Development and application of EST-SSR markers based on transcriptome of Phyllostachys vivax McClure f. aureocaulis N. X. Ma

Based on transcriptome data of Phyllostachys vivax McClure f. aureocaulis N. X. Ma, the distribution and characteristics of simple sequence repeat (SSR) loci were analyzed using bioinformatics. Primers were designed according to the SSR loci in the differentially expressed genes between the “yellow culm type” and “green culm type”. The validity and transferability of the primers within the Phyllostachys genus were determined using samples from Phyllostachys species. Results showed that 12 651 SSR loci were detected in 89 874 unigene sequences of Ph.vivax f. aureocaulis, with a frequency of 14.07%. Among the SSR loci, mononucleotide repeat motifs were the most abundant (51.02%), followed by trinucleotide and dinucleotide repeat motifs (25.61% and 21.94%, respectively). Of the 80 repeat motifs found, the most abundant was A/T (46.60%), followed by AG/CT (13.97%) and CCG/CGG (9.90%). Based on the SSR loci of differentially expressed genes between the “yellow culm type” and “green culm type”, a total of 51 primer pairs were designed, 44 (86.27%) of which were able to amplify the expected polymerase chain reaction (PCR) products. Average transferability of the 44 primers pairs in the selected Phyllostachys species was 92.41%, with 39 pairs containing interspecific polymorphisms. These polymorphic-expressed sequence tag-derived EST-SSR markers could effectively distinguish different bamboo species in Phyllostachys but could not effectively distinguish intraspecific germplasm resources.