Euptelea pleiosperma ">Development of polymorphic SSR markers and their applicability in genetic diversity evaluation in Euptelea pleiosperma

[摘要] Euptelea pleiosperma is a characteristic species of East Asian flora with both ornamental and scientific values.Based on the reduced-representation sequencing (RRS) technology of RAD-Seq, this study conducted high-throughputIllumina paired-end sequencing to find SSR marker information in the genome of E. pleiosperma, and to screen and verifypolymorphism of SSR markers. We obtained 5.5G of high-quality data using RAD-Seq. The total number of contigs of theRAD tags was 299,376, with the maximum contig length of 2,062 bp and the average length of 445 bp. From thesesequences, we identified 20,718 SSR loci, with a distribution density of one SSR per 6.45 kb (1/6.45 kb). Among allSSRs, dinucleotides (52.00%) were the most detected SSRs, followed by mononucleotides (21.63%). AG/CT was thedominant motif in the SSR loci, accounting for 34.8%. Primers were successfully designed for 14,593 loci, and 100pairs of these primers were randomly selected for chemical synthesis and validated by SSR-PCR amplification in 20individuals of E. pleiosperma. Seventy-nine primers were able to amplify the target bands. Cervus 3.0 software wasused to analyze the selected 20 SSR loci with good polymorphism. For the 20 SSR markers, the number of allelesranged from 4 to 9, and the observed heterozygosity and expected heterozygosity were from 0.35 to 0.75 and 0.541 to0.875, respectively. The information content of polymorphic loci ranged from 0.463 to 0.848, with an average value of0.638. Among them, there were 18 highly polymorphic loci, and 20 SSR loci did not deviate from the HardyWeinberg equilibrium. Furthermore, the 20 pairs of SSR primers were used to conduct PCoA analysis based on Nei’sgenetic distance of 51 individuals from three populations. The results showed that these SSR markers coulddistinguish genetic differences based on different geographical locations.

[学科分类] 仪器

[关键词] Cluster analysis;E. pleiosperma;RAD-Seq;Rare species;SSR markers