Analysis on SSR loci information in transcriptome of Houttuynia cordata and its polymorphism / 中草药

ABSTRACT

Objective: Simple sequence repeats (SSR) loci information in the transcriptome of Houttuynia cordata was analyzed in this study and the more powerful tools were provided for molecular marker-assisted breeding in this plant. Methods: SSR loci were searched in all 63 954 unigenes by using MISA. SSR loci information was analyzed and SSR primers were designed by Primer 3. Furthermore, 50 pairs of primers were randomly selected for the polymorphic analysis on 16 H. cordata plants collected from different habitats. Results: A total of 4 800 SSRs were found in the transcriptome of H. cordata, which distributed in 4 413 unigenes with the distribution frequency of 7.51%. Tri-nucleotide repeat was the main type, accounted for as much as 41.54% of all SSRs, followed by mono-nucleotide repeat motif (27.35%). The mononucleotide repeat motifs of A/T were the predominant repeat type (27.0%). A total of 3068 pairs of SSR primers were designed by using Primer 3. For validating the availability of those SSR primers, 50 pairs of primers were randomly selected for PCR amplification. Among them, 43 pairs of primers (86.0%) produced clear and reproductive bands, which showed polymorphism, and 16 H. cordata plants collected from different places were divided into two groups by UPGMA. Conclusion: There are numerous SSRs in H. cordata transcriptome with high frequency and various types, this will provide the basis for study on genetic diversity and genetic map for H. cordata.