MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China.
Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China.
Zool Res. 2024 Mar 18;45(2):329-340. doi: 10.24272/j.issn.2095-8137.2023.270.
The leopard coral grouper ( ) is a species of significant economic importance. Although artificial cultivation of has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for , we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( ) and fixation index ( ) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to . This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting .
波纹唇鱼（）是一种具有重要经济意义的物种。尽管近年来人工养殖取得了蓬勃发展，但由于缺乏全面的群体基因组数据，选择性育种的进展受到了阻碍。在这项研究中，我们通过对 326 个个体进行全基因组重测序，鉴定出超过 873 万个单核苷酸多态性（SNPs）。此外，我们根据遗传特征和系统发育关系，将 226 个具有高覆盖测序深度（≥14×）的个体分为八个聚类。值得注意的是，其中四个聚类与其他群体相比表现出明显的遗传分化。为了识别对 的有利基因座，我们通过分析这四个聚类中的核苷酸多样性（）和固定指数（），研究了基因组中表现出选择清除的区域。利用这些高覆盖重测序数据，我们成功构建了第一个特定于 的单倍型参考面板。这一成就有望实现高质量、低成本的基因分型方法。此外，我们结合低覆盖测序数据和基因分型技术进行了全基因组关联研究，旨在鉴定与生长性状相关的候选 SNP 基因座。这些基因主要集中在 17 号染色体上，该染色体主要参与骨骼肌肉和胚胎发育以及细胞增殖。值得注意的是，我们对八个聚类中的生长相关 SNP 进行了详细调查，结果表明聚类 5 蕴藏着最有希望的候选 SNP，为遗传选择育种提供了潜力。这些发现为管理种质资源和针对 的基因组驱动的育种计划提供了一个强大的工具包和有价值的见解。
