title: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing.
abstract: 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.
authors.affiliation: DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.|Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Evans
authors.affiliation: DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.|Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Crisovan
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Daum
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Govindarajan
authors.initials: G
authors.lastname: Kunde-Ramamoorthy
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Aruna
authors.initials: A
authors.lastname: Nandety
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Chew Yee
authors.initials: CY
authors.lastname: Ngan
authors.affiliation: DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.|Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
authors.forename: Brieanne
authors.initials: B
authors.lastname: Vaillancourt
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.|HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA.|Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
authors.affiliation: DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA.|USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Casler
authors.affiliation: DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.|Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
authors.forename: Carol Robin
authors.initials: CR
authors.lastname: Buell
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D056915:DNA Copy Number Variations; D017753:Ecosystem; D060146:Ecotype; D059472:Exome / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D005843:Geography; D008897:Panicum / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity; D014481:United States
chemical_list: D010940:Plant Proteins
keywords: PRJNA280418; Panicum virgatum; exome capture; genomics; polyploid; switchgrass