Identification of a Major QTL Associated with Body Color on ChrLG3 in Tilapia by GWAS

Body color is one of the most important traits in fish affecting species recognition, mate selection, and its economic value. Dissecting the genetic architecture underlying the body color diversity is important in tilapia. In this study, we successfully dissected the genetic architecture affecting black spot variation in two mapping populations of tilapia (a full-sib family: N = 103 & a mixed population: N = 290) using ddRAD-seq-based GWAS technology. A major QTL interval for black spot trait on ChrLG3 (9.8-14.2 Mb) with a peak located at ChrLG3_11207231 was identified. The significant correlations (P < 0.001) between genotypes and color data were validated by applying a novel microsatellite marker (SSR-BC-1). A total of 14 genome-wide significant SNPs near or under the peak of the major QTL were located in exons or introns of nfib (6) and dennd4c (8). Furthermore, qRT-PCR analysis indicated both genes were differentially expressed in the skin and brain of black and red tilapia. Our study laid a foundation for exploring the genetic mechanism of body color variation and carrying out genetic improvement for color quality in tilapia.