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Surveying Grassland Islands: the genetics and performance of Appalachian switchgrass (Panicum virgatum L.) collections

Abstract

The interior Southeastern United States could contain novel germplasm for the bioenergy crop switchgrass due to its diverse habitats and geographic location between genetic subpopulations (Atlantic, Midwest, and Gulf). Collections from this region could accelerate breeding progress, contribute to conservation efforts, and improve understanding of isolated grasslands in the region. This study located 22 sites in the Midsouth region and obtained 1,521,210 single nucleotide polymorphism markers of 202 individuals through genotype-by-sequencing. Individuals were evaluated for flowering time, winter survival and tiller number. Comparison to a national diversity panel revealed that branches of two major subpopulations occur in the region with two levels of polyploidy: Atlantic tetraploids and Midwest octoploids. Two locations contained admixed octoploid individuals with Midwest and Gulf genetics. Field performance of the Midwest octoploids conformed with prior reported performance of the Midwest subpopulation, although three sites contained promising late flowering traits. The Atlantic tetraploids had moderate winter survival, short stature, and anomalously early flowering. Atlantic populations mostly occurred in marginal sites and their morphological and flowering time adaptations may be a resource conservation strategy. Demographic inference of historical effective population size variation in a subset of tetraploid locations indicated a widespread recent decline in effective population size. This pattern is consistent with isolation of these switchgrass communities from larger populations and is further supported by evidence of inbreeding within the populations (FI = 0.18). The populations documented in this study contain novel genetic diversity and adaptations to a range of marginal habitats. Therefore, this study provides a new source of germplasm for future breeding and conservation programs.

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Acknowledgements

NWT is grateful for the help of many who provided their time, expertise, and/or collection permits to this project: Mamie Coburn of The Nature Conservancy, Gary Kauffman of the USDA Forest Service, Kyle Pursel of Highlands-Cashiers Land Trust, David Lee with Conserving Carolinas, Wesley Sketo with the North Carolina Department of Agriculture, Rusty Boles with the Tennessee Wildlife Resource Agency, Dwayne Estes with the Southeastern Grasslands Initiative, Alex Faught of the U.S. Forest Service, Dot Fields of the Virginia Department of Conservation and Recreation, David Danley recently from the USDA Forest Service (retired), Alan Weakley, Director of the UNC Herbarium, and Robert Peet, Associate Professor at UNC. I would also like to thank Professor Aaron Ragsdale with assistance interpreting demographic inference methods.

Funding

This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409. This research was also supported by congressionally allocated funds to the USDA-ARS, U.S. Dairy Forage Research Center.

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NT: Conceptualization, data collection and curation, formal analysis, writing. MC: Project conception and direction, funding acquisition, supervision, methodology, review and editing of manuscript.

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Correspondence to Neal W. Tilhou.

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Data availability

Unfiltered SNP calls (in variant call format) and field performance BLUPs will be posted to Dryad Digital Repository. Germplasm from the collected populations can be obtained by contacting the authors and will be deposited into the USDA Germplasm Resources Information Network.

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Code used for this study can be obtained by contacting the authors.

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Supplementary file1 (DOCX 48 kb)

10722_2021_1282_MOESM2_ESM.png

Read count distributions of reference alleles within heterozygote calls for each individual by location. Tetraploids with disomic inheritance should display a peak at 0.50. Octoploid individuals with tetrasomic inheritance should display a peak at 0.75 (PNG 156 kb)

10722_2021_1282_MOESM3_ESM.png

A genetic distance dendrogram constructed using UPGMA (average) hierarchical clustering. Analysis included 731 individuals (202 from the Midsouth collections and 529 from the Lovell et al. diversity panel). A total of 109,729 SNPs were used to calculate the genetic distance among individuals. Individuals from the diversity panel were labeled by the state of origin, while the Midsouth collections were labeled with a site code (PNG 472 kb)

Supplementary file4 (DOCX 14 kb)

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Tilhou, N.W., Casler, M.D. Surveying Grassland Islands: the genetics and performance of Appalachian switchgrass (Panicum virgatum L.) collections. Genet Resour Crop Evol (2021). https://doi.org/10.1007/s10722-021-01282-6

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Keywords

  • Germplasm collection
  • Bioenergy traits
  • Genetic diversity
  • Demographic inference