Genome-wide association study and genomic prediction of resistance to summer mortality in Pacific oyster (Crassostrea gigas) using whole genome resequencing

The Pacific oyster Crassostrea gigas is one of the most important farmed marine shellfish worldwide. However, massive mortality during the summer months caused significant economic losses to the C. gigas farming industry. Understanding the genetic architecture of resistance traits has been an ongoing research issue, and the incorporation of genomic information into breeding programs is expected to accelerate the process of genetic improvement. Genomic selection (GS), as a new approach of genetic improvement, has great potential for breeding new lines with adaptive advantages. In this study, we conducted a genome-wide association study (GWAS) for summer mortality resistance and estimated the accuracy of genomic predictions using different methods. The heritability of the C. gigas summer mortality resistance was low, with heritability of 0.108 ± 0.036, 0.161 ± 0.102 and 0.134 ± 0.043 for PBLUP, GBLUP and ssGBLUP, respectively. In addition, we detected 9,783,674 SNPs and used a mixed linear model to identify 18 significant SNPs associated with summer mortality resistance. The phenotypic variance explained (PVE) for these SNPs ranged from 8.25% to 10.14%. Based on these significantly related SNPs, nine significant candidate genes were identified (TLR4, HEX, SLC22A8, PDE2A, HUWE1, SLMAP, RAD52, TBK1 and RAPH1). The prediction accuracy using PBLUP, GBLUP, ssGBLUP, and weight ssGBLUP (WssGBLUP) was 0.549 ± 0.026, 0.381 ± 0.074, 0.544 ± 0.026, and 0.869 ± 0.018, respectively. Therefore, WssGBLUP models are more suitable for genomic prediction of summer mortality resistance in C. gigas. Our results suggest a polygenic genetic architecture that provide new perspectives for studying candidate genes for resistance to summer mortality, which may facilitate the genetic improvement for resistance lines in C. gigas.