Population Genomic Variation and Genome-Wide Association Study in Prairie Cordgrass.

Prairie cordgrass (Spartina pectinate Link) is a productive warm-season, C4 perennial grass native to North America. Having tolerance to wet, cold, and saline marginal land conditions, along with high biomass yield, prairie cordgrass has potential of being used for both conservation practices and bioenergy production. However, as many other undomesticated grass species, extensive genetic variation of prairie cordgrass provide both merits and difficulties to breed and improve it as a dedicated bioenergy crop. In this study, we are able to explore the population genomic variation and study genome-wide association in prairie cordgrass. In 2014, a total of 200 genotypes from 100 natural populations of prairie cordgrass, including three groups of ploidy levels (2n=4x, 2n=6x, and 2n=8x), were phenotyped and genotyped using an Illumina Hi-Seq 2000 platform in Urbana, IL. Both phenotypic and genotypic results indicated that there is a considerable genetic variation among the natural populations. Phylogenetic analysis identified four primary diversity centers for prairie cordgrass in the central Midwest and east, north Midwest, south Midwest, and a transition zone among three centers. Single-nucleotide-polymorphisms (SNPs) significantly associated with geographical separation and phenotypical traits were captured to provide insights into signatures of genomic adaptive variation. As proved to obtain extensive genetic variability and geographically adaptation, prairie cordgrass can be well developed through a planned breeding program in considerable effectiveness.