Abstract:Scapharca kagoshimensis is a marine shellfish of great economic value. In recent decades, populations of S. kagoshimensis have declined due to environmental destruction and overfishing. To enhance our understanding of the genetic diversity and population-level genetic structure of S. kagoshimensis, microsatellite loci were detected based on the transcriptome data of S. kagoshimensis using MISA software. A total of 3987 Single Sequence Repeats (SSRs) were identified from 35,555 unigenes and the frequency of their occurrence was 11.21%. The main types of repeats were dinucleotides and trinucleotides, which accounted for 58.06% and 19.04%, respectively. A total of 182 types of repeat motifs were classified in all SSRs, and AC/GT was the most abundant among dinucleotide repeats (45.70%). The repeat numbers of SSRs primarily ranged between five and seven, and the number of SSRs gradually decreased as repeat number increased．Motif length was predominantly between 12 and 29 bp, and the SSR polymorphism level was above moderate. Among the 60 designed primer pairs, 14 pairs proved to be polymorphic microsatellite markers and were amplified in 30 wild individuals sampled from Weifang in Shandong Province. The results showed that the average number of alleles (Na), average observed heterozygosity (Ho), average expected heterozygosity (He), and polymorphism information content (PIC) were 15.4, 0.682, 0.852, and 0.817, respectively. All 14 loci were highly polymorphic (PIC≥0.5). After Bonferroni correction, seven of the 14 loci deviated significantly from the Hardy-Weinberg equilibrium (P<0.05). These results indicate that it is feasible to develop microsatellite markers based on the S. kagoshimensis transcriptome. The polymorphic microsatellite loci obtained in this study will facilitate further studies on population genetic management, genetic mapping, and molecular assisted breeding of S. kagoshimensis.
