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

Evans, Joseph; Crisovan, Emily; Barry, Kerrie; Daum, Chris; Jenkins, Jerry; Kunde-Ramamoorthy, Govindarajan; Nandety, Aruna; Ngan, Chew Yee; Vaillancourt, Brieanne; Schmutz, Jeremy; Kaeppler, Shawn M.; Casler, Michael D.; Buell, Carol Robin; Wei, Chia-Lin

doi:10.5061/dryad.nh8ph

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

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Abstract

Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels 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 impact protein function in genes that encode 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 up-copy number variants (CNVs), 112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a total of 9,979 genes, including two upland-specific CNV-clusters.more »« less

Authors:

Evans, Joseph; Crisovan, Emily; Barry, Kerrie; Daum, Chris; Jenkins, Jerry; Kunde-Ramamoorthy, Govindarajan; Nandety, Aruna; Ngan, Chew Yee; Vaillancourt, Brieanne; Schmutz, Jeremy; Kaeppler, Shawn M.; Casler, Michael D.; Buell, Carol Robin; Wei, Chia-Lin

Michigan State Univ., East Lansing, MI (United States); OSTI
Michigan State Univ., East Lansing, MI (United States)
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)
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)

Publication Date:: Thu Sep 15 00:00:00 EDT 2016

DOE Contract Number:: FC02-07ER64494; AC02-05CH11231

Research Org.:: Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Subject:: 09 BIOMASS FUELS

OSTI Identifier:: 1873890

DOI:: https://doi.org/10.5061/dryad.nh8ph

Citation Formats


                    Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., Buell, Carol Robin, and Wei, Chia-Lin. Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing.  United States: N. p., 2016. 
        Web.  doi:10.5061/dryad.nh8ph.

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                    Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., Buell, Carol Robin, & Wei, Chia-Lin. Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing.  United States.  doi:https://doi.org/10.5061/dryad.nh8ph

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                    Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., Buell, Carol Robin, and Wei, Chia-Lin. 2016.  
"Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing".  United States.  doi:https://doi.org/10.5061/dryad.nh8ph.  https://www.osti.gov/servlets/purl/1873890. Pub date:Thu Sep 15 00:00:00 EDT 2016

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@article{osti_1873890,

  title        = {Data from: 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 Schmutz, Jeremy and Kaeppler, Shawn M. and Casler, Michael D. and Buell, Carol Robin and Wei, Chia-Lin},

  abstractNote = {Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels 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 impact protein function in genes that encode 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 up-copy number variants (CNVs), 112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a total of 9,979 genes, including two upland-specific CNV-clusters. In total, 45,719 genes were impacted by a SNP, CNV, or a PAV across the panel providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.},

  doi          = {10.5061/dryad.nh8ph},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Thu Sep 15 00:00:00 EDT 2016},

  month        = {Thu Sep 15 00:00:00 EDT 2016}

}

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DOI: https://doi.org/10.5061/dryad.nh8ph

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