Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.
Mar Biotechnol (NY). 2021 Feb;23(1):127-139. doi: 10.1007/s10126-020-10007-2. Epub 2020 Nov 16.
Larimichthys crocea is one of the traditional marine culture fishes in China, widely distributed in South China Sea, East Sea, and southern Yellow Sea. Sex dimorphism is evident in this species that females present a substantial growth strength than males, suggesting breeding females could obtain more economic benefits in L. crocea aquaculture industry. With the continuous expansion of aquaculture industry, both identifying sex-associated genome region and understanding the genetic basis underlying gonad differentiation and development matter to not only sex control aquaculture but also breeding industry. Thus, genome-wide association analysis (GWAS) of sex determination was conducted with a random breeding population of 905 individuals (including 463 females and 442 males) by ddRAD sequencing. For sex determination, 21 significant single nucleotide polymorphisms (SNPs) in chromosome (Chr) 22 were identified. Surrounding these SNPs, we founded 14 candidate genes, including dmrt1, dmrt3, and piwil2, fam102a, and odf2. The sex-associated region was narrowed down further to 2.4 Mb on Chr22 through F scanning and insertion-deletion (InDel) analysis. Besides, 3 SNPs in the supposed sex-determining region on Chr22 were identified as highly associated with gonad differentiation through GWAS on gonadosomatic index (GSI) in 350 males and 231 females. Because of the significant difference of GSI between females and males of L. crocea, GWAS on GSI of different genders was also conducted independently. Finally, we identified a SNP in Chr18 showing genome-wide significant association with male GSI (MGSI) and three genes axl, cyp2a10, and cyp2g1 involved in the gonadal development regulation process of aromatase. Overall, this study explored the genetic basis of sex determination mechanism and provided novel insights into gonad differentiation and development, offering solid genetic support for sex control breeding, marker-assisted selection, and marine resources conservation.
大黄鱼是中国传统的海水养殖鱼类之一，广泛分布于南海、东海和黄海南部。该物种存在明显的性别二态性，雌性的生长力明显强于雄性，这表明在大黄鱼养殖产业中，养殖雌性可以获得更多的经济效益。随着水产养殖业的不断扩大，鉴定与性别相关的基因组区域和了解性腺分化和发育的遗传基础不仅对控制性水产养殖，而且对养殖产业都具有重要意义。因此，通过 ddRAD 测序对一个由 905 个个体（包括 463 个雌性和 442 个雄性）组成的随机繁殖群体进行了性别决定的全基因组关联分析（GWAS）。为了进行性别鉴定，在染色体（Chr）22 上鉴定出 21 个显著的单核苷酸多态性（SNP）。围绕这些 SNP，我们发现了 14 个候选基因，包括 dmrt1、dmrt3 和 piwil2、fam102a 和 odf2。通过 F 扫描和插入缺失（InDel）分析，将与性别相关的区域进一步缩小到 Chr22 上的 2.4 Mb。此外，在 Chr22 上假定的性别决定区域内的 3 个 SNP 通过对 350 个雄性和 231 个雌性的性腺体指数（GSI）进行 GWAS，被鉴定为与性腺分化高度相关。由于大黄鱼雌、雄个体间 GSI 存在显著差异，因此还分别对雌、雄个体的 GSI 进行了 GWAS。最后，我们鉴定出 Chr18 上的一个 SNP 与雄性 GSI（MGSI）具有全基因组显著相关性，以及涉及芳香化酶的性腺发育调控过程的三个基因 axl、cyp2a10 和 cyp2g1。总的来说，本研究探索了性别决定机制的遗传基础，为性腺分化和发育提供了新的见解，为控制性繁殖、标记辅助选择和海洋资源保护提供了坚实的遗传支持。
