仿刺参疣足数量SNP遗传力评估

Estimating SNP heritability for papillae number in sea cucumber Apostichopus japonicus

中文关键词: 遗传力  REML  SNP  仿刺参  疣足数量

英文关键词: Heritability  REML  SNP  Apostichopus japonicus  Papillae number

中文摘要:

      随着测序技术的发展，基于单核苷酸多态性(SNP)分子标记的遗传力估计比传统法准确性更高，已被广泛应用于动植物育种中。本研究对不同地理仿刺参(Apostichopus japonicus)群体的疣足数量进行重测序全基因组水平的SNP遗传力估计，结果显示，次等位基因频率(Minor allele frequency, MAF) >0.05时，在50K SNP基础上均匀抽样，不同SNP密度的仿刺参疣足数量SNP遗传力估计均值范围为(0.566±0.022)~(0.612±0.003)；MAF>0.1时，SNP遗传力估计均值范围为(0.586±0.015)~(0.615±0.016)，说明50K低密度SNP标记足够捕获数量性状基因座(QTL)大效应和小效应；同时，染色体水平SNP遗传力估计值显示，单个染色体对遗传力的贡献和其长度显著相关，暗示仿刺参疣足数量是一个复杂的数量性状，与该性状相关的基因效应位点散布在各染色体，并由多基因共同作用。本研究结果可为海参低密度SNP芯片的设计开发及海参遗传参数评估提供一定的理论依据。

英文摘要:

      The estimation of heritability is a fundamental task in the selective breeding of aquatic animals. With the development of sequencing technology, the estimation of heritability based on single nucleotide polymorphism (SNP) markers has been widely used in breeding since it is more accurate than the traditional method. In this study, the genome-wide SNP heritabilities for papillae number in Apostichopus japonicus from different geographic locations were estimated, and the results showed that the estimated mean SNP heritabilities with different SNP densities at MAF (minor allele frequency)>0.05 ranged from 0.566±0.022 to 0.612±0.003, and the estimated mean SNP heritabilities with different SNP densities at MAF>0.1 ranged from 0.586±0.015 to 0.615±0.016 when sampled uniformly on 50K SNPs, indicating that 50K low-density SNP markers are sufficient to capture both large and small effects of the quantitative trait locus. Chromosome-wise SNP heritability estimates showed that the contribution of an individual chromosome was significantly correlated to its length, suggesting that the papillae number is a complex quantitative trait with effect sites scattered across the chromosomes and shared by multiple genes. The results of this study provide a theoretical basis for the design and development of A. japonicus low-density SNP chips and the evaluation of A. japonicus genetic parameters.