Validation of SNPs Associated with Important Economic Traits of Sea Cucumber (Apostichopus japonicus)

Abstract:

Based on the high-density genetic linkage map and QTL of the sea cucumber (Apostichopus japonicus), we selected 26 candidate SNPs associated with body length, body weight, body breadth, pallet number, and disease resistance. Thirteen pairs of primers were successfully designed, which could be used for high resolution melting (HRM) detection. The 13 candidate SNPs associated with important economic traits were validated and analyzed with phenotypic data using genotyping of HRM in the expanded population. Polymorphic analysis results showed 3 loci were monomorphic sites and the other 10 loci possessed polymorphic minor allele frequency (MAF) at the 10 polymorphic sites, which ranged from 0.016 (SNP113) to 0.332 (SNP160), with an average of 0.173. Observed heterozygosity (Ho) ranged from 0.031 (SNP113) to 0.818 (SNP9), with an average of 0.433. Expected heterozygosity (He) ranged from 0.031 (SNP113) to 0.834 (SNP160), with an average of 0.402. The polymorphism information content (PIC) value ranged from 0.030 to 0.393, with an average of 0.284. Six loci departed from the Hardy Weinberg equilibrium. The results of QTL verification indicated that loci SNP40 and SNP160 associated with growth traits (body length, body weight, body breadth) with the dominant genotypes SNP40 (CC), SNP160 (AA). SNP88, SNP112, and SNP126 were associated with disease resistance. The dominant genotypes were SNP88 (CC), SNP112 (AA), and SNP126 (TT). Diplotypes were constructed based on the five SNPs and association analyses revealed that K1 (CC AA TT) was best for disease resistance, and S1 (CC AA) and S3 (CC AC) were dominant diplotypes for growth traits. These results provide basic data for marker-assisted selection in sea cucumber breeding.