Transferability of rice SSR markers to Miscanthus sinensis, a potential biofuel crop

Miscanthus sinensis (M. sinensis) is a perennial C₄ photosynthesis grass, with high yield, high efficiency of water usage, low fertilizer requirement, tolerance to extreme environments, and is one of the plant species with good biofuel potential. Simple sequence repeat (SSR) markers are highly informative and widely used in plant genetic studies. In this study, 88 SSR primer pairs derived from the rice genome, including 47 EST-SSRs (eSSRs) and 41 genomic SSRs (gSSRs), were evaluated for cross-species transferability to M. sinensis. Forty-one SSR primer pairs in total could successfully amplify DNA fragments in M. sinensis, showing an overall transferability rate of 46.6 % between rice and M. sinensis. The transferability rate of eSSR (51.1 %) was higher than that of gSSR (41.5 %). A total of 140 SSR loci and 340 alleles in the set of rice and M. sinensis germplasm collections were detected. Nei’s gene diversity varied from 0 to 0.72 and averaged 0.35. Shannon’s information index varied from 0 to 1.49 and averaged 0.56. The observed heterozygosity ranged from 0 to 0.95 and averaged 0.08. Thirty-nine loci (27.86 %) were shown heterozygosity out of 140 SSR loci. A dendrogram based on genetic distance showed a significant geographic differentiation. Our results indicated that 46.6% of the rice SSR markers are transferable to M. sinensis, and are useful for germplasm evaluation and genetic analysis in M. sinensis.