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

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.