A Genome-Wide Association Study Reveals That Genes with Functions for Bone Development Are Associated with Body Conformation in Catfish

Body conformation is of great scientific and commercial interest for aquaculture fish species because it affects biological adaptation of the organism to environments, and is of economic importance to the aquaculture industry considering its direct effect on fillet yield. Catfish is the primary aquaculture species in the USA. Two major species used in the aquaculture industry, channel catfish and blue catfish, differ in body shape and therefore the backcross progenies serve as a good model for quantitative trait locus (QTL) analysis. Here, a genome-wide association study (GWAS) with hybrid catfish was conducted to identify the QTL for body conformation, including deheaded body length (DBL), body length (BL), body depth (BD), and body breadth (BB), which were all standardized by cubic root of body weight. Overall, the results indicate that the traits are polygenic. For DBL, linkage group (LG) 2 and LG 24 contain significant QTL, and LG 13 and LG 26 contain suggestively associated QTL (-log(10)(P value) > 4.5). Compared with DBL, additional SNPs were identified to be associated with body length on LG 2, LG 7, and LG 18. Although no significant QTL for body depth was found, three suggestively associated QTLs were identified on LG 5, LG 13, and LG 14. No SNP for body breadth reached the threshold for suggestive association. Genes close to the associated SNPs were determined, many of which are known to be involved in bone development. This work therefore provides the basis for future identification of causal genes for the control of body conformation.