Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

Lu, Fei; Lipka, Alexander E.; Glaubitz, Jeff; Elshire, Rob; Cherney, Jerome H.; Casler, Michael D.; Buckler, Edward S.; Costich, Denise E.

doi:10.1371/journal.pgen.1003215

Title: Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

Journal Article · Thu Jan 17 00:00:00 EST 2013 · PLoS Genetics

DOI:https://doi.org/10.1371/journal.pgen.1003215· OSTI ID:1904732

Lu, Fei ^[1]; Lipka, Alexander E. ^[2]; Glaubitz, Jeff ^[1]; Elshire, Rob ^[1]; Cherney, Jerome H. ^[1]; Casler, Michael D. ^[3]; Buckler, Edward S. ^[2]; Costich, Denise E. ^[2]

Cornell University, Ithaca, NY (United States)
Cornell University, Ithaca, NY (United States); US Department of Agriculture (USDA), Ithaca, NY (United States). Agricultural Research Service
US Department of Agriculture (USDA), Madison, WI (United States). Agricultural Research Service; University of Wisconsin, Madison, WI (United States)

Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of switchgrass.

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Research Organization:: US Deptartment of Agriculture (USDA), Washington, DC (United States). Agricultural Research Service

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF); US Department of Agriculture (USDA)

Grant/Contract Number:: AI02-07ER64454; 0820619; 0965342

OSTI ID:: 1904732

Journal Information:: PLoS Genetics, Vol. 9, Issue 1; ISSN 1553-7404

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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