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Title: Extensive Genetic Diversity is Present within North American Switchgrass Germplasm

Abstract

Switchgrass ( Panicum virgatum L) is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1.9 million high-confidence SNPs were obtained from 1169 individuals from 140 populations (67 upland, 65 lowland, 8 admixed) were used in downstream analyses of genetic diversity and population structure. Seven separate population groups were identified with moderate genetic differentiation [mean fixation index (Fst) estimate of 0.06] between the lowland and the upland populations. Ecotype-specific and population-specific SNPs were identified for use in germplasm evaluations. Relative to rice ( Oryza sativa L.), maize ( Zea mays L.), soybean [ Glycine max (L.) Merr.], and Medicago truncatula Gaertn., analyses of nucleotide diversity revealed a high degree of genetic diversity (0.0135) across all individuals, consistent with the outcrossing mode of reproduction andmore » the polyploidy of switchgrass. This study supports the hypothesis that repeated glaciation events, ploidy barriers, and restricted gene flow caused by flowering time differences have resulted in distinct gene pools across ecotypes and geographic regions. These data provide a resource to associate alleles with traits of interest for forage, restoration, and biofuel feedstock efforts in switchgrass.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [2];  [2];  [3];  [2];  [2];  [1];  [4];  [5];  [6];  [7];  [8];  [9];  [1]
  1. Michigan State Univ., East Lansing, MI (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  4. Univ. of Georgia, Athens, GA (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  6. Noble Research Institute, Ardmore, OK (United States)
  7. Univ. of Wisconsin, Madison, WI (United States)
  8. Univ. of California, Davis, CA (United States)
  9. Univ. of Wisconsin, Madison, WI (United States); USDA-ARS, U.S. Dairy Forage Research Center, Madison, WI (United States)
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States); Univ. of California, Davis, CA (United States); UT-Batelle, Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1499380
Grant/Contract Number:  
FC02-07ER64494; AC02-05CH11231; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
The Plant Genome
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1940-3372
Publisher:
Alliance of Crop, Soil, and Environmental Science Societies
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS

Citation Formats

Evans, Joseph, Sanciangco, Millicent D., Lau, Kin H., Crisovan, Emily, Barry, Kerrie, Daum, Chris, Hundley, Hope, Jenkins, Jerry, Kennedy, Megan, Kunde-Ramamoorthy, Govindarajan, Vaillancourt, Brieanne, Acharya, Ananta, Schmutz, Jeremy, Saha, Malay, Kaeppler, Shawn M., Brummer, E. Charles, Casler, Michael D., and Buell, C. Robin. Extensive Genetic Diversity is Present within North American Switchgrass Germplasm. United States: N. p., 2017. Web. doi:10.3835/plantgenome2017.06.0055.
Evans, Joseph, Sanciangco, Millicent D., Lau, Kin H., Crisovan, Emily, Barry, Kerrie, Daum, Chris, Hundley, Hope, Jenkins, Jerry, Kennedy, Megan, Kunde-Ramamoorthy, Govindarajan, Vaillancourt, Brieanne, Acharya, Ananta, Schmutz, Jeremy, Saha, Malay, Kaeppler, Shawn M., Brummer, E. Charles, Casler, Michael D., & Buell, C. Robin. Extensive Genetic Diversity is Present within North American Switchgrass Germplasm. United States. doi:10.3835/plantgenome2017.06.0055.
Evans, Joseph, Sanciangco, Millicent D., Lau, Kin H., Crisovan, Emily, Barry, Kerrie, Daum, Chris, Hundley, Hope, Jenkins, Jerry, Kennedy, Megan, Kunde-Ramamoorthy, Govindarajan, Vaillancourt, Brieanne, Acharya, Ananta, Schmutz, Jeremy, Saha, Malay, Kaeppler, Shawn M., Brummer, E. Charles, Casler, Michael D., and Buell, C. Robin. Thu . "Extensive Genetic Diversity is Present within North American Switchgrass Germplasm". United States. doi:10.3835/plantgenome2017.06.0055. https://www.osti.gov/servlets/purl/1499380.
@article{osti_1499380,
title = {Extensive Genetic Diversity is Present within North American Switchgrass Germplasm},
author = {Evans, Joseph and Sanciangco, Millicent D. and Lau, Kin H. and Crisovan, Emily and Barry, Kerrie and Daum, Chris and Hundley, Hope and Jenkins, Jerry and Kennedy, Megan and Kunde-Ramamoorthy, Govindarajan and Vaillancourt, Brieanne and Acharya, Ananta and Schmutz, Jeremy and Saha, Malay and Kaeppler, Shawn M. and Brummer, E. Charles and Casler, Michael D. and Buell, C. Robin},
abstractNote = {Switchgrass (Panicum virgatum L) is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1.9 million high-confidence SNPs were obtained from 1169 individuals from 140 populations (67 upland, 65 lowland, 8 admixed) were used in downstream analyses of genetic diversity and population structure. Seven separate population groups were identified with moderate genetic differentiation [mean fixation index (Fst) estimate of 0.06] between the lowland and the upland populations. Ecotype-specific and population-specific SNPs were identified for use in germplasm evaluations. Relative to rice (Oryza sativa L.), maize (Zea mays L.), soybean [Glycine max (L.) Merr.], and Medicago truncatula Gaertn., analyses of nucleotide diversity revealed a high degree of genetic diversity (0.0135) across all individuals, consistent with the outcrossing mode of reproduction and the polyploidy of switchgrass. This study supports the hypothesis that repeated glaciation events, ploidy barriers, and restricted gene flow caused by flowering time differences have resulted in distinct gene pools across ecotypes and geographic regions. These data provide a resource to associate alleles with traits of interest for forage, restoration, and biofuel feedstock efforts in switchgrass.},
doi = {10.3835/plantgenome2017.06.0055},
journal = {The Plant Genome},
number = 1,
volume = 11,
place = {United States},
year = {2017},
month = {12}
}

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