title: Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data.
abstract: Flowering time is a major determinant of biomass yield in switchgrass (Panicum virgatum), a perennial bioenergy crop, because later flowering allows for an extended period of vegetative growth and increased biomass production. A better understanding of the genetic regulation of flowering time in switchgrass will aid the development of switchgrass varieties with increased biomass yields, particularly at northern latitudes, where late-flowering but southern-adapted varieties have high winter mortality. We use genotypes derived from recently published exome-capture sequencing, which mitigates challenges related to the large, highly repetitive and polyploid switchgrass genome, to perform genome-wide association studies (GWAS) using flowering time data from a switchgrass association panel in an effort to characterize the genetic architecture and genes underlying flowering time regulation in switchgrass. We identify associations with flowering time at multiple loci, including in a homolog of FLOWERING LOCUS T and in a locus containing TIMELESS, a homolog of a key circadian regulator in animals. Our results suggest that flowering time variation in switchgrass is due to variation at many positions across the genome. The relationship of flowering time and geographic origin indicates likely roles for genes in the photoperiod and autonomous pathways in generating switchgrass flowering time variation.
authors.affiliation: US Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr. W, Madison, WI, 53706, USA.
authors.forename: Paul P
authors.identifier: 0000-0002-4372-0847
authors.initials: PP
authors.lastname: Grabowski
authors.affiliation: DuPont Pioneer, Johnston, IA, 50131, USA.|Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.|DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Evans
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Daum
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Shweta
authors.initials: S
authors.lastname: Deshpande
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Kerrie W
authors.initials: KW
authors.lastname: Barry
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Megan
authors.initials: M
authors.lastname: Kennedy
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr, Madison, WI, 53706, USA.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Ramstein
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr, Madison, WI, 53706, USA.|DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.|DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.affiliation: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.
authors.forename: Yiwei
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: US Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr. W, Madison, WI, 53706, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Casler
mesh_terms: D000483:Alleles; D059472:Exome / Q000235:genetics*; D035264:Flowers / Q000235:genetics* / Q000502:physiology*; D017343:Genes, Plant; D056726:Genetic Association Studies; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005838:Genotype; D005843:Geography; D015810:Linkage Disequilibrium / Q000235:genetics; D008897:Panicum / Q000235:genetics*; D010641:Phenotype; D012621:Seasons; D013696:Temperature; D013997:Time Factors; D000073359:Exome Sequencing / Q000379:methods*
keywords: Panicum virgatum (switchgrass); bioenergy; exome-capture; flowering time; genome-wide association studies (GWAS)