Microsatellite Development for Genetic Diversity Analysis of Erianthus germplasm Collection in Thailand

Erianthus is a member of the Saccharum complex and is of interest as a potential resource for sugarcane improvement and as a bioenergy crop. Two species, Erianthus arundinaceus (2n = 40, 60) and E. procerus (2n = 40), are widely distributed across Thailand. To utilize wild relatives for sugarcane improvement, we analyzed the genetic diversity among 190 Saccharum complex accessions, including 151 Erianthus accessions collected in Thailand: we used microsatellite (simple sequence repeat; SSR) markers developed from Japanese Erianthus. An accession of E. arundinaceus in Japan was used to identify the microsatellites with pyrosequencing technology on the 454 GS FLX system. A total of 1682 primers characterized by di- to hexanucleotide repeats were designed, of which 1392 were selected through the use of agarose gel electrophoresis. Of these, 242 primers that amplified di- and trinucleotide repeat regions with 5–19 repetitions were further screened for their reproducibility and positions on the Erianthus linkage map. Finally, 41 primers were selected for the analysis of genetic diversity. These primers, with amplification products of 100–300 bp, were used to characterize heterozygosity, cross-transferability, and phylogenetic relationships of the Thai Erianthus collection. The results provide an efficient set of microsatellite markers for genetic diversity assessment of Erianthus and related genera.