High-throughput and cost-effective genotyping by low-coverage whole genome sequencing with genotype imputation in Pacific oyster, Crassostrea gigas.

In order to improve the application of genomic resources in genomic selection breeding of aquaculture species, it is imperative to develop high throughput genotyping methods that are suitable for aquatic species with highly heterozygous and complex genomes. This study aimed to address the issue of accurate genotype imputation for lcWGS (low coverage whole genome sequencing) without reference panel in aquatic species. We performed lcWGS with an average depth of 2.8× on 360 individuals of Crassostrea gigas , then performed genotype imputation through reference-free method to achieve genome-wide genotyping. The results demonstrated that STITCH showed outstanding performance in conducting genotype imputation without reference panel, with R2 of 0.860 ± 0.055 and GC of 0.936 ± 0.022. The comparison of accuracy among different populations indicated that the selected breeding population with higher level of linkage disequilibrium within the population showed significant improvement in imputation accuracy compared to the wild population (P < 0.01). The diminishing marginal utility in accuracy beyond 300 samples suggested that hundreds of individuals were adequate for accurate genotyping by lcWGS. The imputed genotypes showed high accuracy in identifying genetic relationships and potential application in selection breeding. This study provides valuable information toward application of high-throughput and cost-effective genotyping in accelerating genetic analysis and genomic selection of economic traits in aquaculture species. • STITCH showed high imputation accuracy for lcWGS (low coverage whole genome sequencing) data without reference panels. • High linkage disequilibrium strength within the selected population genome was beneficial for performing genotype imputation. • The genotype imputation accuracy tended to stabilize after the sample size used for imputation reached 300. • The imputed genotype showed high accuracy in identifying genetic relationships and for genetic breeding of aquatic species. [ABSTRACT FROM AUTHOR]