Estimating SNP heritability for papillae number in sea cucumber Apostichopus japonicus

Abstract:

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.