Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (<i>Micropterus</i> <i>salmoides</i>)

Largemouth bass ( Micropterussalmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.大口黑鲈( Micropterus salmoides)在北美、欧洲和中国已经成为一种重要的经济鱼类。各种遗传改良和驯化过程可以改变物种的基因序列，在基因组上留下了可以检测到的核苷酸改变的信号。在该研究中，我们对5个大口黑鲈群体的149个个体进行了全基因组重测序，包括原种（从美国引进群体）和改良群体（来自中国的4个国内育种群体）。我们检测到一些基因组变异区域含有某些与改良性状相关的基因，这些变异区域可能成为大口黑鲈遗传改良的分子标记。遗传多样性和群体结构分析表明，国内4个改良群体经历了更严格的遗传选择。通过选择性信号分析，我们在大口黑鲈基因组中确定了数百个选择性信号区域，并在这些选择区域中筛选到103个相关基因，其中有多个与生长（ psst1和 grb10）、早期发育（ klf9、 sp4和 sp8）和免疫（ pkn2、 sept2、 bcl6和 ripk2）有关。综上所述，该研究提供了大口黑鲈在全基因组水平上的遗传变异和选择信号，为了解大口黑鲈驯化和遗传改良的遗传机制提供了新的见解，同时为大口黑鲈的遗传改良提供理论依据。.