Genome wide association study for growth and carcass traits in the Amazon fish Colossoma macropomum

Abstract

Background Growth and carcasses yield are economically important traits for the Amazon fish tambaqui (Colossoma macropomum). However, carcasses yield has received little attention in breeding programs because it is difficult to measure on many fish and it cannot be directly measured on breeding candidates. The goal of this study was to unravel the genetic architecture of growth and carcasses yield traits, as well as to identify candidate genes influencing these traits, in an experimental tambaqui population in Southeastern Brazil, by using ddRAD-sequencing (double digest restriction-site associated DNA) and GWAS (genome-wide association study) methods.Methods and Results Phenotype data from 11 full-sib families, with a total of 365 individuals, were evaluated for 15 months. Eight growth characteristics were measured. Each fish was processed in the following body regions: head, rib, loin, R + L (rib + loin). GWAS analysis identified a total of 3 SNPs with chromosome significance, which were associated with six growth/yield traits (HL, SL, Body weight, R + L weight, Head weight and Rib weight), distributed into two linkage groups (LG 11 and 19). We highlighted three genes (ptpre, glrx3, and ebf3a) close to the QTLs that represents candidates for further functional validation to uncover biological mechanisms underlying variation for these traits in tambaqui.Conclusions In conclusion, our results indicated that growth and carcasses yield traits are polygenic in tambaqui, with the most important loci explaining only 0.2% of the genetic variance for the trait.