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

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 genomemore » (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.« less

Authors:
 [1];  [1];  [2];  [2];  [3];  [2];  [4];  [2];  [1];  [2];  [5];  [6];  [7];  [1]
  1. Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Plant Biology
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  4. Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  6. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Agronomy
  7. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; USDA-ARS Dairy Forage Research Center, Madison, WI (United States)
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Michigan State Univ., East Lansing, MI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1438259
Grant/Contract Number:  
FC02-07ER64494; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Volume: 84; Journal Issue: 4; Journal ID: ISSN 0960-7412
Publisher:
Society for Experimental Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; Panicum virgatum; exome capture; switchgrass; polyploid; genomics; PRJNA280418

Citation Formats

Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Wei, Chia-Lin, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., and Buell, Carol Robin. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. United States: N. p., 2015. Web. doi:10.1111/tpj.13041.
Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Wei, Chia-Lin, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., & Buell, Carol Robin. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. United States. doi:10.1111/tpj.13041.
Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Wei, Chia-Lin, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., and Buell, Carol Robin. Thu . "Diversity and population structure of northern switchgrass as revealed through exome capture sequencing". United States. doi:10.1111/tpj.13041. https://www.osti.gov/servlets/purl/1438259.
@article{osti_1438259,
title = {Diversity and population structure of northern switchgrass as revealed through exome capture sequencing},
author = {Evans, Joseph and Crisovan, Emily and Barry, Kerrie and Daum, Chris and Jenkins, Jerry and Kunde-Ramamoorthy, Govindarajan and Nandety, Aruna and Ngan, Chew Yee and Vaillancourt, Brieanne and Wei, Chia-Lin and Schmutz, Jeremy and Kaeppler, Shawn M. and Casler, Michael D. and Buell, Carol Robin},
abstractNote = {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.},
doi = {10.1111/tpj.13041},
journal = {The Plant Journal},
number = 4,
volume = 84,
place = {United States},
year = {Thu Oct 01 00:00:00 EDT 2015},
month = {Thu Oct 01 00:00:00 EDT 2015}
}

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