Cross-taxon transferability of sugarcane expressed sequence tags derived microsatellite (EST-SSR) markers across the related cereal grasses

Sugarcane is a crop of economic importance providing sugar and bioenergy resource which has a substantial contribution to the national GDP of India as well as other countries. Genomes of the several grasses have co-evolved which share large-scale synteny and genome collinearity; hence it is possible to employ EST-SSR markers of one grass species for genetic study of other related species. A set of sixty potentially informative EST-derived microsatellite (SSR) markers were employed to examine their cross-taxa transferability across the limit of taxonomic boundaries of different grass genomes. The high (96.6%) rate of SSRs cross-transferability observed in genus Saccharum followed by Erianthus (93.3%), Narenga (88.3%), Sclerostachya (86.3%), and Miscanthus (83.3%). Relatively lower rates of cross amplification were observed in other cereal crops including Sorghum bicolor, Pennisetum glaucum, Zea mays, Triticum aestivum, Oryza sativa, and Avena sativa. Cross-transferable EST-SSR markers were utilized to evaluate phylogenetic relationships among genus Saccharum, closely related genera of Saccharum complex, and other allied cereal grasses. The polymorphic information content values ranged from 0.35 to 0.95, with an average of 0.71. Such a high rates of cross-taxa transferability of the EST-SSRs make them a potent tool for genetic studies and comparative genomics across wide evolutionary distances within and across genera along with technologically simplicity and cost effectiveness. EST-SSRs will facilitate to devise potent tools for genetic improvement through advance molecular breeding of such crops for high grain productivity and better quality. They will especially be useful for the orphan grass species, which contribute a major part of the global food security.