Astragali Radix is regarded as an important traditional medicinal plant and has been widely used as a Qi-Invigoratin medicine for more than 2000 years. However, the mechanism of its medicinal and nutritional components in different accessions unexplored. Moreover, the lack of SSR markers for Astragali Radix has stalled genetic breeding and variety identification. To develop EST-SSRs, transcriptome sequencing was performed based on the Illumina platform.

Approximately 99.6 million raw data points were collected, and 296,618 unigenes with an average length of 1,459 bp were obtained. A total of 71,207 SSR loci within 56,097 SSR-containing unigenes were identified. Of these SSR-containing unigenes, 26,188 (46.7%), 16,736 (29.8%) and 8,858 (15.8%) were related to items in the GO database, KEGG database and COG database, respectively. The motifs A/T, AG/CT, AT/AT and AAT/ATT were the most common types, accounting for 39.78%, 19.14%, 10.12% and 4.60%, respectively, and the average length of the EST-SSRs was 17.16 bp. We acquired 8 functional markers linked to key genes correlated with the biosynthesis of flavonoids. The genetic similarity among the 60 AR varietal resources ranged from 0.2692 to 0.8077, with an average of 0.5742. The dendrogram results indicated that the 60 AR samples tested had high levels of genetic similarity.

The 71,207 EST-SSR loci identified here offer valuable source of DNA markers for the genetic diversity identification of 60 Astragali Radix varieties. These results will facilitate genetic map construction, functional gene identification, variety identification, molecular marker-assisted breeding and genetic diversity analysis in Astragali Radix.