Zhu Xinghai, Ni Ping, Sturrock Marc, Wang Yangfan, Ding Jun, Chang Yaqing, Hu Jingjie, Bao Zhenmin
Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China.
Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, D02 YN77 Ireland.
Mar Life Sci Technol. 2022 Aug 23;4(3):343-355. doi: 10.1007/s42995-022-00139-w. eCollection 2022 Aug.
The papilla number is one of the most economically important traits of sea cucumber in the China marketing trade. However, the genetic basis for papilla number diversity in holothurians is still scarce. In the present study, we conducted genome-wide association studies (GWAS) for the trait papilla number of sea cucumbers utilizing a set of 400,186 high-quality SNPs derived from 200 sea cucumbers. Two significant trait-associated SNPs that passed Bonferroni correction ( < 1.25E-7) were located in the intergenic region near and the genic region of , which were reported to play a pivotal role in cell growth and proliferation. The fine-mapping regions around the top two lead SNPs provided precise causative loci/genes related to papilla formation and cellular activity, including , , and . Potential SNPs with < 1E-4 were acquired for the following GO and KEGG enrichment analysis. Moreover, the two lead SNPs were verified in another population of sea cucumber, and the expressive detection of three potential candidate genes , , and that near or cover the two lead SNPs was conducted in papilla tissue of TG (Top papilla number group) and BG (Bottom papilla number group) by qRT-PCR. We found the significantly higher expression profile of (3.34-fold), (4.90-fold), and (4.23-fold) in TG, implying their potential function in papilla polymorphism. The present results provide valuable information to decipher the phenotype differences of the papilla trait and will provide a scientific basis for selective breeding in sea cucumbers.
The online version contains supplementary material available at 10.1007/s42995-022-00139-w.
乳突数量是中国海参市场贸易中最重要的经济性状之一。然而，海参类动物乳突数量多样性的遗传基础仍然匮乏。在本研究中，我们利用从200只海参中获得的一组400,186个高质量单核苷酸多态性（SNP），对海参的乳突数量性状进行了全基因组关联研究（GWAS）。两个经过邦费罗尼校正（<1.25E-7）的与性状显著相关的SNP位于 附近的基因间区域和 的基因区域，据报道它们在细胞生长和增殖中起关键作用。前两个领先SNP周围的精细定位区域提供了与乳突形成和细胞活性相关的精确致病位点/基因，包括 、 和 。获得了P<1E-4的潜在SNP用于以下基因本体（GO）和京都基因与基因组百科全书（KEGG）富集分析。此外，在另一组海参群体中验证了这两个领先SNP，并通过定量逆转录聚合酶链反应（qRT-PCR）在TG（高乳突数量组）和BG（低乳突数量组）的乳突组织中对位于两个领先SNP附近或涵盖这两个领先SNP的三个潜在候选基因 、 和 进行了表达检测。我们发现 （3.34倍）、 （4.90倍）和 （4.23倍）在TG中的表达谱显著更高，这意味着它们在乳突多态性中具有潜在功能。本研究结果为解读乳突性状的表型差异提供了有价值的信息，并将为海参的选择性育种提供科学依据。
在线版本包含可在10.1007/s42995-022-00139-w获取的补充材料。
