Identification of EST–SSRs and molecular diversity analysis in Mentha piperita

Abstract

EST sequences of Mentha piperita available in the public domain (NCBI) were exploited to develop SSR markers. A total of 1316 ESTs were assembled into 155 contigs and 653 singletons and of these, 110 sequences were found to contain 130 SSRs, with a frequency of 1 SSR/3.4 kb. Dinucleotide repeat SSRs were most frequent (72.3%) with the AG/CT (43.8%) repeat motif followed by AT/AT (16.2%). Primers were successfully designed for 68 SSR-containing sequences (62.0%). The 68 primers amplified 13 accessions of M. piperita and 54 produced clear amplicons of the expected size. Of these 54, 33 (61%) were found to be polymorphic among M. piperita accessions, showing from 2 to 4 alleles with an average of 2.33 alleles/SSR, and the polymorphic information content (PIC) value varied between 0.13 and 0.51 (average 0.25). All the amplified SSRs showed transferability among four different species of Mentha, with a highest in Mentha arvensis (87.0%) and minimum in Mentha citrata (37.0%). The newly developed SSRs markers were found to be useful for diversity analysis, as they successfully differentiated among species and accessions of Mentha.