刺参(Apostichopus japonicus)重要经济性状相关SNP标记的验证分析

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

中文关键词: 刺参  QTL位点  SNP  高分辨率熔解曲线  验证

英文关键词: Apostichopus japonicus  Quantitative trait locus (QTL)  Single nucleotide polymorphism (SNP)  High-resolution melting (HRM)  Validation

中文摘要:

      本研究在前期构建的刺参(Apostichopus japonicus)高密度遗传连锁图谱和QTL分析的基础上，筛选出26个与体长、体重、体宽、棘刺总数、抗病力相关的SNP位点，设计出可用于HRM检测的SNP扩增引物13对。在扩大群体中利用HRM小片段法对这13个刺参重要经济性状相关的候选SNP位点进行分型和多态性检测，并结合扩大群体的相关性状数据进行了QTL位点验证。多态性结果显示，13个位点中有3个单态性位点，其余10个多态性位点中有3个位点为低等位多态性，7个位点为中等位多态性。10个多态性位点的最小等位基因频率(MAF)介于0.016(SNP113)~ 0.332(SNP160)之间，平均值为0.173；各位点的观测杂合度(Ho)介于0.031(SNP113)~0.818(SNP9)之间，平均值为0.433；期望杂合度(He)介于0.031(SNP113)~0.834(SNP9)之间，平均值为0.402；多态信息含量(PIC)介于0.030(SNP113)~0.393(SNP160)之间，平均为0.248，有6个位点偏离Hardy- Weinberg平衡。QTL验证结果表明，SNP40和SNP160位点为与生长(体长、体重、体宽)相关的位点，各位点的优势基因型分别为SNP40(CC)和SNP160(AA)；SNP88、SNP112和SNP126这3个位点为与抗病力相关的位点，各位点的优势基因型为SNP88(CC)、SNP112(AA)和SNP126(TT)。基于这5个位点构建生长和抗病二倍型，发现二倍型K1(CC AA TT)抗病力最强，S1(CC AA)、S3(CC AC)在生长方面优势显著，相关研究结果可为分子标记辅助育种在生产中应用提供基础数据。

英文摘要:

      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.