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

Journal Article · · The Plant Genome
 [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)
+ Show Author Affiliations

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.

Research Organization:
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 Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
FC02-07ER64494; AC02-05CH11231; AC05-00OR22725
OSTI ID:
1499380
Alternate ID(s):
OSTI ID: 1616060
Journal Information:
The Plant Genome, Vol. 11, Issue 1; ISSN 1940-3372
Publisher:
Alliance of Crop, Soil, and Environmental Science SocietiesCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 24 works
Citation information provided by
Web of Science

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Cited By (9)

Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars journal September 2019
QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient journal June 2019
Data from: Extensive genetic diversity is present within North American switchgrass germplasm dataset January 2017
Selection for Winter Survivorship in Lowland Switchgrass journal January 2020
Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar journal October 2018
Genomic Prediction for Winter Survival of Lowland Switchgrass in the Northern USA journal June 2019
Benchmarking Parametric and Machine Learning Models for Genomic Prediction of Complex Traits journal November 2019
Quantitative Trait Loci for Freezing Tolerance in a Lowland x Upland Switchgrass Population journal March 2019
Marginal Lands to Grow Novel Bio-Based Crops: A Plant Breeding Perspective journal March 2020

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