Construction of a high-density genetic linkage map and QTL mapping for growth traits in gynogenetic brown-marbled grouper (Epinephelus fuscoguttatus)

Abstract

High-density genetic linkage maps based on single nucleotide polymorphisms (SNPs) are essential for quantitative trait loci (QTL) mapping, trait-related gene identification, marker-assisted selection (MAS), genome assembly, and comparative genomic analysis in aquaculture fish species. Haploid (or gynogenesis) is an excellent germplasm target for mapping genetic linkage maps and MAS breeding. In this study, the high-density genetic linkage map of gynogenetic brown-marbled grouper (Epinephelus fuscoguttatus) based on genotyping by sequencing (GBS) technology was constructed using one F1 gynogenetic family composed of 164 gynogens and their female parents. A high-density linkage map of gynogenetic brown-marbled grouper was constructed with 19,301 SNPs located in 24 linkage groups (LGs). The genetic length of the consensus map was 2343.72 cM, with an average genetic length of 97.655 cM and an average marker interval of 0.12 cM. QTL mapping analysis revealed forty QTLs for body mass and ten phenotypic traits in 9 LGs. Multiple loci were found to be shared on LG3, LG8, LG11, LG16 and LG23, and several important growth-related candidate genes (e.g., mrc1, adgrb3, zbtb38 and adcy3), were identified within QTL regions. These vital SNPs and candidate genes may serve as useful genomic tools for marker-assisted selective breeding. Coupled breeding of MAS and artificial gynogenesis could provide a powerful method for genetic improvement in grouper breeding.