Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Evans, Joseph; Crisovan, Emily; Barry, Kerrie; Daum, Chris; Jenkins, Jerry; Kunde-Ramamoorthy, Govindarajan; Nandety, Aruna; Ngan, Chew Yee; Vaillancourt, Brieanne; Wei, Chia-Lin; Schmutz, Jeremy; Kaeppler, Shawn M.; Casler, Michael D.; Buell, Carol Robin

doi:10.1111/tpj.13041

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Journal Article · Thu Oct 01 00:00:00 EDT 2015 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.13041· OSTI ID:1438259

Evans, Joseph ^[1]; Crisovan, Emily ^[2]; Barry, Kerrie ^[3]; Daum, Chris ^[3]; Jenkins, Jerry ^[4]; Kunde-Ramamoorthy, Govindarajan ^[3]; Nandety, Aruna ^[5]; Ngan, Chew Yee ^[3]; Vaillancourt, Brieanne ^[2]; Wei, Chia-Lin ^[3]; Schmutz, Jeremy ^[6]; Kaeppler, Shawn M. ^[7]; Casler, Michael D. ^[8]; Buell, Carol Robin ^[2]

Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Plant Biology; Michigan State University
Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Plant Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Agronomy
Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; USDA-ARS Dairy Forage Research Center, Madison, WI (United States)

Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Michigan State Univ., East Lansing, MI (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231; FC02-07ER64494

OSTI ID:: 1438259

Alternate ID(s):: OSTI ID: 1616044

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 4 Vol. 84; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations Fiedler, Jason D.; Lanzatella, Christina; Edmé, Serge J. BMC Plant Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12870-018-1360-z	journal	July 2018
Genome-Wide Association Study in Pseudo-F2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates Taylor, Megan; Tornqvist, Carl-Erik; Zhao, Xiongwei Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01250	journal	September 2018
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Quantitative Trait Locus Mapping for Flowering Time in a Lowland × Upland Switchgrass Pseudo-F Population Tornqvist, Carl-Erik; Taylor, Megan; Jiang, Yiwei The Plant Genome, Vol. 11, Issue 2 https://doi.org/10.3835/plantgenome2017.10.0093	journal	January 2018
DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications Loera-Sánchez, Miguel; Studer, Bruno; Kölliker, Roland ETH Zurich https://doi.org/10.3929/ethz-b-000386451	text	January 2019

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09 BIOMASS FUELS
59 BASIC BIOLOGICAL SCIENCES
PRJNA280418
Panicum virgatum
exome capture
genomics
polyploid
switchgrass

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

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