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 genome (down-CNVs) and 14 430 presence/absencemore »
- Authors:
-
- Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Plant Biology
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
- Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
- Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Agronomy
- 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); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1438259
- Alternate Identifier(s):
- OSTI ID: 1616044
- Grant/Contract Number:
- FC02-07ER64494; AC02-05CH11231
- Resource Type:
- 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. https://doi.org/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. https://doi.org/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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