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.

中文翻译：

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南美白对虾主要性别QTL的鉴定

摘要 南美白对虾（Litopenaeus vannamei）是全球养殖最广泛的虾种。近年来，开发选择性育种计划和确定控制南美白对虾性别决定机制的兴趣增加，希望能够提高生产力。南美白对虾表现出雌性二态性，雌性比雄性生长得更快、更大。南美白对虾性别决定所涉及的新基因或区域的发现将使农民能够利用这种自然的性别二态性来提高生产力。本研究利用修改后的南美白对虾遗传连锁图谱（连锁群 42 和 44 合并为 LG42.44）对 20 个全同胞家族进行 QTL 和 GWAS 分析，以确定 20 个作图家族中的一个主要 QTL。QTL 在 LG42.44 上被鉴定，并且在所有家族（428 个后代）中具有 0-12.7 cM 的 95% 置信区间。该区域解释了表型变异的 79.4-100%。1952 个人的独立全基因组关联研究 (GWAS) 确定了位于 LG42.44 (0–12.7 cM) 的 11 个显着 SNP（处于高度连锁不平衡状态），其中一个 SNP 5790_511 的极端 -log10（P 值）为 294。 SNP 5790_511，93% 的纯合基因型是男性，97.6% 的杂合基因型是女性，表明该 SNP 与性别决定位点相对接近。性别表型的 SNP 遗传率为 0.84 +-0.007，表明性别决定有很强的遗传基础。先前描述的女性化基因 Pvfem-1，其特征是参与男性和女性性腺分化，被注释到 LG16；然而，在本研究中，在该区域未发现与性别相关的显着关联或 QTL。尽管在 LG42.44 的 QTL 区域下没有确定已知的性别决定基因，但由 QTL 区域下的显着相关标记解释的大部分表型变异是有希望的，并突出显示该区域可用于进一步精细定位和性别决定基因发现的努力。