - M L Pitt
- Virginia Tech, Blacksburg, Virginia 24061, USA
| | | | | | - B Quinn
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - R Radloff
- Ohio University, Athens, Ohio 45701, USA
| | - S Rahman
- University of Manitoba, Winnipeg, MB R3T2N2 Canada
| | - A Rathnayake
- University of Virginia, Charlottesville, VA 22904, USA
| | - B T Reed
- Indiana University, Bloomington, Indiana 47405, USA
| | - P E Reimer
- Physics Division, Argonne National Laboratory, Lemont, Il 60439
| | - R Richards
- Stony Brook, State University of New York, NY 11794, USA
| | - S Riordan
- Physics Division, Argonne National Laboratory, Lemont, Il 60439
| | - Y Roblin
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - S Seeds
- University of Connecticut, Storrs, CT 06269, USA
| | - A Shahinyan
- A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute), Yerevan 0036, Armenia
| | - P Souder
- Syracuse University, Syracuse, New York 13244, USA
| | - L Tang
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
- Hampton University, Hampton, Virginia 23668, USA
| | - M Thiel
- Institut für Kernphysik, Johannes Gutenberg-Universität, Mainz 55122, Germany
| | - Y Tian
- Syracuse University, Syracuse, New York 13244, USA
| | | | - E W Wertz
- William & Mary, Williamsburg, Virginia 23185, USA
| | - B Wojtsekhowski
- Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606, USA
| | - B Yale
- William & Mary, Williamsburg, Virginia 23185, USA
| | - T Ye
- Stony Brook, State University of New York, NY 11794, USA
| | - A Yoon
- Christopher Newport University, Newport News, Virginia 23606, USA
| | - A Zec
- University of Virginia, Charlottesville, VA 22904, USA
| | - W Zhang
- Stony Brook, State University of New York, NY 11794, USA
| | - J Zhang
- Stony Brook, State University of New York, NY 11794, USA
- Center for Frontiers in Nuclear Science, NY 11794, USA
- Shandong University, Qingdao, Shandong 266237, China
| | - X Zheng
- University of Virginia, Charlottesville, VA 22904, USA
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14
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Ando A, Kirkbride RC, Jones DC, Grimwood J, Chen ZJ. LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation. BMC Genomics 2021; 22:309. [PMID: 33926376 PMCID: PMC8082777 DOI: 10.1186/s12864-021-07579-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/03/2021] [Indexed: 01/21/2023] Open
Abstract
Background Cotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to understand this dramatic developmental shift have been impeded by the difficulty of separation between fiber and epidermal cells. Results Here we employed laser-capture microdissection (LCM) to separate these cell types. RNA-seq analysis revealed transitional differences between fiber and epidermal-layer cells at 0 or 2 days post anthesis. Specifically, down-regulation of putative cell cycle genes was coupled with upregulation of ribosome biosynthesis and translation-related genes, which may suggest their respective roles in fiber cell initiation. Indeed, the amount of fibers in cultured ovules was increased by cell cycle progression inhibitor, Roscovitine, and decreased by ribosome biosynthesis inhibitor, Rbin-1. Moreover, subfunctionalization of homoeologs was pervasive in fiber and epidermal cells, with expression bias towards 10% more D than A homoeologs of cell cycle related genes and 40–50% more D than A homoeologs of ribosomal protein subunit genes. Key cell cycle regulators were predicted to be epialleles in allotetraploid cotton. MYB-transcription factor genes displayed expression divergence between fibers and ovules. Notably, many phytohormone-related genes were upregulated in ovules and down-regulated in fibers, suggesting spatial-temporal effects on fiber cell development. Conclusions Fiber cell initiation is accompanied by cell cycle arrest coupled with active ribosome biosynthesis, spatial-temporal regulation of phytohormones and MYB transcription factors, and homoeolog expression bias of cell cycle and ribosome biosynthesis genes. These valuable genomic resources and molecular insights will help develop breeding and biotechnological tools to improve cotton fiber production. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07579-1.
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Affiliation(s)
- Atsumi Ando
- Department of Molecular Biosciences, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ryan C Kirkbride
- Department of Molecular Biosciences, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Don C Jones
- Agriculture and Environmental Research, Cotton Incorporated, Cary, NC, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
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15
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Balantekin AB, Band HR, Bass CD, Bergeron DE, Berish D, Bowden NS, Brodsky JP, Bryan CD, Classen T, Conant AJ, Deichert G, Diwan MV, Dolinski MJ, Erickson A, Foust BT, Gaison JK, Galindo-Uribarri A, Gilbert CE, Hackett BT, Hans S, Hansell AB, Heeger KM, Heffron B, Jaffe DE, Ji X, Jones DC, Kyzylova O, Lane CE, Langford TJ, LaRosa J, Littlejohn BR, Lu X, Maricic J, Mendenhall MP, Milincic R, Mitchell I, Mueller PE, Mumm HP, Napolitano J, Neilson R, Nikkel JA, Norcini D, Nour S, Palomino-Gallo JL, Pushin DA, Qian X, Romero-Romero E, Rosero R, Surukuchi PT, Tyra MA, Varner RL, White C, Wilhelmi J, Woolverton A, Yeh M, Zhang A, Zhang C, Zhang X. Nonfuel Antineutrino Contributions in the High Flux Isotope Reactor. ACTA ACUST UNITED AC 2020; 101. [PMID: 33336123 DOI: 10.1103/physrevc.101.054605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Reactor neutrino experiments have seen major improvements in precision in recent years. With the experimental uncertainties becoming lower than those from theory, carefully considering all sources of ν ¯ e is important when making theoretical predictions. One source of ν ¯ e that is often neglected arises from the irradiation of the nonfuel materials in reactors. The ν ¯ e rates and energies from these sources vary widely based on the reactor type, configuration, and sampling stage during the reactor cycle and have to be carefully considered for each experiment independently. In this article, we present a formalism for selecting the possible ν ¯ e sources arising from the neutron captures on reactor and target materials. We apply this formalism to the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory, the ν ¯ e source for the the Precision Reactor Oscillation and Spectrum Measurement (PROSPECT) experiment. Overall, we observe that the nonfuel ν ¯ e contributions from HFIR to PROSPECT amount to 1% above the inverse beta decay threshold with a maximum contribution of 9% in the 1.8-2.0 MeV range. Nonfuel contributions can be particularly high for research reactors like HFIR because of the choice of structural and reflector material in addition to the intentional irradiation of target material for isotope production. We show that typical commercial pressurized water reactors fueled with low-enriched uranium will have significantly smaller nonfuel ν ¯ e contribution.
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Affiliation(s)
- A B Balantekin
- Department of Physics, University of Wisconsin, Madison, Madison, WI 53706, USA
| | - H R Band
- Wright Laboratory, Department of Physics, Yale University, New Haven, CT 06520, USA
| | - C D Bass
- Department of Physics, Le Moyne College, Syracuse, NY 13214, USA
| | - D E Bergeron
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - D Berish
- Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - N S Bowden
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - J P Brodsky
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - C D Bryan
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - T Classen
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - A J Conant
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.,High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - G Deichert
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - M V Diwan
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - M J Dolinski
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - A Erickson
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - B T Foust
- Wright Laboratory, Department of Physics, Yale University, New Haven, CT 06520, USA
| | - J K Gaison
- Wright Laboratory, Department of Physics, Yale University, New Haven, CT 06520, USA
| | - A Galindo-Uribarri
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
| | - C E Gilbert
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
| | - B T Hackett
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
| | - S Hans
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A B Hansell
- Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - K M Heeger
- Wright Laboratory, Department of Physics, Yale University, New Haven, CT 06520, USA
| | - B Heffron
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - X Ji
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - D C Jones
- Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - O Kyzylova
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - C E Lane
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - T J Langford
- Wright Laboratory, Department of Physics, Yale University, New Haven, CT 06520, USA
| | - J LaRosa
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - B R Littlejohn
- Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - X Lu
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
| | - J Maricic
- Department of Physics & Astronomy, University of Hawaii, Honolulu, HA 96822, USA
| | - M P Mendenhall
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - R Milincic
- Department of Physics & Astronomy, University of Hawaii, Honolulu, HA 96822, USA
| | - I Mitchell
- Department of Physics & Astronomy, University of Hawaii, Honolulu, HA 96822, USA
| | - P E Mueller
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - H P Mumm
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - J Napolitano
- Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - R Neilson
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - J A Nikkel
- Wright Laboratory, Department of Physics, Yale University, New Haven, CT 06520, USA
| | - D Norcini
- Wright Laboratory, Department of Physics, Yale University, New Haven, CT 06520, USA
| | - S Nour
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - J L Palomino-Gallo
- Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - D A Pushin
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - X Qian
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - E Romero-Romero
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.,Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - R Rosero
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - P T Surukuchi
- Wright Laboratory, Department of Physics, Yale University, New Haven, CT 06520, USA
| | - M A Tyra
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - R L Varner
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - C White
- Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - J Wilhelmi
- Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - A Woolverton
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - M Yeh
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A Zhang
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - C Zhang
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - X Zhang
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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16
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Ghimire NJ, Dally RL, Poudel L, Jones DC, Michel D, Magar NT, Bleuel M, McGuire MA, Jiang JS, Mitchell JF, Lynn JW, Mazin II. Competing magnetic phases and fluctuation-driven scalar spin chirality in the kagome metal YMn 6Sn 6. Sci Adv 2020; 6:6/51/eabe2680. [PMID: 33355145 DOI: 10.1126/sciadv.abe2680] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/02/2020] [Indexed: 05/25/2023]
Abstract
Identification, understanding, and manipulation of novel magnetic textures are essential for the discovery of new quantum materials for future spin-based electronic devices. In particular, materials that manifest a large response to external stimuli such as a magnetic field are subject to intense investigation. Here, we study the kagome-net magnet YMn6Sn6 by magnetometry, transport, and neutron diffraction measurements combined with first-principles calculations. We identify a number of nontrivial magnetic phases, explain their microscopic nature, and demonstrate that one of them hosts a large topological Hall effect (THE). We propose a previously unidentified fluctuation-driven mechanism, which leads to the THE at elevated temperatures. This interesting physics comes from parametrically frustrated interplanar exchange interactions that trigger strong magnetic fluctuations. Our results pave a path to chiral spin textures, promising for novel spintronics.
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Affiliation(s)
- Nirmal J Ghimire
- Department of Physics and Astronomy, George Mason University, Fairfax, VA 22030, USA.
- Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, USA
| | - Rebecca L Dally
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - L Poudel
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - D C Jones
- Department of Physics and Astronomy, George Mason University, Fairfax, VA 22030, USA
- Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, USA
| | - D Michel
- Department of Physics and Astronomy, George Mason University, Fairfax, VA 22030, USA
- Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, USA
| | - N Thapa Magar
- Department of Physics and Astronomy, George Mason University, Fairfax, VA 22030, USA
| | - M Bleuel
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Michael A McGuire
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - J S Jiang
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - J F Mitchell
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Jeffrey W Lynn
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - I I Mazin
- Department of Physics and Astronomy, George Mason University, Fairfax, VA 22030, USA
- Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, USA
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17
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Peng R, Jones DC, Liu F, Zhang B. From Sequencing to Genome Editing for Cotton Improvement. Trends Biotechnol 2020; 39:221-224. [PMID: 32988631 DOI: 10.1016/j.tibtech.2020.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 10/23/2022]
Abstract
Traditional breeding techniques are proven, but additional knowledge learned from genome sequencing provides vast new data that might help identify gene targets for improving cotton sustainability. CRISPR/Cas9 provides a powerful tool for precision cotton breeding. Here, we discuss the opportunities and challenges of genome sequencing and editing for cotton improvement.
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Affiliation(s)
- Renhai Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China.
| | | | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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18
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Chen ZJ, Sreedasyam A, Ando A, Song Q, De Santiago LM, Hulse-Kemp AM, Ding M, Ye W, Kirkbride RC, Jenkins J, Plott C, Lovell J, Lin YM, Vaughn R, Liu B, Simpson S, Scheffler BE, Wen L, Saski CA, Grover CE, Hu G, Conover JL, Carlson JW, Shu S, Boston LB, Williams M, Peterson DG, McGee K, Jones DC, Wendel JF, Stelly DM, Grimwood J, Schmutz J. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet 2020; 52:525-533. [PMID: 32313247 PMCID: PMC7203012 DOI: 10.1038/s41588-020-0614-5] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
Abstract
Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N6-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement. Sequencing and genomic diversification of five allopolyploid cotton species provide insights into polyploid genome evolution and epigenetic landscapes for cotton improvement.
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Affiliation(s)
- Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. .,State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
| | | | - Atsumi Ando
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.,State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Luis M De Santiago
- Department of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USA
| | - Amanda M Hulse-Kemp
- US Department of Agriculture-Agricultural Research Service, Genomics and Bioinformatics Research Unit, Raleigh, NC, USA
| | - Mingquan Ding
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.,College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, China
| | - Wenxue Ye
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Ryan C Kirkbride
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - John Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Yu-Ming Lin
- Department of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USA
| | - Robert Vaughn
- Department of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USA
| | - Bo Liu
- Department of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USA
| | - Sheron Simpson
- US Department of Agriculture-Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Brian E Scheffler
- US Department of Agriculture-Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Li Wen
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Joseph W Carlson
- The US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Shengqiang Shu
- The US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Lori B Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology and Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Keith McGee
- School of Agriculture and Applied Sciences, Alcorn State University, Lorman, MS, USA
| | - Don C Jones
- Agriculture and Environmental Research, Cotton Incorporated, Cary, NC, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,The US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
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19
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Zhang K, Kuraparthy V, Fang H, Zhu L, Sood S, Jones DC. High-density linkage map construction and QTL analyses for fiber quality, yield and morphological traits using CottonSNP63K array in upland cotton (Gossypium hirsutum L.). BMC Genomics 2019; 20:889. [PMID: 31771502 PMCID: PMC6878679 DOI: 10.1186/s12864-019-6214-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
Background Improving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the quantitative trait loci (QTL) for fiber quality and yield traits using the high-density SNP-based genetic maps allows for bridging genomics with cotton breeding through marker assisted and genomic selection. In this study, a recombinant inbred line (RIL) population, derived from cross between two parental accessions, which represent broad allele diversity in Upland cotton, was used to construct high-density SNP-based linkage maps and to map the QTLs controlling important cotton traits. Results Molecular genetic mapping using RIL population produced a genetic map of 3129 SNPs, mapped at a density of 1.41 cM. Genetic maps of the individual chromosomes showed good collinearity with the sequence based physical map. A total of 106 QTLs were identified which included 59 QTLs for six fiber quality traits, 38 QTLs for four yield traits and 9 QTLs for two morphological traits. Sub-genome wide, 57 QTLs were mapped in A sub-genome and 49 were mapped in D sub-genome. More than 75% of the QTLs with favorable alleles were contributed by the parental accession NC05AZ06. Forty-six mapped QTLs each explained more than 10% of the phenotypic variation. Further, we identified 21 QTL clusters where 12 QTL clusters were mapped in the A sub-genome and 9 were mapped in the D sub-genome. Candidate gene analyses of the 11 stable QTL harboring genomic regions identified 19 putative genes which had functional role in cotton fiber development. Conclusion We constructed a high-density genetic map of SNPs in Upland cotton. Collinearity between genetic and physical maps indicated no major structural changes in the genetic mapping populations. Most traits showed high broad-sense heritability. One hundred and six QTLs were identified for the fiber quality, yield and morphological traits. Majority of the QTLs with favorable alleles were contributed by improved parental accession. More than 70% of the mapped QTLs shared the similar map position with previously reported QTLs which suggest the genetic relatedness of Upland cotton germplasm. Identification of QTL clusters could explain the correlation among some fiber quality traits in cotton. Stable and major QTLs and QTL clusters of traits identified in the current study could be the targets for map-based cloning and marker assisted selection (MAS) in cotton breeding. The genomic region on D12 containing the major stable QTLs for micronaire, fiber strength and lint percentage could be potential targets for MAS and gene cloning of fiber quality traits in cotton.
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Affiliation(s)
- Kuang Zhang
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Vasu Kuraparthy
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Hui Fang
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Linglong Zhu
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Shilpa Sood
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA.,4 Cityplace drive, The Climate Corporation (Bayer U.S. Crop Science), St. Louis, MO, 63141, USA
| | - Don C Jones
- Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA
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20
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Ashenfelter J, Balantekin AB, Band HR, Bass CD, Bergeron DE, Berish D, Bowden NS, Brodsky JP, Bryan CD, Cherwinka JJ, Classen T, Conant AJ, Cox AA, Davee D, Dean D, Deichert G, Diwan MV, Dolinski MJ, Erickson A, Febbraro M, Foust BT, Gaison JK, Galindo-Uribarri A, Gilbert CE, Gilje KE, Hackett BT, Hans S, Hansell AB, Heeger KM, Insler J, Jaffe DE, Ji X, Jones DC, Kyzylova O, Lane CE, Langford TJ, LaRosa J, Littlejohn BR, Lu X, Martinez Caicedo DA, Matta JT, McKeown RD, Mendenhall MP, Minock JM, Mueller PE, Mumm HP, Napolitano J, Neilson R, Nikkel JA, Norcini D, Nour S, Pushin DA, Qian X, Romero-Romero E, Rosero R, Sarenac D, Surukuchi PT, Telles AB, Tyra MA, Varner RL, Viren B, White C, Wilhelmi J, Wise T, Yeh M, Yen YR, Zhang A, Zhang C, Zhang X. Measurement of the Antineutrino Spectrum from ^{235}U Fission at HFIR with PROSPECT. Phys Rev Lett 2019; 122:251801. [PMID: 31347897 DOI: 10.1103/physrevlett.122.251801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/22/2019] [Indexed: 06/10/2023]
Abstract
This Letter reports the first measurement of the ^{235}U ν[over ¯]_{e} energy spectrum by PROSPECT, the Precision Reactor Oscillation and Spectrum experiment, operating 7.9 m from the 85 MW_{th} highly enriched uranium (HEU) High Flux Isotope Reactor. With a surface-based, segmented detector, PROSPECT has observed 31678±304(stat) ν[over ¯]_{e}-induced inverse beta decays, the largest sample from HEU fission to date, 99% of which are attributed to ^{235}U. Despite broad agreement, comparison of the Huber ^{235}U model to the measured spectrum produces a χ^{2}/ndf=51.4/31, driven primarily by deviations in two localized energy regions. The measured ^{235}U spectrum shape is consistent with a deviation relative to prediction equal in size to that observed at low-enriched uranium power reactors in the ν[over ¯]_{e} energy region of 5-7 MeV.
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Affiliation(s)
- J Ashenfelter
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - A B Balantekin
- Department of Physics, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
| | - H R Band
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - C D Bass
- Department of Physics, Le Moyne College, Syracuse, New York 13214, USA
| | - D E Bergeron
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - D Berish
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - N S Bowden
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - J P Brodsky
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - C D Bryan
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J J Cherwinka
- Physical Sciences Laboratory, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
| | - T Classen
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - A J Conant
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - A A Cox
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - D Davee
- Department of Physics, College of William and Mary, Williamsburg, Virginia 23187, USA
| | - D Dean
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - G Deichert
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M V Diwan
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - M J Dolinski
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - A Erickson
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M Febbraro
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - B T Foust
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - J K Gaison
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - A Galindo-Uribarri
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - C E Gilbert
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - K E Gilje
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - B T Hackett
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - S Hans
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - A B Hansell
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - K M Heeger
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - J Insler
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - X Ji
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - D C Jones
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - O Kyzylova
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - C E Lane
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - T J Langford
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - J LaRosa
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - B R Littlejohn
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - X Lu
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - D A Martinez Caicedo
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - J T Matta
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R D McKeown
- Department of Physics, College of William and Mary, Williamsburg, Virginia 23187, USA
| | - M P Mendenhall
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - J M Minock
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - P E Mueller
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - H P Mumm
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - J Napolitano
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - R Neilson
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - J A Nikkel
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - D Norcini
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - S Nour
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - D A Pushin
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - X Qian
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - E Romero-Romero
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37916, USA
| | - R Rosero
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - D Sarenac
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - P T Surukuchi
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - A B Telles
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - M A Tyra
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - R L Varner
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - B Viren
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C White
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - J Wilhelmi
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - T Wise
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - M Yeh
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Y-R Yen
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - A Zhang
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C Zhang
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - X Zhang
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
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21
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Thyssen GN, Jenkins JN, McCarty JC, Zeng L, Campbell BT, Delhom CD, Islam MS, Li P, Jones DC, Condon BD, Fang DD. Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.). Theor Appl Genet 2019; 132:989-999. [PMID: 30506522 DOI: 10.1007/s00122-018-3254-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/27/2018] [Indexed: 05/25/2023]
Abstract
Significant associations between candidate genes and six major cotton fiber quality traits were identified in a MAGIC population using GWAS and whole genome sequencing. Upland cotton (Gossypium hirsutum L.) is the world's major renewable source of fibers for textiles. To identify causative genetic variants that influence the major agronomic measures of cotton fiber quality, which are used to set discount or premium prices on each bale of cotton in the USA, we measured six fiber phenotypes from twelve environments, across three locations and 7 years. Our 550 recombinant inbred lines were derived from a multi-parent advanced generation intercross population and were whole-genome-sequenced at 3× coverage, along with the eleven parental cultivars at 20× coverage. The segregation of 473,517 single nucleotide polymorphisms (SNPs) in this population, including 7506 non-synonymous mutations, was combined with phenotypic data to identify seven highly significant fiber quality loci. At these loci, we found fourteen genes with non-synonymous SNPs. Among these loci, some had simple additive effects, while others were only important in a subset of the population. We observed additive effects for elongation and micronaire, when the three most significant loci for each trait were examined. In an informative subset where the major multi-trait locus on chromosome A07:72-Mb was fixed, we unmasked the identity of another significant fiber strength locus in gene Gh_D13G1792 on chromosome D13. The micronaire phenotype only revealed one highly significant genetic locus at one environmental location, demonstrating a significant genetic by environment component. These loci and candidate causative variant alleles will be useful to cotton breeders for marker-assisted selection with minimal linkage drag and potential biotechnological applications.
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Affiliation(s)
- Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
- Cotton Chemistry and Utilization Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | - Johnie N Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Jack C McCarty
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Linghe Zeng
- Crop Genetics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - B Todd Campbell
- Coastal Plain Soil, Water and Plant Conservation Research Unit, USDA-ARS, Florence, SC, 29501, USA
| | - Christopher D Delhom
- Cotton Structure and Quality Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | - Md Sariful Islam
- Sugarcane Production Research Unit, USDA-ARS, Canal Point, FL, 33438, USA
| | - Ping Li
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | | | - Brian D Condon
- Cotton Chemistry and Utilization Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA.
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22
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Ashenfelter J, Balantekin AB, Baldenegro C, Band HR, Bass CD, Bergeron DE, Berish D, Bignell LJ, Bowden NS, Bricco J, Brodsky JP, Bryan CD, Bykadorova Telles A, Cherwinka JJ, Classen T, Commeford K, Conant AJ, Cox AA, Davee D, Dean D, Deichert G, Diwan MV, Dolinski MJ, Erickson A, Febbraro M, Foust BT, Gaison JK, Galindo-Uribarri A, Gilbert CE, Gilje KE, Glenn A, Goddard BW, Hackett BT, Han K, Hans S, Hansell AB, Heeger KM, Heffron B, Insler J, Jaffe DE, Ji X, Jones DC, Koehler K, Kyzylova O, Lane CE, Langford TJ, LaRosa J, Littlejohn BR, Lopez F, Lu X, Martinez Caicedo DA, Matta JT, McKeown RD, Mendenhall MP, Miller HJ, Minock JM, Mueller PE, Mumm HP, Napolitano J, Neilson R, Nikkel JA, Norcini D, Nour S, Pushin DA, Qian X, Romero-Romero E, Rosero R, Sarenac D, Seilhan BS, Sharma R, Surukuchi PT, Trinh C, Tyra MA, Varner RL, Viren B, Wagner JM, Wang W, White B, White C, Wilhelmi J, Wise T, Yao H, Yeh M, Yen YR, Zhang A, Zhang C, Zhang X, Zhao M. First Search for Short-Baseline Neutrino Oscillations at HFIR with PROSPECT. Phys Rev Lett 2018; 121:251802. [PMID: 30608854 DOI: 10.1103/physrevlett.121.251802] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Indexed: 06/09/2023]
Abstract
This Letter reports the first scientific results from the observation of antineutrinos emitted by fission products of ^{235}U at the High Flux Isotope Reactor. PROSPECT, the Precision Reactor Oscillation and Spectrum Experiment, consists of a segmented 4 ton ^{6}Li-doped liquid scintillator detector covering a baseline range of 7-9 m from the reactor and operating under less than 1 m water equivalent overburden. Data collected during 33 live days of reactor operation at a nominal power of 85 MW yield a detection of 25 461±283 (stat) inverse beta decays. Observation of reactor antineutrinos can be achieved in PROSPECT at 5σ statistical significance within 2 h of on-surface reactor-on data taking. A reactor model independent analysis of the inverse beta decay prompt energy spectrum as a function of baseline constrains significant portions of the previously allowed sterile neutrino oscillation parameter space at 95% confidence level and disfavors the best fit of the reactor antineutrino anomaly at 2.2σ confidence level.
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Affiliation(s)
- J Ashenfelter
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - A B Balantekin
- Department of Physics, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
| | - C Baldenegro
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - H R Band
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - C D Bass
- Department of Physics, Le Moyne College, Syracuse, New York 13214, USA
| | - D E Bergeron
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - D Berish
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - L J Bignell
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - N S Bowden
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - J Bricco
- Physical Sciences Laboratory, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
| | - J P Brodsky
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - C D Bryan
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - A Bykadorova Telles
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - J J Cherwinka
- Physical Sciences Laboratory, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
| | - T Classen
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - K Commeford
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - A J Conant
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - A A Cox
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - D Davee
- Department of Physics, College of William and Mary, Williamsburg, Virginia 23185, USA
| | - D Dean
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - G Deichert
- High Flux Isotope Reactor, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - M V Diwan
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - M J Dolinski
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - A Erickson
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M Febbraro
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - B T Foust
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - J K Gaison
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - A Galindo-Uribarri
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - C E Gilbert
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - K E Gilje
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - A Glenn
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - B W Goddard
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - B T Hackett
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - K Han
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - S Hans
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - A B Hansell
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - K M Heeger
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - B Heffron
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - J Insler
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - X Ji
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - D C Jones
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - K Koehler
- Physical Sciences Laboratory, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
| | - O Kyzylova
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - C E Lane
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - T J Langford
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - J LaRosa
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - B R Littlejohn
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - F Lopez
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - X Lu
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - D A Martinez Caicedo
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - J T Matta
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - R D McKeown
- Department of Physics, College of William and Mary, Williamsburg, Virginia 23185, USA
| | - M P Mendenhall
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - H J Miller
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - J M Minock
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - P E Mueller
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - H P Mumm
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - J Napolitano
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - R Neilson
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - J A Nikkel
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - D Norcini
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - S Nour
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - D A Pushin
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - X Qian
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - E Romero-Romero
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - R Rosero
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - D Sarenac
- Institute for Quantum Computing and Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - B S Seilhan
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - R Sharma
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - P T Surukuchi
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - C Trinh
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - M A Tyra
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - R L Varner
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - B Viren
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - J M Wagner
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - W Wang
- Department of Physics, College of William and Mary, Williamsburg, Virginia 23185, USA
| | - B White
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - C White
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - J Wilhelmi
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - T Wise
- Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - H Yao
- Department of Physics, College of William and Mary, Williamsburg, Virginia 23185, USA
| | - M Yeh
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Y-R Yen
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - A Zhang
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C Zhang
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - X Zhang
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - M Zhao
- Brookhaven National Laboratory, Upton, New York 11973, USA
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23
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Saski CA, Scheffler BE, Hulse-Kemp AM, Liu B, Song Q, Ando A, Stelly DM, Scheffler JA, Grimwood J, Jones DC, Peterson DG, Schmutz J, Chen ZJ. Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. Sci Rep 2017; 7:15274. [PMID: 29127298 PMCID: PMC5681701 DOI: 10.1038/s41598-017-14885-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/18/2017] [Indexed: 01/06/2023] Open
Abstract
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.
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Affiliation(s)
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Amanda M Hulse-Kemp
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Bo Liu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Qingxin Song
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA
| | - Atsumi Ando
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Don C Jones
- Agriculture and Environmental Research, Cotton Incorporated, Cary, NC, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology and Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Z Jeffery Chen
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA.
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24
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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25
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Andres RJ, Coneva V, Frank MH, Tuttle JR, Samayoa LF, Han SW, Kaur B, Zhu L, Fang H, Bowman DT, Rojas-Pierce M, Haigler CH, Jones DC, Holland JB, Chitwood DH, Kuraparthy V. Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.). Proc Natl Acad Sci U S A 2017; 114:E57-E66. [PMID: 27999177 PMCID: PMC5224360 DOI: 10.1073/pnas.1613593114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.
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Affiliation(s)
- Ryan J Andres
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
| | | | | | - John R Tuttle
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
| | - Luis Fernando Samayoa
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Raleigh, NC 27695-7620
| | - Sang-Won Han
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | - Baljinder Kaur
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
| | - Linglong Zhu
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
| | - Hui Fang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
| | - Daryl T Bowman
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
| | - Marcela Rojas-Pierce
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | - Candace H Haigler
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | | | - James B Holland
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Raleigh, NC 27695-7620
| | | | - Vasu Kuraparthy
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620;
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26
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Islam MS, Thyssen GN, Jenkins JN, Zeng L, Delhom CD, McCarty JC, Deng DD, Hinchliffe DJ, Jones DC, Fang DD. A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC Genomics 2016; 17:903. [PMID: 27829353 PMCID: PMC5103610 DOI: 10.1186/s12864-016-3249-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/02/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders' ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution. RESULTS An Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars. CONCLUSION Using GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality.
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Affiliation(s)
- Md Sariful Islam
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
| | - Gregory N. Thyssen
- Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
| | - Johnie N. Jenkins
- Genetics & Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS 39762 USA
| | - Linghe Zeng
- Crop Genetics Research Unit, USDA-ARS, Stoneville, MS 38772 USA
| | - Christopher D. Delhom
- Cotton Structure and Quality Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
| | - Jack C. McCarty
- Genetics & Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS 39762 USA
| | - Dewayne D. Deng
- Genetics & Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS 39762 USA
| | - Doug J. Hinchliffe
- Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
| | | | - David D. Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
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27
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López-Álvarez MR, Jiang W, Jones DC, Jayaraman J, Johnson C, Cookson WO, Moffatt MF, Trowsdale J, Traherne JA. LILRA6 copy number variation correlates with susceptibility to atopic dermatitis. Immunogenetics 2016; 68:743-7. [PMID: 27333811 PMCID: PMC5026711 DOI: 10.1007/s00251-016-0924-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023]
Abstract
Leukocyte immunoglobulin-like receptors (LILR) are expressed mostly on myelomonocytic cells where they are mediators of immunological tolerance. Two LILR genes, LILRA3 and LILRA6, exhibit marked copy number variation. We assessed the contribution of these genes to atopic dermatitis (AD) by analysing transmission in 378 AD families. The data indicated that copies of LILRA6 were over-transmitted to affected patients. They are consistent with a contribution of LILR genes to AD. They could affect the equilibrium between activating and inhibitory signals in the immune response.
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Affiliation(s)
- M R López-Álvarez
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - W Jiang
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - D C Jones
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - J Jayaraman
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - C Johnson
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.,Molecular Genetics and Genomics Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK
| | - W O Cookson
- Molecular Genetics and Genomics Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK
| | - M F Moffatt
- Molecular Genetics and Genomics Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK
| | - J Trowsdale
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - J A Traherne
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK. .,Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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28
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Jones DC, Mistry IN, Tavassoli A. Post-translational control of protein function with light using a LOV-intein fusion protein. Mol Biosyst 2016; 12:1388-93. [PMID: 26940144 DOI: 10.1039/c6mb00007j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methods for the post-translational control of protein function with light hold much value as tools in cell biology. To this end, we report a fusion protein that consists of DnaE split-inteins, flanking the light sensitive LOV2 domain of Avena sativa. The resulting chimera combines the activities of these two unrelated proteins to enable controlled formation of a functional protein via upregulation of intein splicing with blue light in bacterial and human cells.
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Affiliation(s)
- D C Jones
- Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.
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29
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Hinze LL, Gazave E, Gore MA, Fang DD, Scheffler BE, Yu JZ, Jones DC, Frelichowski J, Percy RG. Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set. J Hered 2016; 107:274-86. [PMID: 26774060 DOI: 10.1093/jhered/esw004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/04/2016] [Indexed: 11/14/2022] Open
Abstract
A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources.
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Affiliation(s)
- Lori L Hinze
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones).
| | - Elodie Gazave
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Michael A Gore
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - David D Fang
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Brian E Scheffler
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - John Z Yu
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Don C Jones
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - James Frelichowski
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Richard G Percy
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
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30
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Ashrafi H, Hulse-Kemp AM, Wang F, Yang SS, Guan X, Jones DC, Matvienko M, Mockaitis K, Chen ZJ, Stelly DM, Van Deynze A. A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery. Plant Genome 2015; 8:eplantgenome2014.10.0068. [PMID: 33228299 DOI: 10.3835/plantgenome2014.10.0068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/17/2015] [Indexed: 06/11/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) has a narrow germplasm base, which constrains marker development and hampers intraspecific breeding. A pressing need exists for high-throughput single nucleotide polymorphism (SNP) markers that can be readily applied to germplasm in breeding and breeding-related research programs. Despite progress made in developing new sequencing technologies during the past decade, the cost of sequencing remains substantial when one is dealing with numerous samples and large genomes. Several strategies have been proposed to lower the cost of sequencing for multiple genotypes of large-genome species like cotton, such as transcriptome sequencing and reduced-representation DNA sequencing. This paper reports the development of a transcriptome assembly of the inbred line Texas Marker-1 (TM-1), a genetic standard for cotton, its usefulness as a reference for RNA sequencing (RNA-seq)-based SNP identification, and the availability of transcriptome sequences of four other cotton cultivars. An assembly of TM-1 was made using Roche 454 transcriptome reads combined with an assembly of all available public expressed sequence tag (EST) sequences of TM-1. The TM-1 assembly consists of 72,450 contigs with a total of 70 million bp. Functional predictions of the transcripts were estimated by alignment to selected protein databases. Transcriptome sequences of the five lines, including TM-1, were obtained using an Illumina Genome Analyzer-II, and the short reads were mapped to the TM-1 assembly to discover SNPs among the five lines. We identified >14,000 unfiltered allelic SNPs, of which ∼3,700 SNPs were retained for assay development after applying several rigorous filters. This paper reports availability of the reference transcriptome assembly and shows its utility in developing intraspecific SNP markers in upland cotton.
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Affiliation(s)
- Hamid Ashrafi
- Univ. of California-Davis, Dep. of Plant Sciences and Seed Biotechnology Center, One Shields Ave., Davis, CA, 95616
| | | | - Fei Wang
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - S Samuel Yang
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - Xueying Guan
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The Univ. of Texas at Austin, Austin, TX, 78712
| | | | - Marta Matvienko
- Univ. of California-Davis, Genome Center, One Shields Ave., Davis, CA, 95616
| | | | - Z Jeffrey Chen
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The Univ. of Texas at Austin, Austin, TX, 78712
| | - David M Stelly
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - Allen Van Deynze
- Univ. of California-Davis, Dep. of Plant Sciences and Seed Biotechnology Center, One Shields Ave., Davis, CA, 95616
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31
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Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3 (Bethesda) 2015; 5:1187-209. [PMID: 25908569 PMCID: PMC4478548 DOI: 10.1534/g3.115.018416] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/11/2015] [Indexed: 11/18/2022]
Abstract
High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - Jana Lemm
- TraitGenetics GmbH, 06466 Gatersleben, Germany
| | | | - Hamid Ashrafi
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Ramesh Buyyarapu
- Dow AgroSciences, Trait Genetics and Technologies, Indianapolis, Indiana 46268
| | - David D Fang
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - James Frelichowski
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO, Brazil
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Lori L Hinze
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Kelli J Kochan
- Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Penny K Riggs
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Jodi A Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, Mississippi 38776
| | - Joshua A Udall
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Mauricio Ulloa
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Shirley S Wang
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Qian-Hao Zhu
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Sumit K Bag
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Archana Bhardwaj
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - John J Burke
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Robert L Byers
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | | | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - David B Harker
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Md S Islam
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - Johnie N Jenkins
- USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762
| | - Don C Jones
- Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513
| | | | - Danny J Llewellyn
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Richard G Percy
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Alan E Pepper
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jesse A Poland
- Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
| | - Krishan Mohan Rai
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Samir V Sawant
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Sunil Kumar Singh
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Andrew Spriggs
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Jen M Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Fei Wang
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Scott M Yourstone
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Xiuting Zheng
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | | | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Iain W Wilson
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - David M Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
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Xie F, Jones DC, Wang Q, Sun R, Zhang B. Small RNA sequencing identifies miRNA roles in ovule and fibre development. Plant Biotechnol J 2015; 13:355-69. [PMID: 25572837 DOI: 10.1111/pbi.12296] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/15/2014] [Accepted: 10/20/2014] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) have been found to be differentially expressed during cotton fibre development. However, which specific miRNAs and how they are involved in fibre development is unclear. Here, using deep sequencing, 65 conserved miRNA families were identified and 32 families were differentially expressed between leaf and ovule. At least 40 miRNAs were either leaf or ovule specific, whereas 62 miRNAs were shared in both leaf and ovule. qRT-PCR confirmed these miRNAs were differentially expressed during fibre early development. A total of 820 genes were potentially targeted by the identified miRNAs, whose functions are involved in a series of biological processes including fibre development, metabolism and signal transduction. Many predicted miRNA-target pairs were subsequently validated by degradome sequencing analysis. GO and KEGG analyses showed that the identified miRNAs and their targets were classified to 1027 GO terms including 568 biological processes, 324 molecular functions and 135 cellular components and were enriched to 78 KEGG pathways. At least seven unique miRNAs participate in trichome regulatory interaction network. Eleven trans-acting siRNA (tasiRNA) candidate genes were also identified in cotton. One has never been found in other plant species and two of them were derived from MYB and ARF, both of which play important roles in cotton fibre development. Sixteen genes were predicted to be tasiRNA targets, including sucrose synthase and MYB2. Together, this study discovered new miRNAs in cotton and offered evidences that miRNAs play important roles in cotton ovule/fibre development. The identification of tasiRNA genes and their targets broadens our understanding of the complicated regulatory mechanism of miRNAs in cotton.
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Affiliation(s)
- Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC, USA
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Sun R, Wang K, Guo T, Jones DC, Cobb J, Zhang B, Wang Q. Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii. Funct Integr Genomics 2015; 15:481-93. [PMID: 25809690 DOI: 10.1007/s10142-015-0437-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/02/2015] [Accepted: 03/09/2015] [Indexed: 12/17/2022]
Abstract
Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In this study, a total of 35 ARF genes, named as GrARFs, were identified in a diploid cotton species Gossypium raimondii. The 35 ARF genes were located in 12 of the 13 cotton chromosomes; the intron/exon distribution of the GrARF genes was similar among sister pairs, whereas the divergence of some GrARF genes suggests the possibility of functional diversification. Our results show that the middle domains of nine GrARF proteins rich in glutamine (Q) are activators, while 26 other GrARF proteins rich in proline (P), serine (S), and threonine (T) are repressors. Our results also show that the expression of GrARF genes is diverse in different tissues. The expression of GrARF1 was significantly higher in leaves, whereas GrARF2a had higher expression level in shoots, which implicates different roles in the tested tissues. The GrARF11 has a higher expression level in buds than that in leaves, while GrARF19.2 shows contrasting expression patterns, having higher expression in leaves than that in buds. This suggests that they play different roles in leaves and buds. During long-term evolution of G. raimondii, some ARF genes were lost and some arose. The identification and characterization of the ARF genes in G. raimondii elucidate its important role in cotton that ARF genes regulate the development of flower buds, sepals, shoots, and leaves.
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Affiliation(s)
- Runrun Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
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Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda ABV, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics 2014. [PMID: 25359292 DOI: 10.1186/1471‐2164‐15‐945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. RESULTS Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3-79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. CONCLUSIONS This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
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Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda ABV, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics 2014; 15:945. [PMID: 25359292 PMCID: PMC4298081 DOI: 10.1186/1471-2164-15-945] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 10/03/2014] [Indexed: 11/18/2022] Open
Abstract
Background Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. Results Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3–79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. Conclusions This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-945) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
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Ma J, Wang Q, Sun R, Xie F, Jones DC, Zhang B. Genome-wide identification and expression analysis of TCP transcription factors in Gossypium raimondii. Sci Rep 2014; 4:6645. [PMID: 25322260 PMCID: PMC5377578 DOI: 10.1038/srep06645] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/30/2014] [Indexed: 12/04/2022] Open
Abstract
Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play versatile functions in multiple aspects of plant growth and development. However, no systematical study has been performed in cotton. In this study, we performed for the first time the genome-wide identification and expression analysis of the TCP transcription factor family in Gossypium raimondii. A total of 38 non-redundant cotton TCP encoding genes were identified. The TCP transcription factors were divided into eleven subgroups based on phylogenetic analysis. Most TCP genes within the same subfamily demonstrated similar exon and intron organization and the motif structures were highly conserved among the subfamilies. Additionally, the chromosomal distribution pattern revealed that TCP genes were unevenly distributed across 11 out of the 13 chromosomes; segmental duplication is a predominant duplication event for TCP genes and the major contributor to the expansion of TCP gene family in G. raimondii. Moreover, the expression profiles of TCP genes shed light on their functional divergence.
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Affiliation(s)
- Jun Ma
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qinglian Wang
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, P. R. China
| | - Runrun Sun
- 1] Department of Biology, East Carolina University, Greenville, NC 27858, USA [2] Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, P. R. China
| | - Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | | | - Baohong Zhang
- 1] Department of Biology, East Carolina University, Greenville, NC 27858, USA [2] Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, P. R. China
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Jones DC, Bennett CR, Smith MA, Scott AM. High-power beam transport through a hollow-core photonic bandgap fiber. Opt Lett 2014; 39:3122-3125. [PMID: 24875992 DOI: 10.1364/ol.39.003122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We investigate the use of a seven-cell hollow-core photonic bandgap fiber for transport of CW laser radiation from a single-mode, narrow-linewidth, high-power fiber laser amplifier. Over 90% of the amplifier output was coupled successfully and transmitted through the fiber in a near-Gaussian mode, with negligible backreflection into the source. 100 W of power was successfully transmitted continuously without damage and 160 W of power was transmitted briefly before the onset of thermal lensing in the coupling optics.
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Hunt CG, Houtman CJ, Jones DC, Kitin P, Korripally P, Hammel KE. Spatial mapping of extracellular oxidant production by a white rot basidiomycete on wood reveals details of ligninolytic mechanism. Environ Microbiol 2012. [PMID: 23206186 DOI: 10.1111/1462-2920.12039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Oxidative cleavage of the recalcitrant plant polymer lignin is a crucial step in global carbon cycling, and is accomplished most efficiently by fungi that cause white rot of wood. These basidiomycetes secrete many enzymes and metabolites with proposed ligninolytic roles, and it is not clear whether all of these agents are physiologically important during attack on natural lignocellulosic substrates. One new approach to this problem is to infer properties of ligninolytic oxidants from their spatial distribution relative to the fungus on the lignocellulose. We grew Phanerochaete chrysosporium on wood sections in the presence of oxidant-sensing beads based on the ratiometric fluorescent dye BODIPY 581/591. The beads, having fixed locations relative to the fungal hyphae, enabled spatial mapping of cumulative extracellular oxidant distributions by confocal fluorescence microscopy. The results showed that oxidation gradients occurred around the hyphae, and data analysis using a mathematical reaction-diffusion model indicated that the dominant oxidant during incipient white rot had a half-life under 0.1 s. The best available hypothesis is that this oxidant is the cation radical of the secreted P. chrysosporium metabolite veratryl alcohol.
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Abstract
INTRODUCTION The elderly represent an increasing proportion of society. Management of maxillofacial trauma in this population may be complicated by coexisting medical conditions, requiring multi-disciplinary care. METHODS This retrospective audit assesses the incidence and pattern of maxillofacial trauma in elderly patients (≥60 years) presented to the Merseyside Regional Maxillofacial Unit. Over the time period of 2003, 2004 and 2005, 7905 trauma patients presented to the accident and emergency department, of whom 757 were elderly (10%). RESULTS Results indicated that the male to female ratio was 1:1.4. The commonest cause of injury was a fall (83%) followed by an assault (6%); the majority of falls occurring in the home. CONCLUSION Management of maxillofacial injuries in this population should focus on targeted prevention programmes, which address known risk factors for falling. We believe that this is a public health issue. Members of the maxillofacial team should be aware of common risk factors of falls in elderly. Better collaboration with the Medicine for Elderly team should be considered at an early stage on managing these patients.
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Mirik M, Jones DC, Price JA, Workneh F, Ansley RJ, Rush CM. Satellite Remote Sensing of Wheat Infected by Wheat streak mosaic virus. Plant Dis 2011; 95:4-12. [PMID: 30743657 DOI: 10.1094/pdis-04-10-0256] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The prevalence of wheat streak mosaic, caused by Wheat streak mosaic virus, was assessed using Landsat 5 Thematic Mapper (TM) images in two counties of the Texas Panhandle during the 2005-2006 and 2007-2008 crop years. In both crop years, wheat streak mosaic was widely distributed in the counties studied. Healthy and diseased wheat were separated on the images using the maximum likelihood classifier. The overall classification accuracies were between 89.47 and 99.07% for disease detection when compared to "ground truth" field observations. Omission errors (i.e., pixels incorrectly excluded from a particular class and assigned to other classes) varied between 0 and 12.50%. Commission errors (i.e., pixels incorrectly assigned to a particular class that actually belong to other classes) ranged from 0 to 23.81%. There were substantial differences between planted wheat acreage reported by the United States Department of Agriculture-National Agricultural Statistics Service (USDA-NASS) and that detected by image analyses. However, harvested wheat acreage reported by USDA-NASS and that detected by image classifications were closely matched. These results indicate that the TM image can be used to accurately detect and quantify incidence of wheat streak mosaic over large areas. This method appears to be one of the best currently available for identification and mapping disease incidence over large and remote areas by offering a repeatable, inexpensive, and synoptic strategy during the course of a growing season.
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Affiliation(s)
- M Mirik
- Texas AgriLife Research, Vernon 76385
| | - D C Jones
- Texas AgriLife Research, Bushland 79012
| | - J A Price
- Texas AgriLife Research, Bushland 79012
| | - F Workneh
- Texas AgriLife Research, Bushland 79012
| | | | - C M Rush
- Texas AgriLife Research, Bushland 79012
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Workneh F, Price JA, Jones DC, Rush CM. Wheat Streak Mosaic: A Classic Case of Plant Disease Impact on Soil Water Content and Crop Water-Use Efficiency. Plant Dis 2010; 94:771-774. [PMID: 30754315 DOI: 10.1094/pdis-94-6-0771] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- F Workneh
- Texas AgriLife Research, Amarillo, TX 79106
| | - J A Price
- Texas AgriLife Research, Amarillo, TX 79106
| | - D C Jones
- Texas AgriLife Research, Amarillo, TX 79106
| | - C M Rush
- Texas AgriLife Research, Amarillo, TX 79106
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Price JA, Workneh F, Evett SR, Jones DC, Arthur J, Rush CM. Effects of Wheat streak mosaic virus on Root Development and Water-Use Efficiency of Hard Red Winter Wheat. Plant Dis 2010; 94:766-770. [PMID: 30754301 DOI: 10.1094/pdis-94-6-0766] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Greenhouse and field studies were conducted to determine the effects of Wheat streak mosaic virus (WSMV), a member of the family Potyviridae, on root development and water-use efficiency (WUE) of two hard red winter wheat (Triticum aestivum) cultivars, one susceptible and one resistant to WSMV. In the greenhouse studies, wheat cultivars were grown under three water regimes of 30, 60, and 80% soil saturation capacity. After inoculation with WSMV, plants were grown for approximately 4 weeks and then harvested. Root and shoot weights were measured to determine the effect of the disease on biomass. In all water treatments, root biomass and WUE of inoculated susceptible plants were significantly less (P < 0.05) than those of the noninoculated control plants. However, in the resistant cultivar, significance was only found in the 30 and 60% treatments for root weight and WUE, respectively. Field studies were also conducted under three water regimes based on reference evapotranspiration rates. Significant reductions in forage, grain yield, and crop WUE were observed in the inoculated susceptible plots compared with the noninoculated plots. Both studies demonstrated that wheat streak mosaic reduces WUE, which is a major concern in the Texas Panhandle because of limited availability of water.
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Affiliation(s)
- J A Price
- Texas AgriLife Research, Amarillo 79106
| | - F Workneh
- Texas AgriLife Research, Amarillo 79106
| | - S R Evett
- United States Department of Agriculture-Agricultural Research Service Conservation & Production Research Laboratory, Bushland, TX 79012
| | | | - J Arthur
- Texas AgriLife Research, Amarillo
| | - C M Rush
- Texas AgriLife Research, Amarillo
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Allen TW, Jones DC, Boratynski TN, Ykema RE, Rush CM. Application of the Humid Thermal Index for Relating Bunted Kernel Incidence to Soilborne Tilletia indica Teliospores in an Arizona Durum Wheat Field. Plant Dis 2009; 93:713-719. [PMID: 30764364 DOI: 10.1094/pdis-93-7-0713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A study was conducted to determine the relationship between soilborne Tilletia indica teliospore density and Karnal bunt incidence in an Arizona durum wheat field in 2005 and 2006. Soil samples were collected from 507 sample points according to a grid marked in a 7.7-ha field. Approximately 500 g of soil from the top 5 cm was collected from each sample point, and teliospores were recovered from 25-g aliquots by a modified size-selective sieving, sucrose centrifugation procedure. Twenty-five and 50 wheat heads were collected from a 1-m2 area around each sample point in May 2005 and June 2006, respectively. Wheat head samples from each sample point were bulked, threshed, and examined for the presence of bunted kernels. Additionally, data for soilborne teliospores and percent bunted kernels from 70 sample points in 2005 and 2006 that corresponded to sample points from a 2004 bunted kernel survey conducted by the USDA and Arizona Department of Agriculture were analyzed. Soilborne teliospore numbers ranged from 6 to 1,000 per 25-g soil sample in the 2-year study. No bunted kernels were recovered in 2005; however, two sample points yielded bunted kernels in 2006. Weather data from three time periods in 2004, 2005, and 2006 were applied to the humid thermal index model and suggested that a conducive environment for disease development existed in 2005. Based on the data from this research, we concluded that even though high numbers of soilborne teliospores were present in the field, and although a conducive environment was present for disease to develop on only one occasion, a direct relationship between soilborne teliospores and disease incidence may not exist.
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Affiliation(s)
- T W Allen
- Texas AgriLife Research, 2301 Experiment Station Road, Bushland 79012-0010
| | - D C Jones
- Texas AgriLife Research, 2301 Experiment Station Road, Bushland 79012-0010
| | | | - R E Ykema
- Arizona Department of Agriculture, Phoenix 85009-2701
| | - C M Rush
- Texas AgriLife Research, 2301 Experiment Station Road, Bushland 79012-0010
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Workneh F, Jones DC, Rush CM. Quantifying wheat yield across the field as a function of wheat streak mosaic intensity: a state space approach. Phytopathology 2009; 99:432-440. [PMID: 19271985 DOI: 10.1094/phyto-99-4-0432] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Wheat streak mosaic virus (WSMV), vectored by the wheat curl mite Aceria tosichella, is one of the major limiting factors in wheat production in the Texas Panhandle. The mites are blown by wind into wheat fields from nearby volunteer wheat fields or fields supporting vegetation which harbor virulent mites. Consequently, gradients of wheat streak severity are often observed stretching from the edges of wheat fields into the center or beyond. To describe the magnitude of the spatial relationships between grain yield and wheat streak intensity across the field, studies were conducted in 2006 and 2007 in three infected fields. Wheat streak severity was quantified with reflectance measurements (remote sensing) at 555-nm wave length using a hand-held radiometer. Measurements were taken in several equally spaced 1 m(2) locations along a total of eight transects and grain yield was assessed from a 0.8 m(2) area of each location. State space analysis was used to describe the relationships in which yield data and reflectance values were used as dependent and explanatory variables, respectively. A structural time series model was formulated as a state space model where the unobserved components were modeled explicitly. In the analysis the state of yield at current location (d) was related to the state of wheat streak intensity either at current locations (d) or lagged locations with autoregressive values of the first order (d-1) or greater. There were significant cross-correlations between yield and wheat streak intensity up to distances of 150 m (P < or = 0.05). Grain yield at the current position was significantly correlated with reflectance values at the same location and/or at lagged locations. The spatial aspects of the yield-reflectance relationships were best described by state space models with stochastic trends without slopes or deterministic trends with or without slopes. The models correctly predicted almost all of the observed yield values as a function of wheat streak intensity across the field within the 95% confidence interval. Results obtained in this study suggest that state space methodology can be a powerful tool in the study of plant disease spread as a function of other variables.
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Jones DC, Lakatos A, Rogge GA, Kuhar MJ. Regulation of cocaine- and amphetamine-regulated transcript mRNA expression by calcium-mediated signaling in GH3 cells. Neuroscience 2009; 160:339-47. [PMID: 19258027 DOI: 10.1016/j.neuroscience.2009.02.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/20/2009] [Accepted: 02/23/2009] [Indexed: 11/28/2022]
Abstract
Cocaine- and amphetamine-regulated-transcript (CART) peptides are associated with multiple physiological processes, including, feeding, body weight, and the response to drugs of abuse. CART mRNA and peptide levels and the expression of the CART gene appears to be under the control of a number of extra- and intra-cellular factors including the transcription factor, cAMP response element binding protein (CREB). Similar to the effects of CART, Ca(2+) signaling leads to the phosphorylation of CREB and has been associated with both feeding and the actions of psychostimulants; therefore, we hypothesized that Ca(2+) may play a role in CART gene regulation. We used real-time PCR (rtPCR) and GH3 cells to examine the effect of ionomycin, which increases intracellular Ca(2+), on CART mRNA levels. Ionomycin increased CART mRNA in a dose- and time-dependent manner. The effect of ionomycin appeared transient as CART mRNA had returned to control levels 3 h following treatment. Calmidazolium and KN93, inhibitors of calmodulin and Ca(2+)-modulated protein (CaM) kinases respectively, attenuated the effect of ionomycin (10 microM) on CART mRNA levels suggesting a calmodulin-dependent mechanism. Western immunoblotting indicated that ionomycin increased phosphorylated cAMP response element binding protein (pCREB) levels and electrophoretic mobility shift assay/supershift assay using antibodies against pCREB demonstrated increased levels of a CART oligo/pCREB protein complex. Finally, we showed that injection of ionomycin into the rat nucleus accumbens increases CART mRNA levels. To our knowledge, this is the first study providing evidence that the CART gene is, in part, regulated by Ca(2+)/CaM/CREB-dependent cell signaling.
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Affiliation(s)
- D C Jones
- Division of Neuroscience, Yerkes National Primate Research Center of Emory University, 945 Gatewood Road, Atlanta, GA 30329, USA.
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Lacey LA, Horton DR, Jones DC, Headrick HL, Neven LG. Efficacy of the biofumigant fungus Muscodor albus (Ascomycota: Xylariales) for control of codling moth (Lepidoptera: Tortricidae) in simulated storage conditions. J Econ Entomol 2009; 102:43-49. [PMID: 19253616 DOI: 10.1603/029.102.0107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), a serious pest of pome fruit, is a threat to exportation of apples (Malus spp.) because of the possibility of shipping infested fruit. The need for alternatives to fumigants such as methyl bromide for quarantine security of exported fruit has encouraged the development of effective fumigants with reduced side effects. The endophytic fungus Muscodor albus Worapong, Strobel and Hess (Ascomycota: Xylariales) produces volatile compounds that are biocidal for several pest organisms, including plant pathogens and insect pests. The objectives of our research were to determine the effects of M. albus volatile organic compounds (VOCs) on codling moth adults, neonate larvae, larvae in infested apples, and diapausing cocooned larvae in simulated storage conditions. Fumigation of adult codling moth with VOCs produced by M. albus for 3 d and incubating in fresh air for 24 h at 25 degrees C resulted in 81% corrected mortality. Four- and 5-d exposures resulted in higher mortality (84 and 100%, respectively), but control mortality was also high due to the short life span of the moths. Exposure of neonate larvae to VOCs for 3 d on apples and incubating for 7 d resulted in 86% corrected mortality. Treated larvae were predominantly first instars, whereas 85% of control larvae developed to second and third instars. Exposure of apples that had been infested for 5 d, fumigated with M. albus VOCs for 3 d, and incubated as described above resulted in 71% corrected larval mortality. Exposure of diapausing cocooned codling moth larvae to VOCs for 7 or 14 d resulted in 31 and 100% mortality, respectively, with negligible control mortality. Our data on treatment of several stages of codling moth with M. albus VOCs indicate that the fungus could provide an alternative to broad spectrum chemical fumigants for codling moth control in storage and contribute to the systems approach to achieve quarantine security of exported apples.
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Affiliation(s)
- L A Lacey
- USDA-ARS, Yakima Agricultural Research Laboratory, 5230 Konnowac Pass Road, Wapato, WA 98951, USA.
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Jones DC, Stacey CD, Scott AM. Phase stabilization of a large-mode-area ytterbium-doped fiber amplifier. Opt Lett 2007; 32:466-8. [PMID: 17392889 DOI: 10.1364/ol.32.000466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Measurements are reported on the open and closed-loop phase stability of a large-mode-area ytterbium-doped fiber amplifier. Phase fluctuations are characterized by a high-frequency low-amplitude jitter superimposed on a slow power-dependent drift. The amplifier may be phase locked to a precision of lambda/20 by using a low-bandwidth feedback loop.
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Affiliation(s)
- D C Jones
- QinetiQ, St. Andrews Road, Malvern, Worcestershire, UK.
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Jones DC, Edgar RS, Ahmad T, Cummings JRF, Jewell DP, Trowsdale J, Young NT. Killer Ig-like receptor (KIR) genotype and HLA ligand combinations in ulcerative colitis susceptibility. Genes Immun 2006; 7:576-82. [PMID: 16929347 DOI: 10.1038/sj.gene.6364333] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Killer immunoglobulin-like receptors (KIRs) are expressed on natural killer cells and some T-cell subsets and produce either activation or inhibitory signals upon binding with the appropriate human leucocyte antigen (HLA) ligand on target cells. Recent genetic association studies have implicated KIR genotype in the development of several inflammatory conditions. Ulcerative colitis (UC) is an inflammatory disorder of the colonic mucosa that results from an inappropriate activation of the immune system driven by host bacterial flora. We developed a polymerase chain reaction-sequence specific primer (SSP)-based assay to genotype 194 UC patients and 216 control individuals for 14 KIR genes, the HLA-Cw ligand epitopes of the KIR2D receptors and a polymorphism of the lectin-like-activating receptor NKG2D. Initial analysis found the phenotype frequency of KIR2DL2 and -2DS2 to be significantly increased in the UC cohort (P=0.030 and 0.038, respectively). Logistic regression analysis revealed a protective effect conferred by KIR2DL3 in the presence of its ligand HLA-Cw group 1 (P=0.019). These results suggest that KIR genotype and HLA ligand interaction may contribute to the genetic susceptibility of UC.
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Affiliation(s)
- D C Jones
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
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Abstract
The authors describe the case of a 10-year-old girl presenting with Axenfeld-Rieger syndrome (ARS), a rare autosomal dominant condition. The patient showed severe hypodontia, microdontia and short roots. Early diagnosis of the syndrome from its dento-facial and systemic features is important so that subsequent ocular complications may be prevented.
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Affiliation(s)
- E M O'Dwyer
- Department of Oral and Maxillofacial Surgery, Arrowe Park Hospital, Upton, UK
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Abstract
We report a case of mediastinitis complicating a dental infection in a 40-year-old male. Despite drainage of the localised neck abscess and the administration of systemic antibiotics, his submandibular abscess extended to involve the pericardial and pleural cavities. Drainage procedures and thoracotomies were required to treat the empyema and purulent pericarditis. Computed tomography was used to follow the progression of disease and assess the efficacy of treatment.
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Affiliation(s)
- H Pappa
- Craniofacial Fellow, Alder Hey Children's Hospital, Eaton Road, Liverpool, L12 2AP.
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