The identification of a major sex QTL in the white-leg shrimp, Litopenaeus vannamei

Abstract The white-leg shrimp, Litopenaeus vannamei, is the most widely farmed shrimp species globally. In recent years, interest in developing selective breeding programs and identifying the mechanisms controlling sex determination in L. vannamei has increased in the hope that improvements can be made on productivity efficiency. L. vannamei exhibits sexual dimorphism whereby females grow faster and larger than males. The discovery of novel genes or regions involved in sex-determination within L. vannamei would allow farmers to exploit this natural sexual dimorphism to enhance productivity. This study utilised a revised genetic linkage map for L. vannamei (whereby linkage groups 42 and 44 were merged as LG42.44) to conduct QTL and GWAS analyses from 20 full-sib families to identify one major QTL across 20 mapping families. The QTL was identified on LG42.44 and had a 95% confidence interval of 0–12.7 cM across all families (428 progeny). This region explained from 79.4–100% of the phenotypic variation. Independent genome wide association studies (GWAS) across 1952 individuals identified 11 significant SNPs (in high linkage disequilibrium) located on LG42.44 (0–12.7 cM) with one SNP 5790_511 with an extreme -log10 (P-value) of 294. For SNP 5790_511, 93% of homozygous genotypes were males and 97.6% of heterozygous were females indicating relatively close proximity of this SNP to the sex-determination locus. The SNP heritability for the sex phenotype was 0.84 +-0.007 suggesting a strong genetic basis of sex determination. A previously described feminisation gene, Pvfem-1, characterised as being involved in male and female gonad differentiation, was annotated to LG16; however no significant associations or QTL for sex were identified at this region in this study. Even though no known sex-determination genes could be identified under the QTL region of LG42.44, the large proportion of phenotypic variance explained by the significantly associated markers underlying the QTL region is promising and highlights this region for further fine mapping and sex-determination gene discovery efforts.