Genome-wide association study identifies loci for body shape in the large yellow croaker (Larimichthys crocea)

Abstract

The large yellow croaker (Larimichthys crocea) is an important maricultured fish species in southeast China. Body shape is an important economic trait for this species, because consumers prefer to purchase fish that have a slender shape. Furthermore, investigating the genetic basis of this trait may be useful for understanding the evolution of fish body shape in general. This study randomly selected 500 large yellow croakers to perform genome-wide association study of this trait. We used Genotyping-By-Sequencing technology combined with a genome-wide prediction model (BayesC) to identify and test QTLs. We also compared the association results using BayesC and single-marker analysis, and found that BayesC outperformed single-marker analysis in detecting significant SNPs explaining a proportion of the total genetic variance in this experiment. Using 124,419 SNP markers, 10 candidate genes, correspond to 4 QTL regions located around 3.5, 1.8, 23.9 and 10.8 Mb on chromosomes 2, 4, 8 and 22 respectively, were suggested to be relevant to the trait. All of these genes may directly or indirectly participate in bone development. These genes may provide a valuable reference for marker-assisted selective breeding and investigating the genetic basis of the evolution of fish body shape.