São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil.
Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile.
BMC Genomics. 2024 Jun 5;25(1):565. doi: 10.1186/s12864-024-10431-x.
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 in order to improve economically relevant traits. Sexual dimorphism exists in Pacific white shrimp, and the mapping of the sex-determination region in this species may help in future reproductive applications. We have constructed male, female, and sex-averaged high-density genetic maps using a 50 K single-nucleotide polymorphism (SNP) array, followed by a genome-wide association study (GWAS) to identify genomic regions associated with sex in white shrimp.
The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The lengths of the male, female, and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. LG18 was found to be the largest for both sexes, whereas LG44 was the shortest for males and LG31 for females. A sex-determining region was found in LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and was able to identify 99% of the males and 88% of the females. Although other significant markers had a lower ability to determine sex, putative genes were intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidates with possible participation in important processes of sexual differentiation in shrimp.
Our results provide novel genomic resources for shrimp, including a high-density linkage map and new insights into the sex-determining region in L. vannamei, which may be usefulfor future genetics and reproduction applications.
为了应用基因组工具来提高经济相关性状，太平洋白对虾（Litopenaeus vannamei）基因组资源的扩展至关重要，例如构建密集的遗传连锁图谱。太平洋白对虾存在性别二态性，该物种的性别决定区域的图谱绘制可能有助于未来的繁殖应用。我们使用 50K 单核苷酸多态性（SNP）阵列构建了雄性、雌性和平均性别的高密度遗传图谱，随后进行了全基因组关联研究（GWAS），以鉴定与白对虾性别相关的基因组区域。
遗传图谱产生了 15256 个分配到 44 个连锁群（LG）的 SNP。雄性、雌性和平均图谱的长度分别为 5741.36、5461.20 和 5525.26cM。LG18 被发现是两性中最大的，而 LG44 是雄性中最短的，LG31 是雌性中最短的。在 LG31 中发现了一个性别决定区域，有 21 个统计学上显著的 SNP。最重要的 SNP 之前被鉴定为性连锁标记，能够识别 99%的雄性和 88%的雌性。尽管其他重要的标记具有较低的性别决定能力，但假定基因被截获或接近它们。章鱼萤光素 2-单加氧酶、丝氨酸/精氨酸重复矩阵蛋白和精脒氧化酶基因被鉴定为可能参与虾类性分化重要过程的候选基因。
我们的结果为虾类提供了新的基因组资源，包括高密度连锁图谱和对 L. vannamei 性别决定区域的新见解，这可能对未来的遗传学和繁殖应用有用。
