Optimizing genotype imputation strategy for low-coverage whole-genome resequencing and investigating genomic selection signatures in domesticated Paralichthys olivaceus

Single nucleotide polymorphisms (SNPs) have been widely used in marker-assisted selection to demonstrate the molecular mechanisms underlying hereditary traits by screening candidate genes. Low-coverage whole genome resequencing (lcWGS) followed by genotype imputation represents an efficient strategy for acquiring abundant SNPs with a low cost. Although this strategy has been successfully implemented in animal husbandry, its optimal applicability in aquaculture breeds still need to be explored. Here, we investigated the optimal prephasing and imputation workflow in Paralichthys olivaceus , an economically important bony fish that requires urgent germplasm improvement. A total of 10.3 million high-quality biallelic SNPs were identified and 90 % sites with higher confidence were phased as the reference haplotype panel from whole genome resequencing (18.63x) of 168 P. olivaceus . It is revealed that the combination of prephasing by SHAPEIT and imputation through GLIMPSE1 demonstrated best performance across all three tested chromosomes. Furthermore, 0.5x coverage was identified as the most cost-effective resequencing coverage. Following optimizing an important imputation parameter “effective population number (ne)”, the median Pearson correlation coefficient reached 90 % at 0.5x. Moreover, a group of lcWGS P. olivaceus (1x) was imputed and added to original 168 individuals for population genetic analysis. Distinct genetic differentiation and faster linkage disequilibrium decay were observed in all cultured populations. Strong selection signals were detected on a 3.59 Mb region with 111 candidate genes on chromosome 14 in a cultured breed. Our study provides valuable practical insights for applying genotype imputation in aquaculture species. The identification of SNPs and candidate genes has greatly enriched the germplasm resource of P. olivaceus , offering candidate markers for molecular breeding and providing valuable resources for its preservation and management. • Optimal SHAPEIT+GLIMPSE1 combination yields the highest imputation accuracy. • 0.5x coverage is most cost-effective, reaching ∼90% accuracy after optimization. • Population analysis reveals strong selection signals on chromosome 14 with 111 candidate genes in domesticated P. olivaceus .