Genome-wide association study identifies loci and candidate genes associated with growth traits in Siniperca...

Growth performance is a key economic trait that determines aquaculture productivity and profitability, and elucidating its genetic mechanisms is of great importance for germplasm improvement and molecular breeding in aquaculture species. Siniperca scherzeri, an important freshwater cultured species in East Asia, exhibits significant individual variation in growth rate. In this study, a genome-wide association study (GWAS) based on a linear mixed model (LMM) was conducted for five major growth traits in S. scherzeri-body weight (BW), extended length (EL), body length (BL), body thickness (BTH), and body height (BH). A total of 17 significant loci associated with growth traits were identified across nine chromosomes. Among them, 13 loci showed significant or suggestive associations with two or more traits, indicating that growth traits in S. scherzeri exhibit polygenic, small-effect, and cross-trait shared genetic characteristics. Genotype-phenotype association analysis confirmed the presence of specific genotypes conferring growth advantages, among which, the AA genotypes at loci Chr13_5825730 and Chr13_5825731 were significantly associated with increased body weight, extended length, and body length in S. scherzeri. Further annotation of candidate genes within the ±50 kb regions surrounding the significant loci identified a total of 55 candidate genes. GO and KEGG enrichment analyses revealed that these genes were significantly enriched in several biological pathways related to energy metabolism and growth regulation, including the insulin signaling pathway, AMPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, and carbohydrate digestion and absorption. These genes and their associated signaling pathways provide important molecular insights into the genetic basis of individual growth differences in S. scherzeri, offering theoretical support and potential targets for marker-assisted selection (MAS) and precision molecular breeding.