Analysis on SSR Loci in Transcriptome and Development of EST-SSR Molecular Markers in <i>Lonicera macranthoides</i>

Abstract

Huizhanmao-rendong ( Lonicera macranthoides ), as a species of original plant of wild honeysuckle flower ( Flos Lonicerae ), the traditional Chinese medicine, is widely distributed in South China and features high medicinal and economic value. In this study, the SSR loci of 74 057 unigenes in the transcriptome of L .  macranthoides  were analyzed by MISA. Among them, 15 587 unigenes contained 20 161 SSR loci, and the frequency of SSR was 21.05%. The types of SSR sites in the transcriptome of L .  macranthoides  were distributed from single nucleotide to six nucleotide repeats. The main repeats were dinucleotide (9 704) and trinucleotide (5 847), accounting for 48.13 % and 29.00 % of the total SSRs, respectively. The main repeat units were AG/CT (6 086), AT/AT (3 071) and A/T (2 826), accounting for 30.79%, 15.23%, and 14.02% of the total SSRs, respectively. There were 4 897 and 3 531 repeats (the numbers of repeats were the most) in 6 and 5 SSR loci, accounting for 24.29 % and 17.51 % of the total SSR number, respectively. By using primer 6.0 software, 17 611 pairs of SSR primers were designed, and 30 pairs of primers were randomly selected for amplification verification. Among them, 14 pairs of amplified bands showed polymorphism, and then the genetic diversity of 6 varieties of L .  macranthoides  was analyzed by using these 14 pairs of primers. The results will provide a scientific basis for species identification, genetic diversity analysis, and molecular marker-assisted breeding of  L .  macranthoides .