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Title: Diversity and population structure of northern switchgrass as revealed though exome capture sequencing

item EVANS, JOSEPH - Michigan State University
item CRISOVAN, EMILY - Michigan State University
item VAILLANCOURT, BRIEANNE - Michigan State University
item SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology
item KAEPPLER, SHAWN - University Of Wisconsin
item Casler, Michael
item BUELL, ROBIN - Michigan State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/3/2015
Publication Date: 10/1/2015
Publication URL:
Citation: Evans, J., Crisovan, E., Vaillancourt, B., Schmutz, J., Kaeppler, S., Casler, M.D., Buell, R. 2015. Diversity and population structure of northern switchgrass as revealed though exome capture sequencing. PLoS One. 84:800-815.

Interpretive Summary: Switchgrass is undergoing intensive development as a perennial biofuel crop. Research efforts are underway to develop selection tools to speed the rate of progress toward reaching the 10-ton-per-acre goal for biomass production. In order to achieve this goal, a reliable DNA marker system must be developed to have broad marker coverage across the entire switchgrass genome. A team of research scientists has utilized advances in human genetics to accomplish this goal. These DNA markers were successfully evaluated on a diversity panel of 532 switchgrass genotypes that originated from 66 populations. The panel possesses a total of 1.6 million DNA markers of use to switchgrass researchers. The markers also identified 144,000 genes that are either duplicated or deleted in some plants. DNA sequence analysis revealed significant variation within several key genes involved in flowering time, a key trait regulating biomass yield. These results will be of great value to scientists involved in breeding, genetics, and genomics of switchgrass and related species.

Technical Abstract: Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels 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 (~2.5 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 distinct 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 impact protein function in genes that encode 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 AP13 reference sequence, 17,228 up-copy number variants (CNVs), 112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a total of 9,979 genes, including two upland-specific CNV-clusters. In total, 45,719 genes were impacted by a SNP, CNV, or a PAV across the panel providing a firm foundation to identify functional variation associated phenotypic traits of interest for biofuel feedstock production.