Genome-wide association study of muscle fiber related traits in large yellow croaker (Larimichthys crocea)

Large yellow croaker (Larimichthys crocea) is an important mariculture fish in China. In recent years, the meat quality of cultured L. crocea has gradually declined due to limited culture conditions. Histological characteristics of muscle fibers are commonly used indexes in meat quality evaluation, especially muscle fiber diameter (FD) and density (Fρ). To identify related SNPs and investigate the potential genetic architecture of meat quality, thereby provide basis for meat quality related selection. We conducted a genome-wide association study (GWAS) on muscle fiber related traits of L. crocea, we collected the dorsal muscle of 500 cultured L. crocea and measured the FD and Fρ by using paraffin section and hematoxylin eosin (H.E) stain. The collected samples were genotyped by ddRAD-seq (double-digest restriction-site associated DNA sequencing), and a total of 25 520 and 25 309 high quality SNPs were obtained for FD and Fρ respectively. GWAS analysis identified 6 significantly associated SNPs on 5 chromosomes, and ten candidate genes including lpin2, adcyap1, btg1, lifr, thbs4, gmeb1, slc2a1, myom1, myom2 and tcp11l2 were detected. These genes are involved in biological processes including muscle fiber growth and development, as well as energy metabolism. This is the first study on genomic mapping and analysis of muscle fiber related traits in L. crocea. No gender difference was found in the muscle fiber related traits of two-year-old mature fish. In addition, genes such as lpin2, lifr and btg1 and biological processes including energy metabolism, muscle fiber growth and development may play a role in determining the physical characteristics of meat quality in L. crocea fiber. The results provide theoretical basis and potential molecular tools for subsequent genetic improvement of meat quality traits in cultured L. crocea.