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Jordan KW, Bradbury PJ, Miller ZR, Nyine M, He F, Fraser M, Anderson J, Mason E, Katz A, Pearce S, Carter AH, Prather S, Pumphrey M, Chen J, Cook J, Liu S, Rudd JC, Wang Z, Chu C, Ibrahim AMH, Turkus J, Olson E, Nagarajan R, Carver B, Yan L, Taagen E, Sorrells M, Ward B, Ren J, Akhunova A, Bai G, Bowden R, Fiedler J, Faris J, Dubcovsky J, Guttieri M, Brown-Guedira G, Buckler E, Jannink JL, Akhunov ED. Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation. G3 (Bethesda) 2021; 12:6423995. [PMID: 34751373 PMCID: PMC9210282 DOI: 10.1093/g3journal/jkab390] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/21/2021] [Indexed: 12/04/2022]
Abstract
To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the Wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01× sequence coverage, which was slightly lower than the accuracy obtained using the 0.5× sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (P-value < 2 × 10−14) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2× GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequilibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.
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Affiliation(s)
- Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Peter J Bradbury
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Zachary R Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Moses Nyine
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Max Fraser
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jim Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Esten Mason
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Arron H Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Samuel Prather
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, 83210, USA
| | - Jason Cook
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Shuyu Liu
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Jackie C Rudd
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Zhen Wang
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Chenggen Chu
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Amir M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Jonathan Turkus
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Eric Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Ragupathi Nagarajan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Brett Carver
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Ellie Taagen
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Mark Sorrells
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Brian Ward
- USDA-ARS, Plant Science Research Unit, Raleigh, NC, 27695, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Integrative Genomics Facility, Kansas State University, Manhattan, KS, 66506 USA
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Integrative Genomics Facility, Kansas State University, Manhattan, KS, 66506 USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Robert Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Jason Fiedler
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Justin Faris
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Mary Guttieri
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | | | - Ed Buckler
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Jean-Luc Jannink
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
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Saintenac C, Cambon F, Aouini L, Verstappen E, Ghaffary SMT, Poucet T, Marande W, Berges H, Xu S, Jaouannet M, Favery B, Alassimone J, Sánchez-Vallet A, Faris J, Kema G, Robert O, Langin T. A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch. Nat Commun 2021; 12:433. [PMID: 33469010 PMCID: PMC7815785 DOI: 10.1038/s41467-020-20685-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 04/07/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
The poverty of disease resistance gene reservoirs limits the breeding of crops for durable resistance against evolutionary dynamic pathogens. Zymoseptoria tritici which causes Septoria tritici blotch (STB), represents one of the most genetically diverse and devastating wheat pathogens worldwide. No fully virulent Z. tritici isolates against synthetic wheats carrying the major resistant gene Stb16q have been identified. Here, we use comparative genomics, mutagenesis and complementation to identify Stb16q, which confers broad-spectrum resistance against Z. tritici. The Stb16q gene encodes a plasma membrane cysteine-rich receptor-like kinase that was recently introduced into cultivated wheat and which considerably slows penetration and intercellular growth of the pathogen.
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Affiliation(s)
- Cyrille Saintenac
- grid.503180.f0000 0004 0613 5360Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France
| | - Florence Cambon
- grid.503180.f0000 0004 0613 5360Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France
| | - Lamia Aouini
- grid.4818.50000 0001 0791 5666Wageningen University and Research (Wageningen Plant Research, Biointeractions and Plant Health), PO Box 16, 6700AA Wageningen, The Netherlands ,grid.169077.e0000 0004 1937 2197Present Address: Department of Agronomy, Purdue University, West Lafayette, IN 47907 USA
| | - Els Verstappen
- grid.4818.50000 0001 0791 5666Wageningen University and Research (Wageningen Plant Research, Biointeractions and Plant Health), PO Box 16, 6700AA Wageningen, The Netherlands
| | - Seyed Mahmoud Tabib Ghaffary
- grid.4818.50000 0001 0791 5666Wageningen University and Research (Wageningen Plant Research, Biointeractions and Plant Health), PO Box 16, 6700AA Wageningen, The Netherlands ,Present Address: Seed and Plant Improvement Research Department, Safiabad Agricultural and Natural Resources Research and Education Center, AREEO, Dezful, Iran
| | - Théo Poucet
- grid.503180.f0000 0004 0613 5360Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France ,grid.11480.3c0000000121671098Present Address: Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain ,grid.412041.20000 0001 2106 639XPresent Address: Université de Bordeaux, 146 rue Leo-Saignat, Bordeaux, Cedex 33076 France
| | - William Marande
- grid.507621.7CNRGV (Centre National des Ressources Génomiques Végétales), INRAE, UPR 1258 Castanet-Tolosan, France
| | - Hélène Berges
- grid.507621.7CNRGV (Centre National des Ressources Génomiques Végétales), INRAE, UPR 1258 Castanet-Tolosan, France ,grid.508749.7Present Address: Inari Agriculture, One Kendall Square Building 600/700, Cambridge, MA 02139 USA
| | - Steven Xu
- grid.463419.d0000 0001 0946 3608United States Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102 USA
| | - Maëlle Jaouannet
- grid.4444.00000 0001 2112 9282INRAE, Université Côte d’Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Bruno Favery
- grid.4444.00000 0001 2112 9282INRAE, Université Côte d’Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Julien Alassimone
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Andrea Sánchez-Vallet
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland ,grid.5690.a0000 0001 2151 2978Present Address: Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA). Campus de Montegancedo-UPM, 28223-Pozuelo de Alarcón Madrid, Spain
| | - Justin Faris
- grid.463419.d0000 0001 0946 3608United States Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102 USA
| | - Gert Kema
- grid.4818.50000 0001 0791 5666Wageningen University and Research (Wageningen Plant Research, Biointeractions and Plant Health), PO Box 16, 6700AA Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University (Laboratory of Phytopathology), 6700AA Wageningen, The Netherlands
| | - Oliver Robert
- Florimond-Desprez, 3 rue Florimond-Desprez, BP 41, 59242 Cappelle-en-Pevele, France
| | - Thierry Langin
- grid.503180.f0000 0004 0613 5360Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France
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3
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Mazzucotelli E, Sciara G, Mastrangelo AM, Desiderio F, Xu SS, Faris J, Hayden MJ, Tricker PJ, Ozkan H, Echenique V, Steffenson BJ, Knox R, Niane AA, Udupa SM, Longin FCH, Marone D, Petruzzino G, Corneti S, Ormanbekova D, Pozniak C, Roncallo PF, Mather D, Able JA, Amri A, Braun H, Ammar K, Baum M, Cattivelli L, Maccaferri M, Tuberosa R, Bassi FM. The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles. Front Plant Sci 2020; 11:569905. [PMID: 33408724 PMCID: PMC7779600 DOI: 10.3389/fpls.2020.569905] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/24/2020] [Indexed: 05/04/2023]
Abstract
Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94-97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970-2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r 2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (F st ) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.
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Affiliation(s)
- Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Anna M. Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Bergamo, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Steven S. Xu
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, Fargo, ND, United States
| | - Justin Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, Fargo, ND, United States
| | - Matthew J. Hayden
- Agriculture Victoria, Agribio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Penny J. Tricker
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida, Departamento de Agronomía, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Ron Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Abdoul A. Niane
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Sripada M. Udupa
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | | | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Simona Corneti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Danara Ormanbekova
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Curtis Pozniak
- Plant Sciences and Crop Development Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - Pablo F. Roncallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida, Departamento de Agronomía, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Diane Mather
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Jason A. Able
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Hans Braun
- Plant Sciences and Crop Development Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - Karim Ammar
- International Maize and Wheat Improvement Center, Texcoco de Mora, Mexico
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
- *Correspondence: Filippo M. Bassi,
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Sosa V, Melkie M, Sulca C, Li J, Tang L, Li J, Faris J, Foley B, Banh T, Kato M, Cheruzel LE. Selective Light-Driven Chemoenzymatic Trifluoromethylation/Hydroxylation of Substituted Arenes. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04160] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor Sosa
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Marya Melkie
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Carolina Sulca
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Jennifer Li
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Lawrence Tang
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Jeffrey Li
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Justin Faris
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Bridget Foley
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Tam Banh
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Mallory Kato
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
| | - Lionel E. Cheruzel
- Department of Chemistry, San José State University, One Washington Square, San
José, California 95192-0101, United States
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5
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Nirmala J, Saini J, Newcomb M, Olivera P, Gale S, Klindworth D, Elias E, Talbert L, Chao S, Faris J, Xu S, Jin Y, Rouse MN. Discovery of a Novel Stem Rust Resistance Allele in Durum Wheat that Exhibits Differential Reactions to Ug99 Isolates. G3 (Bethesda) 2017; 7:3481-3490. [PMID: 28855282 PMCID: PMC5633396 DOI: 10.1534/g3.117.300209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn, can incur yield losses in susceptible cultivars of durum wheat, Triticum turgidum ssp. durum (Desf.) Husnot. Although several durum cultivars possess the stem rust resistance gene Sr13, additional genes in durum wheat effective against emerging virulent races have not been described. Durum line 8155-B1 confers resistance against the P. graminis f. sp. tritici race TTKST, the variant race of the Ug99 race group with additional virulence to wheat stem rust resistance gene Sr24 However, 8155-B1 does not confer resistance to the first-described race in the Ug99 race group: TTKSK. We mapped a single gene conferring resistance in 8155-B1 against race TTKST, Sr8155B1, to chromosome arm 6AS by utilizing Rusty/8155-B1 and Rusty*2/8155-B1 populations and the 90K Infinium iSelect Custom bead chip supplemented by KASP assays. One marker, KASP_6AS_IWB10558, cosegregated with Sr8155B1 in both populations and correctly predicted Sr8155B1 presence or absence in 11 durum cultivars tested. We confirmed the presence of Sr8155B1 in cultivar Mountrail by mapping in the population Choteau/Mountrail. The marker developed in this study could be used to predict the presence of resistance to race TTKST in uncharacterized durum breeding lines, and also to combine Sr8155B1 with resistance genes effective to Ug99 such as Sr13 The map location of Sr8155B1 cannot rule out the possibility that this gene is an allele at the Sr8 locus. However, race specificity indicates that Sr8155B1 is different from the known alleles Sr8a and Sr8b.
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Affiliation(s)
- Jayaveeramuthu Nirmala
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, Minnesota 55108
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Jyoti Saini
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108
| | - Maria Newcomb
- The School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Pablo Olivera
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Sam Gale
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, Minnesota 55108
| | - Daryl Klindworth
- Cereal Crops Research, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58102
| | - Elias Elias
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108
| | - Luther Talbert
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717
| | - Shiaoman Chao
- Cereal Crops Research, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58102
| | - Justin Faris
- Cereal Crops Research, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58102
| | - Steven Xu
- Cereal Crops Research, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58102
| | - Yue Jin
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, Minnesota 55108
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Matthew N Rouse
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, Minnesota 55108
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
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6
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Qureshi N, Bariana H, Forrest K, Hayden M, Keller B, Wicker T, Faris J, Salina E, Bansal U. Fine mapping of the chromosome 5B region carrying closely linked rust resistance genes Yr47 and Lr52 in wheat. Theor Appl Genet 2017; 130:495-504. [PMID: 27866228 DOI: 10.1007/s00122-016-2829-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/12/2016] [Indexed: 05/26/2023]
Abstract
Fine mapping of Yr47 and Lr52 in chromosome arm 5BS of wheat identified close linkage of the marker sun180 to both genes and its robustness for marker-assisted selection was demonstrated. The widely effective and genetically linked rust resistance genes Yr47 and Lr52 have previously been mapped in the short arm of chromosome 5B in two F3 populations (Aus28183/Aus27229 and Aus28187/Aus27229). The Aus28183/Aus27229 F3 population was advanced to generate an F6 recombinant inbred line (RIL) population to identify markers closely linked with Yr47 and Lr52. Diverse genomic resources including flow-sorted chromosome survey sequence contigs representing the orthologous region in Brachypodium distachyon, the physical map of chromosome arm 5BS, expressed sequence tags (ESTs) located in the 5BS6-0.81-1.00 deletion bin and resistance gene analog contigs of chromosome arm 5BS were used to develop markers to saturate the target region. Selective genotyping was also performed using the iSelect 90 K Infinium wheat SNP assay. A set of SSR, STS, gene-based and SNP markers were developed and genotyped on the Aus28183/Aus27229 RIL population. Yr47 and Lr52 are genetically distinct genes that mapped 0.4 cM apart in the RIL population. The SSR marker sun180 co-segregated with Lr52 and mapped 0.4 cM distal to Yr47. In a high resolution mapping population of 600 F2 genotypes Yr47 and Lr52 mapped 0.2 cM apart and marker sun180 was placed 0.4 cM distal to Lr52. The amplification of a different sun180 amplicon (195 bp) than that linked with Yr47 and Lr52 (200 bp) in 204 diverse wheat genotypes demonstrated its robustness for marker-assisted selection of these genes.
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Affiliation(s)
- Naeela Qureshi
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney Plant Breeding Institute, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Harbans Bariana
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney Plant Breeding Institute, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Kerrie Forrest
- Department of Economic Development, Jobs, Transport and Resources, La Trobe University AgriBio, Bundoora, VIC, 3083, Australia
| | - Matthew Hayden
- Department of Economic Development, Jobs, Transport and Resources, La Trobe University AgriBio, Bundoora, VIC, 3083, Australia
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Red River Valley Agricultural Research Center, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA
| | - Elena Salina
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Urmil Bansal
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney Plant Breeding Institute, Private Bag 4011, Narellan, NSW, 2567, Australia.
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Tabernero J, van Geel R, Guren T, Yaeger R, Spreafico A, Faris J, Yoshino T, Yamada Y, Kim Tae W, Bendell J, Schuler M, Lenz HJ, Eskens F, Desai J, Hochster H, Avsar E, Demuth T, Sandor V, Elez E, Schellens J. O-026 Combination of encorafenib and cetuximab with or without alpelisib in patients with advanced BRAF-mutant colorectal cancer (BRAFm CRC): phase 2 results. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw198.25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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8
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Kariyawasam GK, Carter AH, Rasmussen JB, Faris J, Xu SS, Mergoum M, Liu Z. Genetic relationships between race-nonspecific and race-specific interactions in the wheat-Pyrenophora tritici-repentis pathosystem. Theor Appl Genet 2016; 129:897-908. [PMID: 26796533 DOI: 10.1007/s00122-016-2670-x] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/09/2016] [Indexed: 05/15/2023]
Abstract
We identified a major QTL conferring race-nonspecific resistance and revealed its relationships with race-specific interactions in the wheat- Pyrenophora tritici-repentis pathosystem. Tan spot, caused by the fungus Pyrenophora tritici-repentis (Ptr), is a destructive disease of wheat worldwide. The disease system is known to include inverse gene-for-gene, race-specific interactions involving the recognition of fungal-produced necrotrophic effectors (NEs) by corresponding host sensitivity genes. However, quantitative trait loci (QTLs) conferring race-nonspecific resistance have also been identified. In this work, we identified a major race-nonspecific resistance QTL and characterized its genetic relationships with the NE-host gene interactions Ptr ToxA-Tsn1 and Ptr ToxC-Tsc1 in a recombinant inbred wheat population derived from the cross between 'Louise' and 'Penawawa.' Both parental lines were sensitive to Ptr ToxA, but Penawawa and Louise were highly resistant and susceptible, respectively, to conidial inoculations of all races. Resistance was predominantly governed by a major race-nonspecific QTL on chromosome arm 3BL for resistance to all races. Another significant QTL was detected at the distal end of chromosome arm 1AS for resistance to the Ptr ToxC-producing isolates, which corresponded to the known location of the Tsc1 locus. The effects of the 3B and 1A QTLs were largely additive, and the 3B resistance QTL was epistatic to the Ptr ToxA-Tsn1 interaction. Resistance to race 2 in F1 plants was completely dominant; however, race 3-inoculated F1 plants were only moderately resistant because they developed chlorosis presumably due to the Ptr ToxC-Tsc1 interaction. This work provides further understanding of genetic resistance in the wheat-tan spot system as well as important guidance for tan spot resistance breeding.
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Affiliation(s)
- Gayan K Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Arron H Carter
- Department of Crop and Soil Science, Washington State University, Pullman, WA, 99164-6420, USA
| | - Jack B Rasmussen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, 58102, USA
| | - Steven S Xu
- USDA-ARS Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, 58102, USA
| | - Mohamed Mergoum
- Department of Plant Science, North Dakota State University, Fargo, ND, 58108, USA
- Department of Crop and Soil Sciences, University of Georgia, 1109 Experiment St, Griffin, GA, 30223, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.
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Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnol J 2015; 13:648-63. [PMID: 25424506 DOI: 10.1111/pbi.12288] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [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: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 05/20/2023]
Abstract
Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Andrea Ricci
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sara Giulia Milner
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Enrico Noli
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Simone Scalabrin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Vera Vendramin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | | | - Antonio Blanco
- Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Andrea Massi
- Società Produttori Sementi Bologna (PSB), Argelato, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
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Musselman M, Hall Zimmerman L, Saely S, Faris J, Sherwin R, Browning L. 311 Does Etomidate Dosing for Rapid Sequence Intubation Impact Hemodynamics? Ann Emerg Med 2011. [DOI: 10.1016/j.annemergmed.2011.06.342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Faris J. Book Review: Perioperative, Diagnostic and Interventional Ultrasound. Anaesth Intensive Care 2009. [DOI: 10.1177/0310057x0903700324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R, Gornicki P. Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci U S A 2002; 99:8133-8. [PMID: 12060759 PMCID: PMC123033 DOI: 10.1073/pnas.072223799] [Citation(s) in RCA: 524] [Impact Index Per Article: 23.8] [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] [Accepted: 04/12/2002] [Indexed: 11/18/2022] Open
Abstract
The classic wheat evolutionary history is one of adaptive radiation of the diploid Triticum/Aegilops species (A, S, D), genome convergence and divergence of the tetraploid (Triticum turgidum AABB, and Triticum timopheevii AAGG) and hexaploid (Triticum aestivum, AABBDD) species. We analyzed Acc-1 (plastid acetyl-CoA carboxylase) and Pgk-1 (plastid 3-phosphoglycerate kinase) genes to determine phylogenetic relationships among Triticum and Aegilops species of the wheat lineage and to establish the timeline of wheat evolution based on gene sequence comparisons. Triticum urartu was confirmed as the A genome donor of tetraploid and hexaploid wheat. The A genome of polyploid wheat diverged from T. urartu less than half a million years ago (MYA), indicating a relatively recent origin of polyploid wheat. The D genome sequences of T. aestivum and Aegilops tauschii are identical, confirming that T. aestivum arose from hybridization of T. turgidum and Ae. tauschii only 8,000 years ago. The diploid Triticum and Aegilops progenitors of the A, B, D, G, and S genomes all radiated 2.5-4.5 MYA. Our data suggest that the Acc-1 and Pgk-1 loci have different histories in different lineages, indicating genome mosaicity and significant intraspecific differentiation. Some loci of the S genome of Aegilops speltoides and the G genome of T. timophevii are closely related, suggesting the same origin of some parts of their genomes. None of the Aegilops genomes analyzed is a close relative of the B genome, so the diploid progenitor of the B genome remains unknown.
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Affiliation(s)
- Shaoxing Huang
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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14
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Faris J, Sirikhachornkit A, Haselkorn R, Gill B, Gornicki P. Chromosome mapping and phylogenetic analysis of the cytosolic acetyl-CoA carboxylase loci in wheat. Mol Biol Evol 2001; 18:1720-33. [PMID: 11504852 DOI: 10.1093/oxfordjournals.molbev.a003960] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The cytosolic isoform of plant acetyl-CoA carboxylase is a multidomain enzyme involved in the synthesis of very-long-chain fatty acids and in secondary metabolism. Chromosome mapping of wheat identified one locus containing cytosolic acetyl-CoA carboxylase genes (Acc-2) and a related partially processed pseudogene (Psi-Acc-2) in the distal region of the long arm of wheat homoeologous group 3 chromosomes. Multiple copies of the Acc-2 genes, whose presence was suggested by sequence analysis, are likely to be arranged in tandem repeats. At least three out of five genes cloned from hexaploid wheat map to this locus. Another locus containing Acc-2--related sequences is present in the distal region of the long arm of chromosome 5D. The identity of the hybridizing DNA present at this locus remains unknown. A system based on PCR-cloning and DNA sequence analysis of acetyl-CoA carboxylase genes was developed to address various phylogenetic and systematics questions in grasses. It was applied to reconstruct the phylogeny of the Acc-2 genes from D- and S-genome Aegilops and A-genome Triticum diploid species, AABB- and AAGG-genome tetraploid wheat, and AABBDD-genome hexaploid wheat, as well as from rye and barley. The combined cytogenetic and molecular evolution approach allowed assignment of gene sequences included in phylogenetic analysis to specific loci on homoeologous chromosomes. Recurring gene duplication followed by chromosome translocation and/or possible loss of some gene copies, as well as loss of introns, occurred in the gene family in different plant lineages. Two major Acc-2 clades appeared before the divergence of barley and rye. Nucleotide substitution rates in different parts of the Acc-2 gene were assessed. This analysis of the Acc-2 loci provides detailed information regarding evolutionary events at a low--copy-number locus containing important functional genes. These events are likely to be common and to play a significant role in shaping grass genomes.
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Affiliation(s)
- J Faris
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
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15
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Gornicki P, Faris J, King I, Podkowinski J, Gill B, Haselkorn R. Plastid-localized acetyl-CoA carboxylase of bread wheat is encoded by a single gene on each of the three ancestral chromosome sets. Proc Natl Acad Sci U S A 1997; 94:14179-84. [PMID: 9391173 PMCID: PMC28453 DOI: 10.1073/pnas.94.25.14179] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
5'-End fragments of two genes encoding plastid-localized acetyl-CoA carboxylase (ACCase; EC 6.4.1.2) of wheat (Triticum aestivum) were cloned and sequenced. The sequences of the two genes, Acc-1,1 and Acc-1,2, are 89% identical. Their exon sequences are 98% identical. The amino acid sequence of the biotin carboxylase domain encoded by Acc-1,1 and Acc-1,2 is 93% identical with the maize plastid ACCase but only 80-84% identical with the cytosolic ACCases from other plants and from wheat. Four overlapping fragments of cDNA covering the entire coding region were cloned by PCR and sequenced. The wheat plastid ACCase ORF contains 2,311 amino acids with a predicted molecular mass of 255 kDa. A putative transit peptide is present at the N terminus. Comparison of the genomic and cDNA sequences revealed introns at conserved sites found in the genes of other plant multifunctional ACCases, including two introns absent from the wheat cytosolic ACCase genes. Transcription start sites of the plastid ACCase genes were estimated from the longest cDNA clones obtained by 5'-RACE (rapid amplification of cDNA ends). The untranslated leader sequence encoded by the Acc-1 genes is at least 130-170 nucleotides long and is interrupted by an intron. Southern analysis indicates the presence of only one copy of the gene in each ancestral chromosome set. The gene maps near the telomere on the short arm of chromosomes 2A, 2B, and 2D. Identification of three different cDNAs, two corresponding to genes Acc-1,1 and Acc-1,2, indicates that all three genes are transcriptionally active.
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Affiliation(s)
- P Gornicki
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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16
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McCarthy D, Corban R, Legg S, Faris J. Effects of mild hypoxia on perceptual-motor performance: a signal-detection approach. Ergonomics 1995; 38:1979-1992. [PMID: 7588580] [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] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Twelve healthy male subjects were required to make speeded judgements concerning the orientation of visual stimuli while breathing air at reduced partial pressure in a hypobaric chamber at altitudes of 7000 and 12,000 ft. A control condition was also conducted at sea level, and subjects received practice on the task at sea level prior to the commencement of the experiment. Significantly slower response times were obtained at 7000 and 12,000 ft relative to sea level. A signal-detection analysis showed that accuracy of judgement was significantly poorer at 12,000 ft, but oxygen deprivation has no systematic effect on response criterion.
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Affiliation(s)
- D McCarthy
- Department of Psychology, University of Auckland, New Zealand
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17
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Yap MK, Garner LF, Legg S, Faris J. Effects of exposure to simulated altitudes on visual fields, contrast sensitivity, and dazzle recovery. Aviat Space Environ Med 1995; 66:243-6. [PMID: 7661834] [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] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Previous studies have shown that visual performance may be impaired at altitudes above 12,000 ft when supplementary oxygen is not used. What is not known is whether there may be subtle changes in visual function at altitudes to which airline cabins are usually pressurized. In this study, we measured spatial and temporal contrast sensitivity, central visual field thresholds, and macular photostress recovery time in 12 male subjects at sea level and at simulated altitudes of 7000 ft and 12,000 ft. Our results showed insignificant changes in spatial and temporal contrast sensitivity, central visual field thresholds and dazzle recovery time with respect to simulated altitudes.
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Affiliation(s)
- M K Yap
- Centre for Vision Research, University of Auckland, New Zealand
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18
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Solomont A, Faris J. Protection or pink slips--pro/con. Provider 1994; 20:64, 63. [PMID: 10132009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Abstract
Laboratory experiments, in which very small (approximately 20 nm) grains are produced in the presence of a magnetic field on the order of 100 Gauss in a low-pressure hydrogen atmosphere, have demonstrated that such smokes can become permanently magnetized. We show that magnetization results in an enormous enhancement in the coagulation efficiency of such materials even in the absence of external magnetic fields. Small iron grains should have been produced in the solar nebula by thermal processing of preexisting interstellar grains. If such processing occurred via high-energy electromagnetic events then the resultant magnetized grains could have triggered the formation of centimeter- to meter-sized protoplanetessimals by acting as "nets" capable of sweeping up nonconductive silicates suspended in the gas. It is possible that the presence of conductive fractal aggregates observed in modern-day protostellar disks could be explained by the enhanced coagulation efficiency of very small magnetized iron particles.
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Rocco F, Faris J. Executive recruitment. Part III--Evaluation and selection. OH 1976; 20:11-3. [PMID: 10246441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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23
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Rocco F, Faris J. Executive recruitment. Part II--The interview: intermediate stage. OH 1976; 20:10-3. [PMID: 10246436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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24
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Rocco F, Faris J. Executive recruitment. Part I--The planning stage. OH 1976; 20:13-5. [PMID: 10246432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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25
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James BJ, Agogino GA, Bishop CA, Boissevain E, Cohen R, VanStone JW, Driver HE, Faris J, Hickerson H, Howard JH, Kennard EA, Lurie NO, Maher RF, Rubel AJ. Continuity and Emergence in Indian Poverty Culture [and Comments and Reply]. Current Anthropology 1970. [DOI: 10.1086/201145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
We have studied Korotkoff sounds in 10 subjects by recording pressures and sounds simultaneously through a brachial arterial needle at locations both beyond and beneath the inflatable cuff. The Korotkoff sounds coincided with a small dip and ensuing steep rise in pressure immediately beyond the distal edge of the cuff. Sound intensity paralleled not only the rate and the acceleration of this steep ascent, but also the total pressure through which it was maintained. Pressures beneath the midportion of the cuff showed a more pronounced sharp initial negative dip, usually followed by a rapid reversal and steep rise, and the sounds were also recorded here in association with these rapid pressure changes. This study supports the hypothesis that the initial Korotkoff sound is produced by rapid changes of pressure both beneath and distal to the compressing cuff, sufficient in rate to impart sonic vibrations to the vessel wall and surrounding tissues. We have attempted to explain how these rapid pressure changes are produced.
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