A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei)

Abstract

Abstract Background Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei) such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools to improve economic relevant traits. Sexual dimorphism exists in Pacific white shrimp, and mapping of the sex determination region in this species may help in the future reproductive applications for this species. We constructed male, female and sex-averaged high-density genetic maps using a 50K single-nucleotide polymorphism (SNP) array followed by a genome-wide association study (GWAS) to identify genomic regions associated to sex in white shrimp.Results The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The length of the male, female and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. The LG18 was the largest for both sexes while the LG44 was the shortest for males and LG31 for females. A sex determination region was found on LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and it was able to identify 99% of males and 88% of females. Although, the other significant markers had lower ability to determine sex, putative genes were found intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidate with possible participation in important processes of sexual differentiation in shrimp.Conclusions Our results provided novel genomic resources for shrimp, including a high-density linkage map and new insights regarding the sex determining region in L. vannamei, and may be both useful in future genetics and reproduction applications.