A male-specific insert of Opsariichthys bidens identified based on genome-wide association analyses and comparative genomics

Chinese hooksnout carp (Opsariichthys bidens) is an endemic stream fish and has begun to be artificially bred and cultivated due to its superior taste, high economic value and fast growth. An obvious sex dimorphism in growth has been observed in O. bidens. To explore the genetic architecture underlying the sex and growth traits, genome-wide association studies (GWAS) for sex and growth traits with a O. bidens aquaculture population consisting of 99 males and 101 females were performed using whole-genome re-sequencing. For the sex trait, a total of 5744 SNP loci (P value < 1 × 10−6) were found to be significantly associated with sex, 92.41 % (5308) of which were clustered on chromosome 24 within a 15.37 Mb region, and six candidate sex-related genes were detected, including sox4, nr0b2, u2af2a, rspo1, spaca6, tdrp-like. Almost all SNPs significantly associated with sex were heterozygous in males and homozygous in females. Therefore, we speculated that Chinese hooksnout carp had an XX/XY sex determination system. For the growth trait, a total of 80 SNP loci (P value < 1 × 10−6) were found to be significantly associated with the growth trait, which were unevenly distributed on chromosome 17, 11, 4 and 8. Similarly, six candidate growth-related genes were detected, including chst12, neub-like,nckx2, eif3f, eif3b, fgb-like. To develop a sex-specific marker, we performed a genome comparison between male and female genome. A male-specific insert of 2648 bp located on chromosome 24 was detected, and finally a PCR-based sex identification method was constructed based on the male-specific insert. Overall, this study explored the genetic basis of the sex and growth traits in O. bidens, and the identification of a sex-specific marker provided a powerful tool for the breeding of a mono-sexual strain.