Extensive Genetic Diversity is Present within North American Switchgrass Germplasm
Abstract
Switchgrass ( 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 ( L.), maize ( L.), soybean [ (L.) Merr.], and 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 repeatedmore »
- Authors:
-
- Michigan State Univ., East Lansing, MI (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
- Univ. of Georgia, Athens, GA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
- Noble Research Institute, Ardmore, OK (United States)
- Univ. of Wisconsin, Madison, WI (United States)
- Univ. of California, Davis, CA (United States)
- 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); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1499380
- Alternate Identifier(s):
- OSTI ID: 1616060
- 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. https://doi.org/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. https://doi.org/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 ( 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 ( L.), maize ( L.), soybean [ (L.) Merr.], and 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 = {Thu Dec 07 00:00:00 EST 2017},
month = {Thu Dec 07 00:00:00 EST 2017}
}
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