Extreme-Phenotype Genome-Wide Association Analysis for Growth Traits in Spotted Sea Bass (Lateolabrax maculatus) Using Whole-Genome Resequencing

Simple Summary Fish farming provides an efficient means of obtaining high-quality protein for humans. However, the decreased growth rate of aquaculture fish due to germplasm degradation often increases production costs and reduces economic benefits. Therefore, it is particularly important to develop fast-growing varieties and elucidate the genetic mechanisms underlying growth traits. In this study, we identified 50 growth-related markers in the genome of Lateolabrax maculatus, an important marine aquaculture species, with the phenotypic variance explained up to 15.82%, which will help in marker-assisted breeding for fast-growing varieties. Additionally, 47 growth-related candidate genes were annotated, and the functions of some of these genes in growth traits have been confirmed in mice or zebrafish through gene knockout or knockdown experiments. The 47 candidate genes are mainly associated with the metabolism of energy, glucose, and lipids and the development of musculoskeletal and nervous systems, which may act as drivers for the growth of L. maculatus. Altogether, our study identified growth-related markers and candidate genes, which will help develop the fast-growing varieties of L. maculatus and elucidate genetic mechanisms underlying its growth traits.Abstract Spotted sea bass (Lateolabrax maculatus) is an important marine economic fish in China, ranking third in annual production among marine fish. However, a declined growth rate caused by germplasm degradation has severely increased production costs and reduced economic benefits. There is an urgent need to develop the fast-growing varieties of L. maculatus and elucidate the genetic mechanisms underlying growth traits. Here, whole-genome resequencing technology combined with extreme phenotype genome-wide association analysis (XP-GWAS) was used to identify candidate markers and genes associated with growth traits in L. maculatus. Two groups of L. maculatus, consisting of 100 fast-growing and 100 slow-growing individuals with significant differences in body weight, body length, and carcass weight, underwent whole-genome resequencing. A total of 4,528,936 high-quality single nucleotide polymorphisms (SNPs) were used for XP-GWAS. These SNPs were evenly distributed across all chromosomes without large gaps, and the average distance between SNPs was only 175.8 bp. XP-GWAS based on the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (Blink) and Fixed and random model Circulating Probability Unification (FarmCPU) identified 50 growth-related markers, of which 17 were related to body length, 19 to body weight, and 23 to carcass weight. The highest phenotypic variance explained (PVE) reached 15.82%. Furthermore, significant differences were observed in body weight, body length, and carcass weight among individuals with different genotypes. For example, there were highly significant differences in body weight among individuals with different genotypes for four SNPs located on chromosome 16: chr16:13133726, chr16:13209537, chr16:14468078, and chr16:18537358. Additionally, 47 growth-associated genes were annotated. These genes are mainly related to the metabolism of energy, glucose, and lipids and the development of musculoskeletal and nervous systems, which may regulate the growth of L. maculatus. Our study identified growth-related markers and candidate genes, which will help to develop the fast-growing varieties of L. maculatus through marker-assisted breeding and elucidate the genetic mechanisms underlying the growth traits.