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Ludwig E, Sumner J, Berry J, Polydore S, Ficor T, Agnew E, Haines K, Greenham K, Fahlgren N, Mockler TC, Gehan MA. Natural variation in Brachypodium distachyon responses to combined abiotic stresses. Plant J 2024; 117:1676-1701. [PMID: 37483133 DOI: 10.1111/tpj.16387] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023]
Abstract
The demand for agricultural production is becoming more challenging as climate change increases global temperature and the frequency of extreme weather events. This study examines the phenotypic variation of 149 accessions of Brachypodium distachyon under drought, heat, and the combination of stresses. Heat alone causes the largest amounts of tissue damage while the combination of stresses causes the largest decrease in biomass compared to other treatments. Notably, Bd21-0, the reference line for B. distachyon, did not have robust growth under stress conditions, especially the heat and combined drought and heat treatments. The climate of origin was significantly associated with B. distachyon responses to the assessed stress conditions. Additionally, a GWAS found loci associated with changes in plant height and the amount of damaged tissue under stress. Some of these SNPs were closely located to genes known to be involved in responses to abiotic stresses and point to potential causative loci in plant stress response. However, SNPs found to be significantly associated with a response to heat or drought individually are not also significantly associated with the combination of stresses. This, with the phenotypic data, suggests that the effects of these abiotic stresses are not simply additive, and the responses to the combined stresses differ from drought and heat alone.
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Affiliation(s)
- Ella Ludwig
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Joshua Sumner
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Jeffrey Berry
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
- Bayer Crop Sciences, St. Louis, Missouri, 63017, USA
| | - Seth Polydore
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Tracy Ficor
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Erica Agnew
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Kristina Haines
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Kathleen Greenham
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
- University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
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2
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Gao M, Lu Y, Geng F, Klose C, Staudt AM, Huang H, Nguyen D, Lan H, Lu H, Mockler TC, Nusinow DA, Hiltbrunner A, Schäfer E, Wigge PA, Jaeger KE. Phytochromes transmit photoperiod information via the evening complex in Brachypodium. Genome Biol 2023; 24:256. [PMID: 37936225 PMCID: PMC10631206 DOI: 10.1186/s13059-023-03082-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD1 (PPD1) and EARLY FLOWERING3 (ELF3) have been selected for in adapting barley and wheat to northern latitudes. How monocot plants sense photoperiod and integrate this information into growth and development is not well understood. RESULTS We find that phytochrome C (PHYC) is essential for flowering in Brachypodium distachyon. Conversely, ELF3 acts as a floral repressor and elf3 mutants display a constitutive long day phenotype and transcriptome. We find that ELF3 and PHYC occur in a common complex. ELF3 associates with the promoters of a number of conserved regulators of flowering, including PPD1 and VRN1. Consistent with observations in barley, we are able to show that PPD1 overexpression accelerates flowering in short days and is necessary for rapid flowering in response to long days. PHYC is in the active Pfr state at the end of the day, but we observe it undergoes dark reversion over the course of the night. CONCLUSIONS We propose that PHYC acts as a molecular timer and communicates information on night-length to the circadian clock via ELF3.
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Affiliation(s)
- Mingjun Gao
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yunlong Lu
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany
| | - Feng Geng
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Cornelia Klose
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
| | - Anne-Marie Staudt
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
| | - He Huang
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Duy Nguyen
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Hui Lan
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Han Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | | | - Andreas Hiltbrunner
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - Eberhard Schäfer
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, Freiburg, 79104, Germany
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK.
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany.
| | - Katja E Jaeger
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK.
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany.
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3
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Zhang Z, Pope M, Shakoor N, Pless R, Mockler TC, Stylianou A. Comparing Deep Learning Approaches for Understanding Genotype × Phenotype Interactions in Biomass Sorghum. Front Artif Intell 2022; 5:872858. [PMID: 35860344 PMCID: PMC9289439 DOI: 10.3389/frai.2022.872858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
We explore the use of deep convolutional neural networks (CNNs) trained on overhead imagery of biomass sorghum to ascertain the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. We consider both CNNs trained explicitly on the classification task of predicting whether an image shows a plant with a reference or alternate version of various SNPs as well as CNNs trained to create data-driven features based on learning features so that images from the same plot are more similar than images from different plots, and then using the features this network learns for genetic marker classification. We characterize how efficient both approaches are at predicting the presence or absence of a genetic markers, and visualize what parts of the images are most important for those predictions. We find that the data-driven approaches give somewhat higher prediction performance, but have visualizations that are harder to interpret; and we give suggestions of potential future machine learning research and discuss the possibilities of using this approach to uncover unknown genotype × phenotype relationships.
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Affiliation(s)
- Zeyu Zhang
- Department of Computer Science, George Washington University, Washington, DC, United States
| | - Madison Pope
- Department of Computer Science, Saint Louis University, Saint Louis, MO, United States
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, Mockler Lab, Saint Louis, MO, United States
| | - Robert Pless
- Department of Computer Science, George Washington University, Washington, DC, United States
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, Mockler Lab, Saint Louis, MO, United States
| | - Abby Stylianou
- Department of Computer Science, Saint Louis University, Saint Louis, MO, United States
- *Correspondence: Abby Stylianou
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4
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Muleta KT, Felderhoff T, Winans N, Walstead R, Charles JR, Armstrong JS, Mamidi S, Plott C, Vogel JP, Lemaux PG, Mockler TC, Grimwood J, Schmutz J, Pressoir G, Morris GP. The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange. Sci Adv 2022; 8:eabj4633. [PMID: 35138897 PMCID: PMC8827733 DOI: 10.1126/sciadv.abj4633] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Rapid environmental change can lead to population extinction or evolutionary rescue. The global staple crop sorghum (Sorghum bicolor) has recently been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). We characterized genomic signatures of adaptation in a Haitian breeding population that had rapidly adapted to SCA infestation, conducting evolutionary population genomics analyses on 296 Haitian lines versus 767 global accessions. Genome scans and geographic analyses suggest that SCA adaptation has been conferred by a globally rare East African allele of RMES1, which spread to breeding programs in Africa, Asia, and the Americas. De novo genome sequencing revealed potential causative variants at RMES1. Markers developed from the RMES1 sweep predicted resistance in eight independent commercial and public breeding programs. These findings demonstrate the value of evolutionary genomics to develop adaptive trait technology and highlight the benefits of global germplasm exchange to facilitate evolutionary rescue.
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Affiliation(s)
- Kebede T. Muleta
- Department of Agronomy, Kansas State University, Manhattan, KS 66502, USA
| | - Terry Felderhoff
- Department of Agronomy, Kansas State University, Manhattan, KS 66502, USA
| | - Noah Winans
- Department of Agronomy, Kansas State University, Manhattan, KS 66502, USA
| | - Rachel Walstead
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jean Rigaud Charles
- Chibas and Faculty of Agriculture and Environmental Sciences, Quisqueya University, Port-au-Prince, Haiti
| | - J. Scott Armstrong
- U.S. Department of Agriculture, Agricultural Research Service, Wheat, Peanut and Other Field Crops Research Unit, 1301 North Western Rd., Stillwater, OK 74075, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - John P. Vogel
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peggy G. Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gael Pressoir
- Chibas and Faculty of Agriculture and Environmental Sciences, Quisqueya University, Port-au-Prince, Haiti
| | - Geoffrey P. Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66502, USA
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO 80526, USA
- Corresponding author.
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5
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Shakoor N, Mockler TC. Wireless Fixed Camera Network for Greenhouse-Based Plant Phenotyping. Methods Mol Biol 2022; 2539:49-56. [PMID: 35895195 DOI: 10.1007/978-1-0716-2537-8_6] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An indoor wireless fixed camera network was developed for an efficient, cost-effective method of extracting informative plant phenotypes in a controlled greenhouse environment. Deployed at the Donald Danforth Plant Science Center (DDPSC), this fixed camera platform implements rapid and automated plant phenotyping. The platform uses low-cost Raspberry Pi computers and digital cameras to monitor aboveground morphological and developmental plant phenotypes. The Raspberry Pi is a readily programmable, credit card-sized computer board with remote accessibility. A standard camera module connects to the Raspberry Pi computer board and generates eight-megapixel resolution images. With a fixed array, or "bramble," of Raspberry Pi computer boards and camera modules placed strategically in a greenhouse, we can capture automated, high-resolution images for 3D reconstructions of individual plants on timescales ranging from minutes to hours, capturing temporal changes in plant phenotypes.
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Affiliation(s)
- Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
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6
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Weissmann S, Huang P, Wiechert MA, Furuyama K, Brutnell TP, Taniguchi M, Schnable JC, Mockler TC. DCT4-A New Member of the Dicarboxylate Transporter Family in C4 Grasses. Genome Biol Evol 2021; 13:6126432. [PMID: 33587128 PMCID: PMC7883667 DOI: 10.1093/gbe/evaa251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Accepted: 11/24/2020] [Indexed: 11/15/2022] Open
Abstract
Malate transport shuttles atmospheric carbon into the Calvin–Benson cycle during NADP-ME C4 photosynthesis. Previous characterizations of several plant dicarboxylate transporters (DCT) showed that they efficiently exchange malate across membranes. Here, we identify and characterize a previously unknown member of the DCT family, DCT4, in Sorghum bicolor. We show that SbDCT4 exchanges malate across membranes and its expression pattern is consistent with a role in malate transport during C4 photosynthesis. SbDCT4 is not syntenic to the characterized photosynthetic gene ZmDCT2, and an ortholog is not detectable in the maize reference genome. We found that the expression patterns of DCT family genes in the leaves of Zea mays, and S. bicolor varied by cell type. Our results suggest that subfunctionalization, of members of the DCT family, for the transport of malate into the bundle sheath plastids, occurred during the process of independent recurrent evolution of C4 photosynthesis in grasses of the PACMAD clade. We also show that this subfunctionalization is lineage independent. Our results challenge the dogma that key C4 genes must be orthologues of one another among C4 species, and shed new light on the evolution of C4 photosynthesis.
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Affiliation(s)
- Sarit Weissmann
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Pu Huang
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | | | - Koki Furuyama
- Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Thomas P Brutnell
- Chinese Academy of Agricultural Sciences, Biotechnology Research Institute, Beijing, China
| | - Mitsutaka Taniguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - James C Schnable
- Computational Sciences Initiative, Center for Plant Science Innovation, Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Nebraska, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
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7
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Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe F, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JR, Martienssen RA, Lam E. Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Res 2021; 31:225-238. [PMID: 33361111 PMCID: PMC7849404 DOI: 10.1101/gr.266429.120] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/16/2020] [Indexed: 11/24/2022]
Abstract
Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
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Affiliation(s)
- Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Evan Ernst
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nolan Hartwick
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Philomena Chu
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Douglas Bryant
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Stefan Ortleb
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Erin L Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye, Kerala 671316, India
| | | | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Florian Jupe
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Justin P Sandoval
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Ljudmylla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Joseph R Ecker
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Robert A Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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8
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Wang Q, Shakoor N, Boyher A, Veley KM, Berry JC, Mockler TC, Bart RS. Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response. PLoS Pathog 2021; 17:e1009175. [PMID: 33428681 PMCID: PMC7822516 DOI: 10.1371/journal.ppat.1009175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/25/2020] [Revised: 01/22/2021] [Accepted: 11/19/2020] [Indexed: 11/22/2022] Open
Abstract
The zig-zag model of host-pathogen interaction describes the relative strength of defense response across a spectrum of pathogen-induced plant phenotypes. A stronger defense response results in increased resistance. Here, we investigate the strength of pathogen virulence during disease and place these findings in the context of the zig-zag model. Xanthomonas vasicola pv. holcicola (Xvh) causes sorghum bacterial leaf streak. Despite being widespread, this disease has not been described in detail at the molecular level. We divided diverse sorghum genotypes into three groups based on disease symptoms: water-soaked lesions, red lesions, and resistance. Bacterial growth assays confirmed that these three phenotypes represent a range of resistance and susceptibility. To simultaneously reveal defense and virulence responses across the spectrum of disease phenotypes, we performed dual RNA-seq on Xvh-infected sorghum. Consistent with the zig-zag model, the expression of plant defense-related genes was strongest in the resistance interaction. Surprisingly, bacterial virulence genes related to the type III secretion system (T3SS) and type III effectors (T3Es) were also most highly expressed in the resistance interaction. This expression pattern was observed at multiple time points within the sorghum-Xvh pathosystem. Further, a similar expression pattern was observed in Arabidopsis infected with Pseudomonas syringae for effector-triggered immunity via AvrRps4 but not AvrRpt2. Specific metabolites were able to repress the Xvh virulence response in vitro and in planta suggesting a possible signaling mechanism. Taken together, these findings reveal multiple permutations of the continually evolving host-pathogen arms race from the perspective of host defense and pathogen virulence responses. The arms race between plants and pathogens is a complex process. To dissect the plant defense and pathogen virulence responses simultaneously, we used sorghum and Xanthomonas vasicola pv. holcicola, as a model pathosystem. We performed dual RNA-seq on infected sorghum with a range of disease phenotypes. Our characterization of this pathosystem demonstrates that genes related to the plant defense and pathogen virulence responses are most highly induced during a resistance interaction. We observed a similar pattern of escalation in Arabidopsis infected with Pseudomonas syringae. These observations support a conceptual model of fluidity between the different stages of plant immunity and pathogen virulence.
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Affiliation(s)
- Qi Wang
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Adam Boyher
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Kira M Veley
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Jeffrey C Berry
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Todd C Mockler
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
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9
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Lozano R, Gazave E, Dos Santos JPR, Stetter MG, Valluru R, Bandillo N, Fernandes SB, Brown PJ, Shakoor N, Mockler TC, Cooper EA, Taylor Perkins M, Buckler ES, Ross-Ibarra J, Gore MA. Comparative evolutionary genetics of deleterious load in sorghum and maize. Nat Plants 2021; 7:17-24. [PMID: 33452486 DOI: 10.1038/s41477-020-00834-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Sorghum and maize share a close evolutionary history that can be explored through comparative genomics1,2. To perform a large-scale comparison of the genomic variation between these two species, we analysed ~13 million variants identified from whole-genome resequencing of 499 sorghum lines together with 25 million variants previously identified in 1,218 maize lines. Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the domestication-cost hypothesis that predicts a higher deleterious burden among domesticates compared with wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy greater than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing these variants for removal through genome editing and breeding.
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Affiliation(s)
- Roberto Lozano
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Elodie Gazave
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Jhonathan P R Dos Santos
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Markus G Stetter
- Botanical Institute, Biozentrum, University of Cologne, Cologne, Germany
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- University of Lincoln, Lincoln, UK
| | - Nonoy Bandillo
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patrick J Brown
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Elizabeth A Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Taylor Perkins
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Edward S Buckler
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R. W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA.
- Center for Population Biology and Genome Center, University of California Davis, Davis, CA, USA.
| | - Michael A Gore
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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10
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Greenham K, Sartor RC, Zorich S, Lou P, Mockler TC, McClung CR. Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns. eLife 2020; 9:e58993. [PMID: 32996462 PMCID: PMC7655105 DOI: 10.7554/elife.58993] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/29/2020] [Indexed: 02/02/2023] Open
Abstract
An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here we describe the circadian transcriptome in the polyploid crop Brassica rapa. Strikingly, almost three-quarters of the expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of the circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal evidence for divergence between B. rapa paralogs that may be driven in part by variation in conserved non-coding sequences (CNS). Additionally, differential drought response among retained paralogous pairs suggests further functional diversification. These findings support the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new approach for assessing paralog activity at the transcript level.
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Affiliation(s)
- Kathleen Greenham
- Department of Plant and Microbial Biology, University of MinnesotaSaint PaulUnited States
| | - Ryan C Sartor
- Crop and Soil Sciences, North Carolina State UniversityRaleighUnited States
| | - Stevan Zorich
- Department of Plant and Microbial Biology, University of MinnesotaSaint PaulUnited States
| | - Ping Lou
- Department of Biological Sciences, Dartmouth CollegeHanoverUnited States
| | - Todd C Mockler
- Donald Danforth Plant Science CenterSt. LouisUnited States
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11
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Herritt MT, Pauli D, Mockler TC, Thompson AL. Chlorophyll fluorescence imaging captures photochemical efficiency of grain sorghum ( Sorghum bicolor) in a field setting. Plant Methods 2020; 16:109. [PMID: 32793296 PMCID: PMC7419188 DOI: 10.1186/s13007-020-00650-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/01/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Photosynthesis is one of the most important biological reactions and forms the basis of crop productivity and yield on which a growing global population relies. However, to develop improved plant cultivars that are capable of increased productivity, methods that can accurately and quickly quantify photosynthetic efficiency in large numbers of genotypes under field conditions are needed. Chlorophyll fluorescence imaging is a rapid, non-destructive measurement that can provide insight into the efficiency of the light-dependent reactions of photosynthesis. RESULTS To test and validate a field-deployed fluorescence imaging system on the TERRA-REF field scanalyzer, leaves of potted sorghum plants were treated with a photosystem II inhibitor, DCMU, to reduce photochemical efficiency (FV/FM). The ability of the fluorescence imaging system to detect changes in fluorescence was determined by comparing the image-derived values with a handheld fluorometer. This study demonstrated that the imaging system was able to accurately measure photochemical efficiency (FV/FM) and was highly correlated (r = 0.92) with the handheld fluorometer values. Additionally, the fluorescence imaging system was able to track the decrease in photochemical efficiency due to treatment of DCMU over a 7 day period. CONCLUSIONS The system's ability to capture the temporal dynamics of the plants' response to this induced stress, which has comparable dynamics to abiotic and biotic stressors found in field environments, indicates the system is operating correctly. With the validation of the fluorescence imaging system, physiological and genetic studies can be undertaken that leverage the fluorescence imaging capabilities and throughput of the field scanalyzer.
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Affiliation(s)
- Matthew T. Herritt
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Arid-Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - Duke Pauli
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
| | - Todd C. Mockler
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
- Donald Danforth Plant Science Center, Saint Louis, MO 63132 USA
| | - Alison L. Thompson
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Arid-Land Agricultural Research Center, Maricopa, AZ 85138 USA
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12
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Carter KA, Liston A, Bassil NV, Alice LA, Bushakra JM, Sutherland BL, Mockler TC, Bryant DW, Hummer KE. Target Capture Sequencing Unravels Rubus Evolution. Front Plant Sci 2019; 10:1615. [PMID: 31921259 PMCID: PMC6933950 DOI: 10.3389/fpls.2019.01615] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/15/2019] [Indexed: 05/09/2023]
Abstract
Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.
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Affiliation(s)
- Katherine A. Carter
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Aaron Liston
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Nahla V. Bassil
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - Lawrence A. Alice
- Department of Biology, Western Kentucky University, Bowling Green, KY, United States
| | - Jill M. Bushakra
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - Brittany L. Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Todd C. Mockler
- Mockler Lab, Donald Danforth Plant Sciences Center, St. Louis, MO, United States
| | - Douglas W. Bryant
- Mockler Lab, Donald Danforth Plant Sciences Center, St. Louis, MO, United States
| | - Kim E. Hummer
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
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13
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Wai CM, Weise SE, Ozersky P, Mockler TC, Michael TP, VanBuren R. Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album. PLoS Genet 2019; 15:e1008209. [PMID: 31199791 PMCID: PMC6594660 DOI: 10.1371/journal.pgen.1008209] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 01/28/2019] [Revised: 06/26/2019] [Accepted: 05/24/2019] [Indexed: 12/22/2022] Open
Abstract
Plants with facultative crassulacean acid metabolism (CAM) maximize performance through utilizing C3 or C4 photosynthesis under ideal conditions while temporally switching to CAM under water stress (drought). While genome-scale analyses of constitutive CAM plants suggest that time of day networks are shifted, or phased to the evening compared to C3, little is known for how the shift from C3 to CAM networks is modulated in drought induced CAM. Here we generate a draft genome for the drought-induced CAM-cycling species Sedum album. Through parallel sampling in well-watered (C3) and drought (CAM) conditions, we uncover a massive rewiring of time of day expression and a CAM and stress-specific network. The core circadian genes are expanded in S. album and under CAM induction, core clock genes either change phase or amplitude. While the core clock cis-elements are conserved in S. album, we uncover a set of novel CAM and stress specific cis-elements consistent with our finding of rewired co-expression networks. We identified shared elements between constitutive CAM and CAM-cycling species and expression patterns unique to CAM-cycling S. album. Together these results demonstrate that drought induced CAM-cycling photosynthesis evolved through the mobilization of a stress-specific, time of day network, and not solely the phasing of existing C3 networks. These results will inform efforts to engineer water use efficiency into crop plants for growth on marginal land.
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Affiliation(s)
- Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Sean E. Weise
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Philip Ozersky
- Donald Danforth Plant Science Center, St. Louis MO, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis MO, United States of America
| | - Todd P. Michael
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States of America
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14
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VanBuren R, Wai CM, Colle M, Wang J, Sullivan S, Bushakra JM, Liachko I, Vining KJ, Dossett M, Finn CE, Jibran R, Chagné D, Childs K, Edger PP, Mockler TC, Bassil NV. A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. Gigascience 2018; 7:5069394. [PMID: 30107523 PMCID: PMC6131213 DOI: 10.1093/gigascience/giy094] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [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: 01/29/2018] [Accepted: 07/10/2018] [Indexed: 11/13/2022] Open
Abstract
Background The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies. Findings Here, we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing an ∼200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high-quality V4 woodland strawberry genome (Fragaria vesca) revealed near-perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis. Conclusions The improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.
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Affiliation(s)
- Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.,Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Marivi Colle
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Jill M Bushakra
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Rd., Corvallis, OR, 97333, USA
| | | | - Kelly J Vining
- Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research Centre, BC V0M 1A0, Canada
| | - Michael Dossett
- Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research Centre, BC V0M 1A0, Canada
| | - Chad E Finn
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97330, USA
| | - Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4474, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4474, New Zealand
| | - Kevin Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Todd C Mockler
- The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Rd., Corvallis, OR, 97333, USA
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15
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Torello Marinoni D, Valentini N, Portis E, Acquadro A, Beltramo C, Mehlenbacher SA, Mockler TC, Rowley ER, Botta R. High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L. PLoS One 2018; 13:e0195408. [PMID: 29608620 PMCID: PMC5880404 DOI: 10.1371/journal.pone.0195408] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 11/11/2017] [Accepted: 03/21/2018] [Indexed: 01/25/2023] Open
Abstract
The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection. The objectives of this study were to enrich a previous linkage map and confirm QTL related to time of leaf budburst, using an F1 population obtained by crossing Tonda Gentile delle Langhe with Merveille de Bollwiller. Genotyping-by-Sequencing was used to identify a total of 9,999 single nucleotide polymorphism markers. Well saturated linkage maps were constructed for each parent using the double pseudo-testcross mapping strategy. A reciprocal translocation was detected in Tonda Gentile delle Langhe between two non-homologous chromosomes. Applying a bioinformatic approach, we were able to disentangle ‘pseudo-linkage’ between markers, removing markers around the translocation breakpoints and obtain a linear order of the markers for the two chromosomes arms, for each linkage group involved in the translocation. Twenty-nine QTL for time of leaf budburst were identified, including a stably expressed region on LG_02 of the Tonda Gentile delle Langhe map. The stability of these QTL and their coding sequence content indicates promise for the identification of specific chromosomal regions carrying key genes involved in leaf budburst.
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Affiliation(s)
- Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Nadia Valentini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
- * E-mail:
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Chiara Beltramo
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Shawn A. Mehlenbacher
- Department of Horticulture, Oregon State University, Corvallis, Oregon, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Erik R. Rowley
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
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16
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Jibran R, Dzierzon H, Bassil N, Bushakra JM, Edger PP, Sullivan S, Finn CE, Dossett M, Vining KJ, VanBuren R, Mockler TC, Liachko I, Davies KM, Foster TM, Chagné D. Chromosome-scale scaffolding of the black raspberry ( Rubus occidentalis L.) genome based on chromatin interaction data. Hortic Res 2018; 5:8. [PMID: 29423238 PMCID: PMC5802725 DOI: 10.1038/s41438-017-0013-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/06/2017] [Accepted: 12/10/2017] [Indexed: 05/23/2023]
Abstract
Black raspberry (Rubus occidentalis L.) is a niche fruit crop valued for its flavor and potential health benefits. The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome. The recently released draft genome for black raspberry (ORUS 4115-3) lacks assembly of scaffolds to chromosome scale. We used high-throughput chromatin conformation capture (Hi-C) and Proximity-Guided Assembly (PGA) to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes. The seven pseudo-chromosomes cover ~97.2% of the total contig length (~223.8 Mb). Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map. Centromeric regions were inferred from recombination frequencies of genetic markers, alignment of 303 bp centromeric sequence with the PGA, and heat map showing the physical contact matrix over the entire genome. We demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry (Fragaria vesca L.) assembled using only PacBio long-read sequences. We conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.
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Affiliation(s)
- Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4474 New Zealand
| | - Helge Dzierzon
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4474 New Zealand
| | - Nahla Bassil
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333 USA
| | - Jill M. Bushakra
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333 USA
| | - Patrick P. Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824-2604 USA
| | | | - Chad E. Finn
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97330 USA
| | - Michael Dossett
- B.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research Centre, Agassiz, BC V0M 1A0 Canada
| | - Kelly J. Vining
- B.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research Centre, Agassiz, BC V0M 1A0 Canada
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824-2604 USA
| | - Todd C. Mockler
- The Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
| | - Ivan Liachko
- Phase Genomics, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Kevin M. Davies
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4474 New Zealand
| | - Toshi M. Foster
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4474 New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4474 New Zealand
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17
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VanBuren R, Wai CM, Ou S, Pardo J, Bryant D, Jiang N, Mockler TC, Edger P, Michael TP. Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla. Nat Commun 2018; 9:13. [PMID: 29296019 PMCID: PMC5750206 DOI: 10.1038/s41467-017-02546-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [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: 09/21/2017] [Accepted: 12/08/2017] [Indexed: 01/10/2023] Open
Abstract
Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content. Here we report the small 109 Mb genome of Selaginella lepidophylla, a clubmoss with extreme desiccation tolerance. Single-molecule sequencing enables accurate haplotype assembly of a single heterozygous S. lepidophylla plant, revealing extensive structural variation. We observe numerous haplotype-specific deletions consisting of largely repetitive and heavily methylated sequences, with enrichment in young Gypsy LTR retrotransposons. Such elements are active but rapidly deleted, suggesting "bloat and purge" to maintain a small genome size. Unlike all other land plant lineages, Selaginella has no evidence of a whole-genome duplication event in its evolutionary history, but instead shows unique tandem gene duplication patterns reflecting adaptation to extreme drying. Gene expression changes during desiccation in S. lepidophylla mirror patterns observed across angiosperm resurrection plants.
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Affiliation(s)
- Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Shujun Ou
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Jeremy Pardo
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Doug Bryant
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Patrick Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
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18
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Huang H, Gehan MA, Huss SE, Alvarez S, Lizarraga C, Gruebbling EL, Gierer J, Naldrett MJ, Bindbeutel RK, Evans BS, Mockler TC, Nusinow DA. Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. Plant Direct 2017; 1:e00018. [PMID: 31245666 PMCID: PMC6508535 DOI: 10.1002/pld3.18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/10/2017] [Accepted: 09/13/2017] [Indexed: 05/03/2023]
Abstract
Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant Arabidopsis thaliana (Arabidopsis) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside of Arabidopsis, however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function of Brachypodium distachyon (Brachypodium) and Setaria viridis (Setaria) orthologs of EARLY FLOWERING 3, a key clock gene in Arabidopsis. To identify both cycling genes and putative ELF3 functional orthologs in Setaria, a circadian RNA-seq dataset and online query tool (Diel Explorer) were generated to explore expression profiles of Setaria genes under circadian conditions. The function of ELF3 orthologs from Arabidopsis, Brachypodium, and Setaria was tested for complementation of an elf3 mutation in Arabidopsis. We find that both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time, and arrhythmic clock phenotypes. Using affinity purification and mass spectrometry, our data indicate that BdELF3 and SvELF3 could be integrated into similar complexes in vivo as AtELF3. Thus, we find that, despite 180 million years of separation, BdELF3 and SvELF3 can functionally complement loss of ELF3 at the molecular and physiological level.
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Affiliation(s)
- He Huang
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | | | - Sophie Alvarez
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of Nebraska‐LincolnLincolnNEUSA
| | | | | | - John Gierer
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Michael J. Naldrett
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of Nebraska‐LincolnLincolnNEUSA
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19
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VanBuren R, Wai CM, Zhang Q, Song X, Edger PP, Bryant D, Michael TP, Mockler TC, Bartels D. Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomaeum. Plant Cell Environ 2017; 40:2292-2306. [PMID: 28730594 DOI: 10.1111/pce.13027] [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] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 05/24/2023]
Abstract
Resurrection plants desiccate during periods of prolonged drought stress, then resume normal cellular metabolism upon water availability. Desiccation tolerance has multiple origins in flowering plants, and it likely evolved through rewiring seed desiccation pathways. Oropetium thomaeum is an emerging model for extreme drought tolerance, and its genome, which is the smallest among surveyed grasses, was recently sequenced. Combining RNA-seq, targeted metabolite analysis and comparative genomics, we show evidence for co-option of seed-specific pathways during vegetative desiccation. Desiccation-related gene co-expression clusters are enriched in functions related to seed development including several seed-specific transcription factors. Across the metabolic network, pathways involved in programmed cell death inhibition, ABA signalling and others are activated during dehydration. Oleosins and oil bodies that typically function in seed storage are highly abundant in desiccated leaves and may function for membrane stability and storage. Orthologs to seed-specific LEA proteins from rice and maize have neofunctionalized in Oropetium with high expression during desiccation. Accumulation of sucrose, raffinose and stachyose in drying leaves mirrors sugar accumulation patterns in maturing seeds. Together, these results connect vegetative desiccation with existing seed desiccation and drought responsive pathways and provide some key candidate genes for engineering improved drought tolerance in crop plants.
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Affiliation(s)
- Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48823, USA
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
| | - Qingwei Zhang
- IMBIO, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Xiaomin Song
- IMBIO, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48823, USA
| | - Doug Bryant
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Dorothea Bartels
- IMBIO, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
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20
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Begemann MB, Gray BN, January E, Gordon GC, He Y, Liu H, Wu X, Brutnell TP, Mockler TC, Oufattole M. Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases. Sci Rep 2017; 7:11606. [PMID: 28912524 PMCID: PMC5599503 DOI: 10.1038/s41598-017-11760-6] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [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: 03/09/2017] [Accepted: 08/30/2017] [Indexed: 12/26/2022] Open
Abstract
Precise genome editing of plants has the potential to reshape global agriculture through the targeted engineering of endogenous pathways or the introduction of new traits. To develop a CRISPR nuclease-based platform that would enable higher efficiencies of precise gene insertion or replacement, we screened the Cpf1 nucleases from Francisella novicida and Lachnospiraceae bacterium ND2006 for their capability to induce targeted gene insertion via homology directed repair. Both nucleases, in the presence of a guide RNA and repairing DNA template flanked by homology DNA fragments to the target site, were demonstrated to generate precise gene insertions as well as indel mutations at the target site in the rice genome. The frequency of targeted insertion for these Cpf1 nucleases, up to 8%, is higher than most other genome editing nucleases, indicative of its effective enzymatic chemistry. Further refinements and broad adoption of the Cpf1 genome editing technology have the potential to make a dramatic impact on plant biotechnology.
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Affiliation(s)
- Matthew B Begemann
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA.
| | - Benjamin N Gray
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA
| | - Emma January
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA
| | - Gina C Gordon
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA
| | - Yonghua He
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA
| | - Haijun Liu
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA
| | - Xingrong Wu
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA
| | - Thomas P Brutnell
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA
- Donald Danforth Plant Science Center, 975N, Warson Road, St. Louis, MO, 63132, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, 975N, Warson Road, St. Louis, MO, 63132, USA
| | - Mohammed Oufattole
- Benson Hill Biosystems, 1100 Corporate Square Dr, St. Louis, MO, 63132, USA
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21
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Greenham K, Guadagno CR, Gehan MA, Mockler TC, Weinig C, Ewers BE, McClung CR. Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa. eLife 2017; 6:e29655. [PMID: 28826479 PMCID: PMC5628015 DOI: 10.7554/elife.29655] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [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: 06/15/2017] [Accepted: 08/11/2017] [Indexed: 11/13/2022] Open
Abstract
The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity. Underlying drought responses are circadian and diel control of gene expression that regulate daily variations in metabolic and physiological pathways. To identify transcriptomic changes that occur in the crop Brassica rapa during initial perception of drought, we applied a co-expression network approach to associate rhythmic gene expression changes with physiological responses. Coupled analysis of transcriptome and physiological parameters over a two-day time course in control and drought-stressed plants provided temporal resolution necessary for correlation of network modules with dynamic changes in stomatal conductance, photosynthetic rate, and photosystem II efficiency. This approach enabled the identification of drought-responsive genes based on their differential rhythmic expression profiles in well-watered versus droughted networks and provided new insights into the dynamic physiological changes that occur during drought.
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Affiliation(s)
- Kathleen Greenham
- Department of Biological SciencesDartmouth CollegeHanoverUnited States
| | | | - Malia A Gehan
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Todd C Mockler
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Cynthia Weinig
- Department of BotanyUniversity of WyomingLaramieUnited States
- Department of Molecular BiologyUniversity of WyomingLaramieUnited States
- Program in EcologyUniversity of WyomingLaramieUnited States
| | - Brent E Ewers
- Department of BotanyUniversity of WyomingLaramieUnited States
- Program in EcologyUniversity of WyomingLaramieUnited States
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22
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Shakoor N, Lee S, Mockler TC. High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field. Curr Opin Plant Biol 2017; 38:184-192. [PMID: 28738313 DOI: 10.1016/j.pbi.2017.05.006] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/17/2017] [Indexed: 05/18/2023]
Abstract
Effective implementation of technology that facilitates accurate and high-throughput screening of thousands of field-grown lines is critical for accelerating crop improvement and breeding strategies for higher yield and disease tolerance. Progress in the development of field-based high throughput phenotyping methods has advanced considerably in the last 10 years through technological progress in sensor development and high-performance computing. Here, we review recent advances in high throughput field phenotyping technologies designed to inform the genetics of quantitative traits, including crop yield and disease tolerance. Successful application of phenotyping platforms to advance crop breeding and identify and monitor disease requires: (1) high resolution of imaging and environmental sensors; (2) quality data products that facilitate computer vision, machine learning and GIS; (3) capacity infrastructure for data management and analysis; and (4) automated environmental data collection. Accelerated breeding for agriculturally relevant crop traits is key to the development of improved varieties and is critically dependent on high-resolution, high-throughput field-scale phenotyping technologies that can efficiently discriminate better performing lines within a larger population and across multiple environments.
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Affiliation(s)
| | - Scott Lee
- Donald Danforth Plant Science Center, United States
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23
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Agnew E, Bray A, Floro E, Ellis N, Gierer J, Lizárraga C, O'Brien D, Wiechert M, Mockler TC, Shakoor N, Topp CN. Whole-Plant Manual and Image-Based Phenotyping in Controlled Environments. Curr Protoc Plant Biol 2017; 2:1-21. [PMID: 31725975 DOI: 10.1002/cppb.20044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Phenotypic measurements and images of crops grown under controlled-environment conditions can be analyzed to compare plant growth and other phenotypes from diverse varieties. Those demonstrating the most favorable phenotypic traits can then be used for crop improvement strategies. This article details a protocol for image-based root and shoot phenotyping of plants grown in the greenhouse to compare traits among different varieties. Diverse maize lines were grown in the greenhouse in large 8-gallon treepots in a clay granule substrate. Replicates of each line were harvested at 4 weeks, 6 weeks, and 8 weeks after planting to capture developmental information. Whole-plant phenotypes include biomass accumulation, ontogeny, architecture, and photosynthetic efficiency of leaves. Image analysis was used to measure leaf surface area and tassel size and to extract shape variance information from complex 3D root architectures. Notably, this framework is extensible to any number of above- or below-ground phenotypes, both morphological and physiological. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Erica Agnew
- Donald Danforth Plant Science Center, St. Louis, Missouri
| | - Adam Bray
- Donald Danforth Plant Science Center, St. Louis, Missouri
| | - Eric Floro
- Donald Danforth Plant Science Center, St. Louis, Missouri
| | - Nate Ellis
- Donald Danforth Plant Science Center, St. Louis, Missouri
| | - John Gierer
- Donald Danforth Plant Science Center, St. Louis, Missouri
| | | | - Darren O'Brien
- Donald Danforth Plant Science Center, St. Louis, Missouri
| | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, Missouri
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24
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Michael TP, Bryant D, Gutierrez R, Borisjuk N, Chu P, Zhang H, Xia J, Zhou J, Peng H, El Baidouri M, Ten Hallers B, Hastie AR, Liang T, Acosta K, Gilbert S, McEntee C, Jackson SA, Mockler TC, Zhang W, Lam E. Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies. Plant J 2017; 89:617-635. [PMID: 27754575 DOI: 10.1111/tpj.13400] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 07/10/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 05/15/2023]
Abstract
Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family.
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Affiliation(s)
- Todd P Michael
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
- IBIS Bioscience, Carlsbad, CA, USA
| | - Douglas Bryant
- IBIS Bioscience, Carlsbad, CA, USA
- Donald Danforth Center for Plant Science, St. Louis, MO, USA
| | - Ryan Gutierrez
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Nikolai Borisjuk
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Philomena Chu
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Hanzhong Zhang
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, China
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, China
| | - Moaine El Baidouri
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | | | | | - Kenneth Acosta
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Sarah Gilbert
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | | | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Todd C Mockler
- Donald Danforth Center for Plant Science, St. Louis, MO, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, China
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA
| | - Eric Lam
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
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25
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Boyle G, Richter K, Priest HD, Traver D, Mockler TC, Chang JT, Kay SA, Breton G. Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes. PLoS One 2017; 12:e0169923. [PMID: 28076377 PMCID: PMC5226840 DOI: 10.1371/journal.pone.0169923] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/23/2016] [Indexed: 11/18/2022] Open
Abstract
From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology. One potential reason is the sheer size of the output network. Diurnal/circadian transcriptomic studies are reporting that around 10% of the expressed genome is rhythmically controlled. Zebrafish is an important model system for the study of the core circadian mechanism in vertebrate. As Zebrafish share more than 70% of its genes with human, it could also be an additional model in addition to rodent for exploring the diurnal/circadian output with potential for translational relevance. Here we performed comparative diurnal/circadian transcriptome analysis with established mouse liver and other tissue datasets. First, by combining liver tissue sampling in a 48h time series, transcription profiling using oligonucleotide arrays and bioinformatics analysis, we profiled rhythmic transcripts and identified 2609 rhythmic genes. The comparative analysis revealed interesting features of the output network regarding number of rhythmic genes, proportion of tissue specific genes and the extent of transcription factor family expression. Undoubtedly, the Zebrafish model system will help identify new vertebrate outputs and their regulators and provides leads for further characterization of the diurnal cis-regulatory network.
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Affiliation(s)
- Greg Boyle
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America
| | - Kerstin Richter
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Henry D. Priest
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - David Traver
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Jeffrey T. Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America
| | - Steve A. Kay
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ghislain Breton
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas, United States of America
- * E-mail:
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26
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VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER, Priest HD, Michael TP, Lyons E, Filichkin SA, Dossett M, Finn CE, Bassil NV, Mockler TC. The genome of black raspberry (Rubus occidentalis). Plant J 2016; 87:535-47. [PMID: 27228578 DOI: 10.1111/tpj.13215] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 01/05/2016] [Revised: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 05/02/2023]
Abstract
Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein-coding genes, we identified 290 very recent small-scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars.
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Affiliation(s)
- Robert VanBuren
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Doug Bryant
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Jill M Bushakra
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA
| | - Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
| | - Erik R Rowley
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Henry D Priest
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | | | - Eric Lyons
- CyVerse, BIO5, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Sergei A Filichkin
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University Corvallis, Corvallis, OR, 97331, USA
| | - Michael Dossett
- B.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) - Agassiz Research and Development Centre, Agassiz, BC, VOM 1A0, Canada
| | - Chad E Finn
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR, 97330, USA
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
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27
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Sebastian J, Yee MC, Goudinho Viana W, Rellán-Álvarez R, Feldman M, Priest HD, Trontin C, Lee T, Jiang H, Baxter I, Mockler TC, Hochholdinger F, Brutnell TP, Dinneny JR. Grasses suppress shoot-borne roots to conserve water during drought. Proc Natl Acad Sci U S A 2016; 113:8861-8866. [PMID: 27422554 DOI: 10.1073/pnas.160421113] [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] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.
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Affiliation(s)
- Jose Sebastian
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305
| | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305
| | - Willian Goudinho Viana
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305; Coordination for the Improvement of Higher Education Personnel (CAPES) Foundation, Ministry of Education of Brazil, Brasilia-DF 70.040-020, Brazil
| | - Rubén Rellán-Álvarez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305; Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Mexico
| | - Max Feldman
- Donald Danforth Plant Science Center, St. Louis, MO 63162
| | - Henry D Priest
- Donald Danforth Plant Science Center, St. Louis, MO 63162
| | - Charlotte Trontin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305
| | - Tak Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, MO 63162
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO 63162; Plant Physiology and Genetics Research, Agricultural Research Unit, US Department of Agriculture, St. Louis, MO 63132
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO 63162
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, D-53113 Bonn, Germany
| | | | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305;
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28
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Abstract
A report on the 10th plant genome meeting entitled ‘Plant genomes and biotechnology: from genes to networks’, held at Cold Spring Harbor Laboratory, 2–5 December, 2015.
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Affiliation(s)
- Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Panama Street, Stanford, CA, 94305, USA.
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné weg, 50829, Cologne, Germany
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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29
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VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, Mockler TC. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 2015; 527:508-11. [PMID: 26560029 DOI: 10.1038/nature15714] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/10/2015] [Indexed: 12/20/2022]
Abstract
Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.
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Affiliation(s)
- Robert VanBuren
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Doug Bryant
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.,Department of Horticulture, Michigan State University, East Lansing, Michigan 48823, USA
| | - Haibao Tang
- iPlant Collaborative, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.,Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Diane Burgess
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA
| | | | | | - Richard Hall
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Jenny Gu
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Eric Lyons
- iPlant Collaborative, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA
| | | | | | - Alex Hastie
- BioNano Genomics, San Diego, California 92121, USA
| | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
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30
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Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, Chow J, Choi C, Adam C, Cao XH, Fuchs J, Schubert I, Rokhsar D, Schmutz J, Michael TP, Mayer KFX, Messing J. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 2015; 5:3311. [PMID: 24548928 PMCID: PMC3948053 DOI: 10.1038/ncomms4311] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [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: 08/20/2013] [Accepted: 01/24/2014] [Indexed: 11/30/2022] Open
Abstract
The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications. Spirodela, or duckweed, is a basal monocotyledonous plant with both pharmaceutical and commercial value. Here, the authors sequence the genome of Spirodela polyrhiza, suggesting its genome has evolved by neotenous reduction and clonal propagation, and provide a platform for future comparative genomic studies in angiosperms.
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Affiliation(s)
- W Wang
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - G Haberer
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - H Gundlach
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - C Gläßer
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - T Nussbaumer
- MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - M C Luo
- Department of Plant Sciences, University of California, 265 Hunt Hall, One Shields Avenue, Davis, California 95616, USA
| | - A Lomsadze
- Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332, USA
| | - M Borodovsky
- Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332, USA
| | - R A Kerstetter
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - J Shanklin
- Brookhaven National Laboratory, 50 Bell Ave, Upton, New York 11973, USA
| | - D W Byrant
- Donald Danforth Plant Science Center, 975N Warson Road, St. Louis, Missouri 63132, USA
| | - T C Mockler
- Donald Danforth Plant Science Center, 975N Warson Road, St. Louis, Missouri 63132, USA
| | - K J Appenroth
- Department of Plant Physiology, University of Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - J Grimwood
- 1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - J Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - J Chow
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - C Choi
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - C Adam
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - X-H Cao
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - J Fuchs
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - I Schubert
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - D Rokhsar
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - J Schmutz
- 1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - T P Michael
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - K F X Mayer
- MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - J Messing
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
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31
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Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, Hill ST, McEntee CJ, Warnasooriya SN, Kumar I, Ficor T, Turnipseed S, Gilbert KB, Brutnell TP, Carrington JC, Mockler TC, Baxter I. A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria. Mol Plant 2015; 8:1520-35. [PMID: 26099924 DOI: 10.1016/j.molp.2015.06.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [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: 05/05/2015] [Revised: 05/28/2015] [Accepted: 06/08/2015] [Indexed: 05/18/2023]
Abstract
Phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping Platform for controlled-environment plant growth and automated multimodal phenotyping is described. The system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision (PlantCV) was developed as open-source, hardware platform-independent software for quantitative image analysis. In a 4-week experiment, wild Setaria viridis and domesticated Setaria italica had fundamentally different temporal responses to water availability. While both lines produced similar levels of biomass under limited water conditions, Setaria viridis maintained the same water-use efficiency under water replete conditions, while Setaria italica shifted to less efficient growth. Overall, the Bellwether Phenotyping Platform and PlantCV software detected significant effects of genotype and environment on height, biomass, water-use efficiency, color, plant architecture, and tissue water status traits. All ∼ 79,000 images acquired during the course of the experiment are publicly available.
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Affiliation(s)
- Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | - Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | - Christine Shyu
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | - Steven T Hill
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | | | - Indrajit Kumar
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Tracy Ficor
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | | | | | | | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Ivan Baxter
- USDA-ARS, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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32
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Bushakra JM, Bryant DW, Dossett M, Vining KJ, VanBuren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV. A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica. Theor Appl Genet 2015; 128:1631-46. [PMID: 26037086 PMCID: PMC4477079 DOI: 10.1007/s00122-015-2541-x] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/18/2015] [Indexed: 05/07/2023]
Abstract
We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3-4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F1 population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly.
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Affiliation(s)
- Jill M Bushakra
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Rd., Corvallis, OR, 97333, USA,
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33
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Carbonell A, Fahlgren N, Mitchell S, Cox KL, Reilly KC, Mockler TC, Carrington JC. Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors. Plant J 2015; 82:1061-1075. [PMID: 25809382 PMCID: PMC4464980 DOI: 10.1111/tpj.12835] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 01/28/2015] [Revised: 03/11/2015] [Accepted: 03/19/2015] [Indexed: 05/17/2023]
Abstract
Artificial microRNAs (amiRNAs) are used for selective gene silencing in plants. However, current methods to produce amiRNA constructs for silencing transcripts in monocot species are not suitable for simple, cost-effective and large-scale synthesis. Here, a series of expression vectors based on Oryza sativa MIR390 (OsMIR390) precursor was developed for high-throughput cloning and high expression of amiRNAs in monocots. Four different amiRNA sequences designed to target specifically endogenous genes and expressed from OsMIR390-based vectors were validated in transgenic Brachypodium distachyon plants. Surprisingly, amiRNAs accumulated to higher levels and were processed more accurately when expressed from chimeric OsMIR390-based precursors that include distal stem-loop sequences from Arabidopsis thaliana MIR390a (AtMIR390a). In all cases, transgenic plants displayed the predicted phenotypes induced by target gene repression, and accumulated high levels of amiRNAs and low levels of the corresponding target transcripts. Genome-wide transcriptome profiling combined with 5'-RLM-RACE analysis in transgenic plants confirmed that amiRNAs were highly specific.
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Affiliation(s)
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Skyler Mitchell
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Kevin L Cox
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Kevin C Reilly
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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34
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Lee I, Mockler TC. Editorial overview: genome studies and molecular genetics: data-driven approaches to genotype-to-phenotype studies in crops. Curr Opin Plant Biol 2015; 24:iv-vi. [PMID: 25817324 DOI: 10.1016/j.pbi.2015.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Insuk Lee
- Yonsei University, Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea.
| | - Todd C Mockler
- Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO 63131, USA.
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35
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Filichkin S, Priest HD, Megraw M, Mockler TC. Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress. Curr Opin Plant Biol 2015; 24:125-35. [PMID: 25835141 DOI: 10.1016/j.pbi.2015.02.008] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 05/20/2023]
Abstract
In recent years, high-throughput sequencing-based analysis of plant transcriptomes has suggested that up to ∼60% of plant gene loci encode alternatively spliced mature transcripts. These studies have also revealed that alternative splicing in plants can be regulated by cell type, developmental stage, the environment, and the circadian clock. Alternative splicing is coupled to RNA surveillance and processing mechanisms, including nonsense mediated decay. Recently, non-protein-coding transcripts have also been shown to undergo alternative splicing. These discoveries collectively describe a robust system of post-transcriptional regulatory feedback loops which influence RNA abundance. In this review, we summarize recent studies describing the specific roles alternative splicing and RNA surveillance play in plant adaptation to environmental stresses and the regulation of the circadian clock.
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Affiliation(s)
- Sergei Filichkin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
| | - Henry D Priest
- Division of Biology and Biomedical Sciences, Washington University, Saint Louis, MO 63130, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Molly Megraw
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Todd C Mockler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA; Division of Biology and Biomedical Sciences, Washington University, Saint Louis, MO 63130, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA.
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36
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Gehan MA, Greenham K, Mockler TC, McClung CR. Transcriptional networks-crops, clocks, and abiotic stress. Curr Opin Plant Biol 2015; 24:39-46. [PMID: 25646668 DOI: 10.1016/j.pbi.2015.01.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 05/20/2023]
Abstract
Several factors affect the yield potential and geographical range of crops including the circadian clock, water availability, and seasonal temperature changes. In order to sustain and increase plant productivity on marginal land in the face of both biotic and abiotic stresses, we need to more efficiently generate stress-resistant crops through marker-assisted breeding, genetic modification, and new genome-editing technologies. To leverage these strategies for producing the next generation of crops, future transcriptomic data acquisition should be pursued with an appropriate temporal design and analyzed with a network-centric approach. The following review focuses on recent developments in abiotic stress transcriptional networks in economically important crops and will highlight the utility of correlation-based network analysis and applications.
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Affiliation(s)
- Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, MO 63132, United States
| | - Kathleen Greenham
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, United States
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO 63132, United States
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, United States.
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37
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Filichkin SA, Cumbie JS, Dharmawardhana P, Jaiswal P, Chang JH, Palusa SG, Reddy ASN, Megraw M, Mockler TC. Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis. Mol Plant 2015; 8:207-27. [PMID: 25680774 DOI: 10.1016/j.molp.2014.10.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [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: 10/10/2014] [Revised: 10/10/2014] [Accepted: 10/20/2014] [Indexed: 05/21/2023]
Abstract
Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining (IR) transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad-range thermal cycles triggered a sharp increase in the long IR CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or Pseudomonas syringae infection induced a similar increase. Thermal stress induced a time delay in accumulation of CCA1 I4Rb transcripts, whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out-of-phase oscillations of CCA1 IR transcripts. Taken together, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this splicing factor could be involved in regulation of intron retention. Transcriptomes of nonsense-mediated mRNA decay (NMD)-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.
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Affiliation(s)
- Sergei A Filichkin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
| | - Jason S Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Palitha Dharmawardhana
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Saiprasad G Palusa
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - A S N Reddy
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Molly Megraw
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Todd C Mockler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA.
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38
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Howe GT, Horvath DP, Dharmawardhana P, Priest HD, Mockler TC, Strauss SH. Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus. Front Plant Sci 2015; 6:989. [PMID: 26734012 PMCID: PMC4681841 DOI: 10.3389/fpls.2015.00989] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/29/2015] [Indexed: 05/19/2023]
Abstract
To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.1%) were differentially expressed among the three dormancy states, and 429 (1.0%) were differentially expressed during only one of the two dormancy transitions (FDR p-value < 0.05). Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, which was expected given the lower metabolic activity associated with endodormancy. Dormancy transitions were accompanied by changes in genes associated with DNA methylation (via RNA-directed DNA methylation) and histone modifications (via Polycomb Repressive Complex 2), confirming and extending knowledge of chromatin modifications as major features of dormancy transitions. Among the chromatin-associated genes, two genes similar to SPT (SUPPRESSOR OF TY) were strongly up-regulated during endodormancy. Transcription factor genes and gene sets that were atypically up-regulated during endodormancy include a gene that seems to encode a trihelix transcription factor and genes associated with proteins involved in responses to ethylene, cold, and other abiotic stresses. These latter transcription factors include ETHYLENE INSENSITIVE 3 (EIN3), ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN (EBP), ETHYLENE RESPONSE FACTOR (ERF), ZINC FINGER PROTEIN 10 (ZAT10), ZAT12, and WRKY DNA-binding domain proteins. Analyses of phytohormone-associated genes suggest important changes in responses to ethylene, auxin, and brassinosteroids occur during endodormancy. We found weaker evidence for changes in genes associated with salicylic acid and jasmonic acid, and little evidence for important changes in genes associated with gibberellins, abscisic acid, and cytokinin. We identified 315 upstream sequence motifs associated with eight patterns of gene expression, including novel motifs and motifs associated with the circadian clock and responses to photoperiod, cold, dehydration, and ABA. Analogies between flowering and endodormancy suggest important roles for genes similar to SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL), DORMANCY ASSOCIATED MADS-BOX (DAM), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).
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Affiliation(s)
- Glenn T. Howe
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, USA
| | - David P. Horvath
- Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research ServiceFargo, ND, USA
| | - Palitha Dharmawardhana
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, USA
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Henry D. Priest
- Donald Danforth Plant Science CenterSaint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University in Saint LouisSaint Louis, MO, USA
| | - Todd C. Mockler
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Donald Danforth Plant Science CenterSaint Louis, MO, USA
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, USA
- *Correspondence: Steven H. Strauss,
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39
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Filichkin SA, Cumbie JS, Dharmawadhana JP, Jaiswal P, Chang JH, Palusa SG, Reddy ASN, Megraw M, Mockler TC. Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis. Mol Plant 2014:ssu130. [PMID: 25366180 DOI: 10.1093/mp/ssu130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron retaining (IR) transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad range thermal cycles triggered a sharp increase in the long intron retaining CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or P. syringae infection induced similar increase. Thermal stress induced a time delay in accumulation of CCA1 I4Rb transcripts whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out of phase oscillations of CCA1 IR transcripts. Altogether, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this splicing factor could be involved in regulation of intron retention. Transcriptomes of NMD-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.
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Affiliation(s)
- Sergei A Filichkin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Jason S Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
| | - J Palitha Dharmawadhana
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Saiprasad G Palusa
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - A S N Reddy
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Molly Megraw
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Todd C Mockler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA Donald Danforth Plant Science Center, Saint Louis, Missouri, 63132, USA
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Wang L, Czedik-Eysenberg A, Mertz RA, Si Y, Tohge T, Nunes-Nesi A, Arrivault S, Dedow LK, Bryant DW, Zhou W, Xu J, Weissmann S, Studer A, Li P, Zhang C, LaRue T, Shao Y, Ding Z, Sun Q, Patel RV, Turgeon R, Zhu X, Provart NJ, Mockler TC, Fernie AR, Stitt M, Liu P, Brutnell TP. Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice. Nat Biotechnol 2014; 32:1158-65. [DOI: 10.1038/nbt.3019] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 08/14/2014] [Indexed: 01/29/2023]
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Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin DF, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel JP. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J 2014; 79:361-74. [PMID: 24888695 DOI: 10.1111/tpj.12569] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [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: 11/07/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 05/08/2023]
Abstract
Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.
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Affiliation(s)
- Sean P Gordon
- USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710, USA
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Abstract
The reduced or oxidized state of plastoquinone in chloroplasts regulates splicing in the nucleus to control nuclear gene expression in response to changing environmental conditions.
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Priest HD, Fox SE, Rowley ER, Murray JR, Michael TP, Mockler TC. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PLoS One 2014; 9:e87499. [PMID: 24489928 PMCID: PMC3906199 DOI: 10.1371/journal.pone.0087499] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [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: 11/11/2013] [Accepted: 12/27/2013] [Indexed: 12/01/2022] Open
Abstract
Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.
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Affiliation(s)
- Henry D. Priest
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University, Saint Louis, Missouri, United States of America
| | - Samuel E. Fox
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Erik R. Rowley
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Jessica R. Murray
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Todd P. Michael
- Waksman Institute and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University, Saint Louis, Missouri, United States of America
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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Fox SE, Christie MR, Marine M, Priest HD, Mockler TC, Blouin MS. Sequencing and characterization of the anadromous steelhead (Oncorhynchus mykiss) transcriptome. Mar Genomics 2014; 15:13-5. [PMID: 24440488 DOI: 10.1016/j.margen.2013.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 11/20/2013] [Accepted: 12/02/2013] [Indexed: 12/26/2022]
Abstract
Identifying the traits that differ between hatchery and wild fish may allow for pragmatic changes to hatchery practice. To meet those ends, we sequenced, assembled, and characterized the anadromous steelhead (Oncorhynchus mykiss) transcriptome. Using the Illumina sequencing platform, we sequenced nearly 41million 76-mer reads representing 3.1 Gbp of steelhead transcriptome. Upon final assembly, this sequence data yielded 86,402 transcript scaffolds, of which, 66,530 (77%) displayed homology to proteins of the non-redundant NCBI database. Gene descriptions and gene ontology terms were used to annotate the transcriptome resulting in 4030 unique gene ontology (GO) annotations attributed to the assembled sequences. We also conducted a comparative analysis that identified homologous genes within four other fish species including zebrafish (Danio rerio), stickleback (Gasterosteus aculeatus), and two pufferfish species (Tetraodon nigroviridis and Takifugu rubripes). Comparing our steelhead reference assembly directly to the transcriptome for rainbow trout (the fresh water life-history variant of the same species) revealed that while the steelhead and rainbow trout transcriptomes are complementary, the steelhead data will be useful for investigating questions related to anadromous (ocean-going) fishes. These sequence data and web tools provide a useful set of resources for salmonid researchers and the broader genomics community (available at http://salmon.cgrb.oregonstate.edu).
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Affiliation(s)
- Samuel E Fox
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Mark R Christie
- Department of Zoology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
| | - Melanie Marine
- Department of Zoology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Henry D Priest
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA; Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63110, USA
| | - Todd C Mockler
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA; Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63110, USA
| | - Michael S Blouin
- Department of Zoology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
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Trabucco GM, Matos DA, Lee SJ, Saathoff AJ, Priest HD, Mockler TC, Sarath G, Hazen SP. Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon. BMC Biotechnol 2013; 13:61. [PMID: 23902793 PMCID: PMC3734214 DOI: 10.1186/1472-6750-13-61] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [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: 05/20/2013] [Accepted: 06/11/2013] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Lignin is a significant barrier in the conversion of plant biomass to bioethanol. Cinnamyl alcohol dehydrogenase (CAD) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the pathway of lignin monomer biosynthesis. Brown midrib mutants in Zea mays and Sorghum bicolor with impaired CAD or COMT activity have attracted considerable agronomic interest for their altered lignin composition and improved digestibility. Here, we identified and functionally characterized candidate genes encoding CAD and COMT enzymes in the grass model species Brachypodium distachyon with the aim of improving crops for efficient biofuel production. RESULTS We developed transgenic plants overexpressing artificial microRNA designed to silence BdCAD1 or BdCOMT4. Both transgenes caused altered flowering time and increased stem count and weight. Downregulation of BdCAD1 caused a leaf brown midrib phenotype, the first time this phenotype has been observed in a C3 plant. While acetyl bromide soluble lignin measurements were equivalent in BdCAD1 downregulated and control plants, histochemical staining and thioacidolysis indicated a decrease in lignin syringyl units and reduced syringyl/guaiacyl ratio in the transgenic plants. BdCOMT4 downregulated plants exhibited a reduction in total lignin content and decreased Maule staining of syringyl units in stem. Ethanol yield by microbial fermentation was enhanced in amiR-cad1-8 plants. CONCLUSION These results have elucidated two key genes in the lignin biosynthetic pathway in B. distachyon that, when perturbed, may result in greater stem biomass yield and bioconversion efficiency.
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Affiliation(s)
- Gina M Trabucco
- Biology Department, University of Massachusetts 221 Morrill Science Center III, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Dominick A Matos
- Biology Department, University of Massachusetts 221 Morrill Science Center III, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Scott J Lee
- Biology Department, University of Massachusetts 221 Morrill Science Center III, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Aaron J Saathoff
- USDA-ARS, Grain, Forage, and Bioenergy Research Unit, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Henry D Priest
- The Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Todd C Mockler
- The Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Gautam Sarath
- USDA-ARS, Grain, Forage, and Bioenergy Research Unit, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Samuel P Hazen
- Biology Department, University of Massachusetts 221 Morrill Science Center III, Amherst, MA 01003, USA
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Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH. Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC Plant Biol 2013; 13:92. [PMID: 23799904 PMCID: PMC3728041 DOI: 10.1186/1471-2229-13-92] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 06/12/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation. RESULTS We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes. CONCLUSIONS DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.
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Affiliation(s)
- Kelly Vining
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle R Pomraning
- Molecular and Cellular Biology Program, Corvallis, OR 97331, USA
- Department of Biochemistry and Biophysics, Corvallis, OR 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | | | - Cathleen Ma
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Yanming Di
- Statistics Department, Oregon State University, Corvallis, Oregon, USA
| | - Todd C Mockler
- The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Michael Freitag
- Molecular and Cellular Biology Program, Corvallis, OR 97331, USA
- Department of Biochemistry and Biophysics, Corvallis, OR 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
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Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol 2013; 14:R41. [PMID: 23663246 PMCID: PMC4053705 DOI: 10.1186/gb-2013-14-5-r41] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 05/10/2013] [Indexed: 11/20/2022] Open
Abstract
Background Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan. Results The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101× and 5.2×. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment. Conclusions The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.
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Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS One 2012; 7:e48305. [PMID: 23284615 PMCID: PMC3527432 DOI: 10.1371/journal.pone.0048305] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [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: 07/04/2012] [Accepted: 09/17/2012] [Indexed: 11/19/2022] Open
Abstract
High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.
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Affiliation(s)
- Cameron Peace
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America.
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Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol 2012; 196:713-725. [PMID: 22861491 DOI: 10.1111/j.1469-8137.2012.04258.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
• Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype-genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ≈ 4000-6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.
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Affiliation(s)
- Gancho T Slavov
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Eli Rodgers-Melnick
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | - Mindie F Lipphardt
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | | | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Len A Pennacchio
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lee E Gunter
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kelly Vining
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA
| | - Kyle R Pomraning
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
| | | | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095-1606, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Yousry A El-Kassaby
- Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA
| | - Dan Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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50
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Rowley ER, Fox SE, Bryant DW, Sullivan CM, Priest HD, Givan SA, Mehlenbacher SA, Mockler TC. Assembly and Characterization of the European Hazelnut ‘Jefferson’ Transcriptome. Crop Science 2012; 52:2679-2686. [PMID: 0 DOI: 10.2135/cropsci2012.02.0065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Erik R. Rowley
- Dep. of Botany and Plant Pathology and Center for Genome Research and Biocomputing; Oregon State University; Corvallis OR 97331
- The Donald Danforth Plant Science Center; 975 North Warson Road St. Louis MO 63132
| | - Samuel E. Fox
- Dep. of Botany and Plant Pathology and Center for Genome Research and Biocomputing; Oregon State University; Corvallis OR 97331
| | - Douglas W. Bryant
- The Donald Danforth Plant Science Center; 975 North Warson Road St. Louis MO 63132
| | - Christopher M. Sullivan
- Dep. of Botany and Plant Pathology and Center for Genome Research and Biocomputing; Oregon State University; Corvallis OR 97331
| | - Henry D. Priest
- The Donald Danforth Plant Science Center; 975 North Warson Road St. Louis MO 63132
| | - Scott A. Givan
- Informatics Research Core Facility; Molecular Microbiology and Immunology, University of Missouri; Columbia MO 65201
| | | | - Todd C. Mockler
- Dep. of Botany and Plant Pathology and Center for Genome Research and Biocomputing; Oregon State University; Corvallis OR 97331
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