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Cross-taxon application of sugarcane EST-SSR to genetic diversity analysis of bermudagrass (Cynodon spp.)

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Abstract

Bermudagrass lags in genomic and molecular breeding resources, particularly regarding a critical mass of robust, reproducible, and highly polymorphic molecular markers like simple sequence repeats (SSR). Here, 2017 sugarcane EST-SSR primer pairs (PPs) were screened for transferability and polymorphisms against commercial triploid hybrids and representatives of their parental species, tetraploid Cynodon dactylon and diploid C. transvaalensis. Fifty-four percent of PPs amplified target SSR in at least one of the two species, while 62% of these ‘transferable’ SSR were polymorphic. A subset of 228 polymorphic markers was utilized for genotyping 24 samples that included: 10 ‘Tif’ series cultivars (i.e., released from Tifton, GA), their parental species, 10 F1 hybrids between the two species, and two diverse Sorghum spp. A total of 90 and 144 PPs produced reproducible bands in the bermudagrass samples and the sorghum species, respectively. While 63 (70%) PPs were polymorphic among members of the ‘Tif’ diversity panel, 79 (54.8%) were polymorphic between the sorghum species. Further, 57 PPs polymorphic in the ‘Tif’ diversity panel were genotyped against 3 experimental lines and 7 commercial hybrids including ‘TifTuf’, a recent addition to the ‘Tif’ series. Joint analysis of 24 genotypes grouped bermudagrass accessions into two main clusters, one including C. dactylon and the other including C. transvaalensis. A small set of informative SSR readily differentiated the cultivar groups and identified potentially mischaracterized cultivars, but did not differentiate among mutants within cultivar groups. Heterologous EST-SSR from sugarcane are useful sources of polymorphic markers for cultivar identification in bermudagrass, and build on existing marker resources to facilitate genetic mapping, QTL analysis, and marker assisted selection.

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Acknowledgements

We thank Wayne Hanna for his feedback on the manuscript. This work was financially supported by the United States Golf Association (USGA), Georgia Seed Development Commission (GSDC), Georgia Crop Improvement Association (GCIA), and Georgia Agricultural Experiment Station.

Author contribution

SK was responsible for designing and performing the experiments, data analysis and manuscript writing as a part of his PhD research. BS served as SK’s PhD committee member, provided germplasm included in the study, maintained the mapping population, and provided feedback on the proposed work and manuscript before submission.CK helped in marker screening and reviewed data analysis. SAA, LKR and JA performed experiments. AHP conceived the project, served as SK’s major advisor and revised the manuscript before submission.

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Authors and Affiliations

  1. Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA

    Sameer Khanal, Changsoo Kim, Jeevan Adhikari, Lisa K. Rainville, Susan A. Auckland & Andrew H. Paterson

  2. Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31793, USA

    Brian M. Schwartz

  3. Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, South Korea

    Changsoo Kim

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  1. Sameer Khanal
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Correspondence to Andrew H. Paterson.

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Khanal, S., Schwartz, B.M., Kim, C. et al. Cross-taxon application of sugarcane EST-SSR to genetic diversity analysis of bermudagrass (Cynodon spp.). Genet Resour Crop Evol 64, 2059–2070 (2017). https://doi.org/10.1007/s10722-017-0496-2

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