Genomic diversity and population structure of bermudagrass (Cynodon spp.) revealed by genotyping-by-sequencing

Authors: SINGH, LOVEPREET - Mississippi State University; WU, YANQI - Mississippi State Extension Service; MCCURDY, JAMES - Mississippi State University; STEWART, BARRY - Mississippi State University; Warburton, Marilyn; BALDWIN, BRIAN - Mississippi State University; DONG, HONGXU - Mississippi State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/18/2023
Publication Date: 6/8/2023
Citation: Singh, L., Wu, Y., McCurdy, J.D., Stewart, B.R., Warburton, M.L., Baldwin, B.S., Dong, H. 2023. Genomic diversity and population structure of bermudagrass (Cynodon spp.) revealed by genotyping-by-sequencing. Frontiers in Plant Science. 14. Article 1155721. https://doi.org/10.3389/fpls.2023.1155721.
DOI: https://doi.org/10.3389/fpls.2023.1155721

Interpretive Summary: Bermudagrass is an important turf and forage species, and new cultivars are needed to address challenges due to increasing drought, salinity, disease and insect pests, and other streses. New cultivars require new genetic diversity, and while there is abundant diversity in the species, the lack of understanding of which populations contain what diversity, and what populations are related to what others, slows the progress that can be made by plant breeding. This study was undertaken with genetic markers that read the differences on the chromosomes of 206 total populations of bermudagrasses from around the world, but particularly from Africa, where it originated, to fill in some of the gaps in our understanding of diversity and relationships in and between the populations. Further studies of this panel of bermudagrass populations can elucidate what genes are involved in traits of interest to further speed breeding in the future.

Technical Abstract: Breeding and cultivar development in bermudagrass (Cynodon spp.) is hampered by the limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 Cynodon accessions consisting of 193 common bermudagrass (C. dactylon var. dactylon) and 13 African bermudagrass (C. transvaalensis) accessions of worldwide origin were assembled for this study. Genotyping-by-sequencing (GBS) with ApeKI enzyme was employed for genetic marker development. With a minor allele frequency of 0.05 and a minimum call rate of 0.5, a total of 37,496 raw single nucleotide polymorphisms (SNPs) were called de novo using the TASSEL 3 UNEAK pipeline. Population structure analysis using ADMIXTURE revealed four subpopulations in this germplasm panel, which was consistent with principal component analysis (PCA) and phylogenetic analysis results. The first three principal components explained 15.6 %, 10.1 %, and 3.8 % of the variance in the germplasm panel, respectively. The first subpopulation consists of admixture of C. dactylon accessions from various continents, the second subpopulation comprises mainly C. transvaalensis accessions, the third subpopulation contains C. dactylon accessions primarily of African origin, and the fourth subpopulation represents C. dactylon accessions from the Oklahoma State University bermudagrass breeding program. Genetic diversity parameters including nucleotide diversity or average pairwise divergence (p), estimated mutation rate or expected nucleotide diversity ('), Tajima’s D statistic, and Fst statistic revealed substantial genetic variation in the Cynodon genus, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs.