Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
Genes (Basel). 2024 Oct 10;15(10):1307. doi: 10.3390/genes15101307.
Largemouth bass (), a valuable freshwater fish species, has experienced significant genetic decline in China due to prolonged domestic breeding and limited introduction of new genetic material. It is necessary to have a comprehensive understanding of the genetic status of largemouth bass populations in China. In this study, we conducted population genetic analyses on nine cultured largemouth bass populations using whole genome resequencing. A total of 3.23 Tb of clean bases were generated, with average Q20 and Q30 values of 98.17% and 94.25%, respectively, and 2,140,534 high-quality SNPs were obtained. Relatively high genetic diversity was observed across all populations. Combined with linkage disequilibrium (LD) patterns, the Wanlu (WL) population possessed the highest genetic diversity, and the Longyou (LY) population possessed the lowest genetic diversity. Additionally, population structure analyses, including pairwise F-statistics, phylogenetic trees, PCA, and admixture analysis, revealed significant genetic differentiation, particularly between the WL, LY, and other 7 populations, while also indicating the occurrence of a common admixture event. Finally, TreeMix inferred migration events from the WL to the Chuanlu (CL) population and from the Taiwan breeding population (TWL) to the Guanglu (GL) population. These findings provide a critical foundation for developing conservation and breeding strategies for largemouth bass in China.
大口黑鲈（）是一种有价值的淡水鱼类，由于长期的国内养殖和新遗传物质的引入有限，在中国经历了显著的遗传衰退。全面了解中国大口黑鲈种群的遗传状况是必要的。在这项研究中，我们使用全基因组重测序对 9 个养殖大口黑鲈种群进行了群体遗传分析。共产生了 3.23 Tb 的清洁碱基，平均 Q20 和 Q30 值分别为 98.17%和 94.25%，获得了 2,140,534 个高质量的 SNP。所有种群均表现出较高的遗传多样性。结合连锁不平衡（LD）模式，万禄（WL）种群具有最高的遗传多样性，龙游（LY）种群具有最低的遗传多样性。此外，种群结构分析，包括成对 F-统计量、系统发育树、PCA 和混合分析，揭示了显著的遗传分化，特别是在 WL、LY 和其他 7 个种群之间，同时也表明发生了共同的混合事件。最后，TreeMix 推断了从 WL 到 Chuanlu（CL）种群和从台湾养殖种群（TWL）到 Guanglu（GL）种群的迁移事件。这些发现为中国大口黑鲈的保护和养殖策略的制定提供了重要基础。
