Development and evaluation of a haplotype reference panel of Zhikong scallop (Chlamys farreri) for genotype imputation

Abstract

Single nucleotide polymorphisms (SNPs) across the genome are remarkably useful resources for investigating the genome architecture, studying the genetic basis of complex traits and implementation of genomic selection. However, information on high-density SNPs is unavailable for most aquaculture species owing to the high costs of whole genome sequencing. Genotype imputation is an attractive approach for obtaining large number of genomic variants at a low cost. In this study, the first haplotype reference panel was constructed for Chlamys farreri, an economically important mollusk species and a major contributor to aquaculture in China. A total of 174 scallops from six populations in the main scallop culture area were selected for whole-genome resequencing. More than 87.47 million SNPs were identified and 3,968,417 SNPs genome-wide were selected for constructing the haplotype reference panel for C. farreri. The number of SNPs per chromosome ranged from 125,000 to 279,981 with an average spacing of 242 bases. Several factors were evaluated based on the imputation performance of the reference panel. The imputation accuracies of 19 chromosomes ranged from 0.91 to 0.95, and there were no significant differences among them (p > 0.05). The imputation accuracies of populations could reach 0.95, 0.93, and 0.90 for ZY, PR, and CS respectively, which confirmed a positive relationship between the kinship within the population and the imputation accuracy. The imputation accuracies increased with sequencing depth and plateaued at 0.5×, reaching accuracies of 0.91–0.93 for artificially breeding populations. Taken together, we constructed a haplotype reference panel for C. farreri, which can provide a cost-effective way to extend the limited number of genotypes for boosting the power of downstream analyses such as genome-wide association studies and genomic selection.