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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Dairy Forage Research » Research » Publications at this Location » Publication #303673

Research Project: Redesigning Forage Genetics, Management, and Harvesting for Efficiency, Profit, and Sustainability in Dairy and Bioenergy Production Systems

Location: Dairy Forage Research

Title: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum

Author
item EVANS, JOSEPH - Michigan State University
item KIM, JEONGWOON - Michigan State University
item CHILDS, KEVIN - Michigan State University
item VAILLANCOURT, BRIEANNE - Michigan State University
item CRISOVAN, EMILY - Michigan State University
item RICHMOND, TODD - Roche Nimblegen, Inc
item JEDDELOH, JEFFREY - Roche Nimblegen, Inc
item KAEPPLER, SHAWN - University Of Wisconsin
item Casler, Michael
item BUELL, C. ROBIN - Michigan State University

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/9/2014
Publication Date: 8/15/2014
Publication URL: https://handle.nal.usda.gov/10113/62415
Citation: Evans, J., Kim, J., Childs, K., Vaillancourt, B., Crisovan, E., Richmond, T., Jeddeloh, J., Kaeppler, S., Casler, M.D., Buell, C. 2014. Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum. Plant Journal. 79(6):993-1008.

Interpretive Summary: Switchgrass is undergoing intensive development as a perennial biofuel crop. Research efforts are underway to develop genomic selection models 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 develop an exome capture probe set specifically for switchgrass DNA. The probe set was successfully tested against eight highly divergent switchgrass genotypes that represent the range of DNA variation in the species. The exome capture probe design resulted in 1.4 million genetic markers that are now available for breeding and genetic studies. This probe set will be used in developing genome-wide associations between traits and markers and in developing genomic selection models for both upland and lowland switchgrass to support several switchgrass breeding programs.

Technical Abstract: Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America. Traditionally grown as forage and ground cover, switchgrass has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass, inhabiting the northern and southern regions of the species’ range, respectively. Switchgrass ecotypes vary in ploidy, with upland switchgrass cultivars generally octoploid and lowland cultivars generally tetraploid. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes and contains a significant amount of repetitive sequence, limiting the efficiency of re-sequencing projects focused on determining genome diversity. To assess genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set from a set of transcript assemblies that represent ~50 Mb of annotated switchgrass exome sequences. We then assessed and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next generation sequencing. Using the optimized probe set, we assessed variation in the exomes of eight switchgrass genotypes representing tetraploid lowland and octoploid upland cultivars to benchmark our exome capture probe set design. We were able to identify ample variation in the switchgrass genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8,173 putative copy number variants and 3,336 presence/absence variants. While the majority of the SNPs (84%) detected were bi-allelic, a substantial number were tri-allelic with limited occurrence of tetra-allelic polymorphisms consistent with the heterozygous nature of the switchgrass genome. Comparison of genome-derived SNPs with transcriptome-derived SNPs revealed a substantial number of genes with allele preferential expression. Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in large, repetitive, heterozygous polyploid species.