Analysis on SSR information in transcriptome of Astragalus membranaceus var. mongholicus and its polymorphism

Abstract

In order to enrich the library of SSR and provide more powerful tools for molecular marker-assisted breeding in Astragalus membranaceus var. mongholicus, simple sequence repeats (SSR) loci in its transcriptome were searched in 18 040 unigenes (>=1 kb) by using MISA. SSR loci information was analyzed and SSR primers were designed by Primer 3. Furthermore, 110 pairs of primers were randomly selected for the polymorphic analysis on 20 plants collected from different habitats. A total of 5 640 SSRs were found in the transcriptome of A. membranaceus var. mongholicus, distributed in 4 462 unigenes with the distribution frequency of 31.26%. SSR loci occurred every 6 514 bp. Mono-nucleotide repeat was the main type, accounted for as much as 36.72% of all SSRs, followed by tri-nucleotide(32.57%) and di-nucleotide(27.73%) repeat motif. Among all 75 repeat types, A/T(2 026) was the predominant one followed by AG/CT(1 179), AAG/CTT(477). For validating the availability of the SSR primers designed using Primer 3, 110 pairs of primers were randomly selected for PCR amplification. Among them, 97 pairs of primers (88.18%) produced clear and reproductive bands. Using 19 pairs of primers showed polymorphism, 20 plants were divded into two groups by UPGMA. There are numerous SSRs in A. membranaceus var. mongholicus transcriptome with high frequency and various types, this will provide the abundant candidate molecular markers for genetic diversity, molecular identification, and marker-assisted breeding study for this plant.