Abstract:
【Objective】 Based on the transcriptome sequencing data, SSR loci were excavated and analyzed from the leaves of
Idesia polycarpa, and the availability and polymorphism of SSR markers were evaluated, which provided theoretical reference for the collection and preservation of
Idesia polycarpa germplasm resources and the development of molecular markers. 【Method】 With
Idesia polycarpa leaves as materials, MISA was used to retrieve SSR loci from transcriptome sequencing data and analyze their characteristics. Primer 5.0 was used to design SSR primers, and SSR-PCR was used to verify and develop polymorphic primers. 【Result】 A total of 8182 SSR loci were found in 18300 Unigenes screened by MISA, accounting for 44.71% of the total sequences. A total of 11767 SSR loci were identified, with an average distribution distance of 1.74 kb. There were 10721 complete SSR loci, accounting for 91.11% of the total SSR loci. Among the SSR repeat types, the number of single nucleotide repeats was the largest, with a total of 6384, accounting for 54.25% of the total SSR loci;followed by dinucleotide, a total of 2223 SSR loci, accounting for 18.89% of the total SSR loci; the number of pentanucleotide repeats was the least, only 36, accounting for 0.31% of the total SSR loci. A total of 257 repeat motifs were found. Among the single nucleotide repeat motifs, A/T had the largest number (6222), accoun-ting for 52.88% of the total SSR loci. Among the dinucleotide repeat motifs, CT/AG had the largest number (701), accounting for 5.96% of the total SSR loci, followed by TC/GA, a total of 664, accounting for 5.64% of the total SSR loci. Among the number of motif repeats, the number of SSR loci with a repeat number of 10 was the largest (2434), accounting for 20.68% of the total SSR loci, and the number of single nucleotide repeats was the largest (2263), accoun-ting for 92.97%. The lengths of 10721 SSR loci ranged from 10 to 84 bp, with an average length of 14.99 bp. The length of the loci was mainly concentrated in 10-42 bp. There were 10697 SSR loci in this interval, accounting for 90.91% of the total SSR loci. A total of 1941 SSR loci had high polymorphism (SSR length ≥ 20 bp), accounting for 16.50% of the total SSR loci. Based on 16 germplasm resources of
Idesia polycarpa, 70 pairs of SSR primers were randomly selected for verification. A total of 65 pairs of primers could amplify the target bands, with an effective amplification rate of 92.86%, of which 16 pairs of primers could amplify polymorphic bands. Using 6 pairs of polymorphic primers, a cluster analysis was conducted on 16 samples of
Idesia polycarpa. At the genetic similarity coefficient of 0.78, the 16 samples could be classified into 2 categories. 【Conclusion】 The SSR loci in the leaf transcriptome of
Idesia polycarpa are abundant, and a total of 16 pairs of polymorphic primers have been obtained, which has the potential to be developed into high polymorphic SSR molecular markers. The result lays foundation for genetic diversity analysis, molecular marker bree-ding, and resource protection of
Idesia polycarpa.