SSR marker development and genetic diversity analysis of Stephania kwangsiensis / 中草药

ABSTRACT

Objective To develop simple sequence repeat (SSR) molecular markers based on Stephania kwangsiensis transcriptome and to evaluate genetic diversity of S. kwangsiensis in natural populations. Methods The unigenes from S. kwangsiensis transcriptome were used to explore SSR loci. SSR primers were designed by oligo 7.0. Polymorphic primers were selected by electrophoresis and were applied to the investigation of the genetic diversity of S. kwangsiensis. Results A total of 6 833 SSR loci (33.11%) were obtained from 20 637 unigenes in the S. kwangsiensis transcriptome. Of the 50 SSR markers tested, ten pairs of highly polymorphic primers were selected to analyze the genetic polymorphisms of 63 individuals from five populations. Ten primers produced 83 band loci, all (100%) of which were polymorphic, and the polymorphism information content (PIC) was 0.688 9. At the species level and population level, the Nei’ s gene diversity (H) was 0.725 2 and 0.613 4, respectively; the Shannon’s Information index (I) was 1.576 6 and 1.220 3, respectively; The observed heterozygosity (Ho) was 0.584 5 and 0.558 4, respectively; The expected heterozygosity (He) was 0.731 2 and 0.643 5, respectively. The genetic differentiation coefficient (Fst) was 0.146 5 and the gene flow (Nm) was 1.456 9. Based on UPGMA cluster analysis, the five populations of S. kwangsiensis were divided into three clusters. Conclusion The developed SSR markers were applicable to the genetic diversity evaluation of S. kwangsiensis. The genetic diversity of this plant was relatively high at both species level and population level. The genetic differentiation mainly existed within populations.