Characterization and Primer Design for Simple Sequence Repeat Loci in Salvia miltorrhiza Genome

VernacularTitle:丹参基因组SSR位点的特征分析及引物开发＊
Author: Haibin XU ; Bo WANG ; Chao SUN ; Lifang XIE ; Jingyuan SONG
Publication Type:Journal Article
Keywords: Salvia miltorrhiza; simple sequence repeat; primer design
From: World Science and Technology-Modernization of Traditional Chinese Medicine 2013;(3):367-370
CountryChina
Language:Chinese
Abstract: Salvia miltorrhiza Bge. is a perennial deciduous flowering plant. Its medicinal root and rhizomes part is widely used in the treatment of various diseases. In this study, bioinformatics analysis was performed to identify 4832 genome SSR loci with length longer than or equal to 40 bp from the draft genome assembly of S. miltorrhiza. The re-sults showed that the dinucleotide repeat motifs and trinucleotide repeat motifs constitute the main types of genome SSR loci, accounting for 37.3% and 61.3% respectively. SSR types enriched with A/T bases showed significantly higher abundance than other types, including AT/TA AAT/ATT, ATA/TAT, TAA/TTA, accounting for 30.5%, 21.6%, 17.1%, 20.4% of the total number of SSR loci, respectively. 1079 primer pairs were designed for these genome SSR loci. These primers can be used for genomic diversity analysis, genetic map construction, genetic marker screening. These data could lay the foundation for population genetics and genomics research of S. miltorrhiza.