Extreme-phenotype genome-wide association study of growth traits in golden pompano (Trachinotus blochii) and implications for genomic selection

Genetic improvement of growth is a major objective in aquaculture because it directly enhances production efficiency. Golden pompano ( Trachinotus blochii ) is a fast-growing marine fish of high commercial value, but the genetic architecture of growth remains poorly understood. Growth traits were measured in 703 market-size fish, and 300 extreme-phenotype individuals selected by body weight (BW) were subjected to whole-genome resequencing. After quality control and variant calling, 9,642,743 high-quality SNPs were identified. Genome-wide association analyses for BW, body length (BL), whole length (WL), and body height (BH) revealed three prominent association peaks and 22 genome-wide significant SNPs, each explaining 11%-25% of the additive phenotypic variance. Haplotype-based linkage analysis further defined four linkage blocks and identified 17 candidate genes related to growth. To evaluate their breeding utility, eight evenly spaced SNP-density panels and six genomic selection models were tested. Incorporating the 22 GWAS-significant SNPs improved prediction accuracy for BW by 2.8%-22.0% across models, with gains generally exceeding 13% when marker density was below 3k. These results provide valuable markers and candidate genes for dissecting growth in T. blochii and support the development of cost-effective genomic selection strategies for breeding.