Genome-wide association study of red skin color in leopard coral grouper (Plectropomus leopardus) based on genome resequencing

Leopard coral grouper (Plectropomus leopardus) is an economically important grouper species which is popular in markets because of its red-skin color. However, currently, a large proportion of individuals in the artificial breeding of P. leopardus exhibit non-red skin colors, which increases breeding costs by reducing efficiency and restricts the development of the industry. To identify candidate genes and SNPs associated with the red-skin trait, this study collected 139 P. leopardus individuals from three farms (LED, QHH, and QHL), and performed a genome-wide association study (GWAS) based on whole-genome resequencing. The results identified 10 SNPs that are potentially associated with the red-skin color traits in P. leopardus, and a total of 35 potential genes were annotated within 50 kb of these SNPs. KEGG pathway analysis using these 35 candidate genes showed that natural killer cell mediated cytotoxicity, Ras signaling, MAPK signaling, and other pathways were significantly enriched (p < 0.05). Subsequently, GWAS was used for populations of LED, QHH, and QHL respectively, which showed that 7 genes (MIC13, SPIN1, PRS57, FLOT1, TARS, DHI1L, and FGF10) of the above 35 genes were shared in QHH populations. These results will greatly improve the P. leopardus industry by helping understand the molecular mechanisms underlying red-skin color traits. Furthermore, the identified SNPs can be used as markers to aid targeted breeding for skin color in P. leopardus.