A high-density genetic linkage map and QTL mapping for sex in Clarias fuscus

Abstract

Hong Kong catfish (Clarias fuscus) is a freshwater fish that has economic value and is widely cultured in southern China. C. fuscus has significant sexual growth dimorphism. In this study, full-sib F1 individuals of C. fuscus were used as a mapping family to construct a high-density genetic linkage map, and sex-related quantitative trait loci (QTL) were mapped using single nucleotide polymorphism (SNP) markers by restriction-site associated DNA sequencing (RAD-seq) technology. The genetic map was divided into 28 linkage groups with a total map distance of 4870.15 cM, 6453 markers, and an average genetic distance of 0.75 cM between markers. Based on the genetic linkage map, interval mapping was performed to identify sex-related QTLs. A sex-related QTL, qSEX-1, was successfully mapped to LG13, which contained 225 linked SNP markers. The LOD value for the main QTL peak was 77.18, located at 138.32 cM, and the proportion of phenotypic variance explained (PVE) for sex was 83.1%. A candidate sex-determination region was identified within the qSEX-1 interval, with a total map distance of 16.073 cM and 15 SNP markers. The np544 marker was highly linked to sex. In summary, the first genetic linkage map of C. fuscus was generated based on high-throughput sequencing. Moreover, sex-linked SNP loci and a sex-determining interval were identified, providing methodological guidance and important tools for sex control technology in C. fuscus breeding.