Genomic selection for resistance to Streptococcus agalactiae in GIFT strain of Oreochromis niloticus by GBLUP, wGBLUP, and BayesC pi

China is the largest producer of tilapia in the world, and genetically improved farmed tilapia (GIFT) strain of Oreochromis niloticus is the main breed which is cultured widely in coastal and inland areas of China. Streptococcal disease, caused by Streptococcus agalactiae, is one of the most prevalent diseases in farmed tilapia that causes huge economic loss, leading to urgent needs for disease-resistant breed of tilapia. In view of the predictive accuracy and selective efficiency, genomic selection (GS) could be a feasible and optimal method to improve the S. agalactiae resistance in GITF. In this study, the genetic architecture of resistance to S. agalactiae and the accuracy of three GS methods at improving the resistance in GIFT were investigated by artificial challenge test (for phenotypes) and whole-genome re-sequencing (for genotypes). A total of 897 individuals were genotyped (776 individuals were used as the reference group) and 3,759,557 high-quality SNPs were obtained for downstream analysis. The genome-wide association study (GWAS) using weighted genomic BLUP (wGBLUP) and 1 M SNPs revealed that resistance to S. agalactiae in GIFT belongs to a polygenic genetic architecture. Seven suggestive trait-related SNPs were identified on chromosomes 4, 7, 11, and 18. These SNPs explained more than 1% genetic variance. Three GS (GBLUP, wGBLUP, and BayesC pi) methods had better estimation than pedigree-based BLUP, which indicated that the genomic selection approach could be a feasible and promising method to improve the S. agalactiae resistance in GIFT. Although wGBLUP and BayesC pi resulted in similar estimation accuracy, wGBLUP had priority when estimating time needs to be considered.