Genetic diversity of 1-deoxy-D-xylulose 5-phosphate synthase gene (SmDXS) among the cultivated Danshen (Salvia miltiorrhiza) populations

Abstract

Abstract Danshen, a major traditional medicine for cardio-cerebrovascular disorders with a wide range of pharmacological effects, is the radix of herbal Salvia miltiorrhiza Bunge of the genus Salvia and the family Labiatae. It has abundant and more often species unidentified germplasm resources and related alternatives. In recent years, with the advent of more elderly society and the more market demanding, more and more researches have been focused on the cultivation, germplasm resources protection and molecular identification. In this research, 38 cultivated Danshen populations were collected from 30 regions of China. Based on the cDNA gene of the key enzyme 1-deoxy-D-xylulose 5-phosphate synthase (DXS) in the salvianone biosynthetic pathways, degenerate homologous walking primers were designed and the corresponding genomic SmDXS genes were cloned by PCR, sequenced, spliced, and used for bioinformatic analysis, in hope to understand its genetic diversity, to identify novel Danshen materials, and to find specific and traceable SNP fingerprints. Results showed that SmDXS gene is highly conserved. The full-length SmDXS gene in the majority populations (36) was 3383bp, and two (B-JS-V-2 and W-SCHY-W-1), 3374 and 3322 bp respectively; the SmDXS consisted of 10 exons and 9 introns. The spliced exon sequences were all 2157bp in length, with a total of 48 SNP variation sites distributed in 13 populations and a variation rate of 2.23%. The spliced exon sequences encode 718 amino acid residues with 28 amino acid mutations sites in 8 populations. The introns of SmDXS have 224 SNP variation sites, most of which distributed in W-SCHY-W-1. Thirteen populations can be discriminated by SNP fingerprints based on SmDXS gene, with a discriminate rate of 34.2%. Phylogenetic trees based on various parts of the SmDXS gene or deduced proteins showed similar two-clade architectures. Population B-JS-V-2 in full-length SmDXS and combined intron sequences, W-SCHY-W-1 in the spliced exon sequences all stand alone. Populations B-SD-V-2 and V-HBAG-V-1cluster in the deduced amino acid sequences.