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Plant J. 2015 Nov;84(4):800-15. doi: 10.1111/tpj.13041.

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing.

Author information

1
DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.
2
Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
3
Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
4
HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
5
Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
6
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA.
7
Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA.
8
USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA.

Abstract

Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel 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 (~2.4 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 primary 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 affect the protein function of 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 near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.

KEYWORDS:

PRJNA280418; Panicum virgatum; exome capture; genomics; polyploid; switchgrass

PMID:
26426343
DOI:
10.1111/tpj.13041
[Indexed for MEDLINE]
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