Construction of a high-density genetic linkage map and QTL mapping for growth traits in hybrid Epinephelus fuscoguttatus (9) and Epinephelus tukula (♂) progeny

QTL mapping is an effective method for marker assisted selection (MAS) in animal breeding, and high-density linkage genetic maps are necessary for fine mapping of QTLs. In this study, high-density genetic maps of hybrid Epinephelus fuscoguttatus (9) and Epinephelus tukula (male) progeny (which demonstrated improved growth rates compared with the female parent) were constructed using RAD technology. Sex-average, female-specific, and male-specific linkage maps were composed of 24 linkage groups (LGs). The genetic map developed in this study had the highest number of SNPs among reported genetic maps for groupers. The sex-average linkage map contained 2759 bin makers (150,468 SNPs) and spanned 1627.28 cM, with an average marker interval of 0.59 cM. The female-specific (E. fuscoguttatus) linkage map contained 648 bin makers (38,269 SNPs) and spanned 1414.68 cM, with an average marker interval of 2.22 cM. The male-specific (E. tukula) linkage map contained 2126 bin makers (112,015 SNPs) and spanned 1839.88 cM, with an average marker interval of 0.86 cM. In total, 45 QTLs comprising 318 SNPs for growth-related traits were identified, including 10 QTLs for body weight, 6 QTLs for full length, 7 QTLs for body length, 14 QTLs for head length, 5 QTLs for body height, and 3 QTLs for body thickness. In addition, 56 candidate genes related to growth, metabolism, bone formation, muscle development, and neural regulation were identified, including eight genes associated with growth in other fish. Among these, gpr126, fam20a, fam20c, sox9b, foxm1, foxl1, myf6, zbtb38, and sl should be a focus of further research. These results provide a foundation for fine QTL mapping in grouper, and theoretical guidance for exploring the causes of heterosis, which is of great significance for MAS in the breeding of hybrids and male and female parents.