Genome-wide QTL mapping and RNA-seq reveal the genetic variation influencing growth traits in giant grouper (Epinephelus lanceolatus)

Genetic improvement of growth traits is a major target of grouper aquaculture and breeding. As one of the largest groupers, the giant grouper (Epinephelus lanceolatus) has excellent growth performance, although the genetic basis of its growth traits has been rarely studied. In this study, we successfully constructed a high-density genetic linkage map with 2988 SNPs generated by genotype-by-sequencing of 178 individuals, which belong to an F1 full-sibling family. The length of the map was 3231.5 cM with an average interval of 1.21 cM. Then, we performed genome-wide QTL (quantitative trait locus) mapping for five growth traits including all length, body length, body height, body thickness, and body weight in the giant grouper and identified six growth-associated QTLs, which explained 4.65–12.56% of the phenotypic variance. These QTLs were distributed on five linkage groupers (LGs) of our sex-averaged linkage map with two QTLs on LG11, four QTLs on LG7, LG10, LG15, and LG23. The genes identified within the significant QTLs were validated using qPCR and the results showed six significantly upregulated genes (kalrn, ypel1, supt7l, lacs5, ccnd2, mybpc2) in tissues (muscle, fat, liver, gill, etc.) of the fast vs slow growth groups were highlighted as promising candidates. Further, RNA-seq analysis revealed 484 differentially expressed genes (DEGs) between fast/slow growth groups that play roles in the RNA transport, metabolic pathways, PPAR signaling pathway, and carbon metabolism pathways. Notably, 27 DEGs were detected in the identified growth-associated-QTL regions. Those candidate genes shared between QTL mapping and DEGs may play important roles in regulating cell growth, signal transduction, carbohydrate metabolism and skeletal development. Overall, our findings are useful for improving the genetic process for molecular marker-assisted selection and provide new insights into elucidating the molecular mechanism of growth variation in this species.