Abstract
Characterization of genetic variants is crucial for understanding the molecular mechanisms behind selected traits and enhancing the rate of genetic gain through artificial selection. This study explored the genetic diversity and population structure of blunt snout bream Megalobrama amblycephala, a key freshwater fish in Chinese aquaculture. We conducted whole-genome re-sequencing of individuals from six populations, comprising three natural and three genetically improved strains, to assess genetic diversity, population structure and the impacts of selective breeding. We identified 17,009,590 high-quality biallelic single nucleotide polymorphism (SNP) loci. Genetic diversity assessments revealed low levels of polymorphism across populations, with genetically improved strains showing moderate to high genetic differentiation from their source populations. The study also highlighted runs of homozygosity (ROH) and analyzed linkage disequilibrium (LD) decay, indicating minimal recent inbreeding and diverse recombination events among populations. Selective sweep analyses uncovered significant selection loci associated with growth and hypoxia tolerance traits. Enrichment analyses identified genes involved in olfactory signal transduction, immune response, and metabolism pathways, which are closely related to these selective traits. These findings offer insights into the genetic basis of critical traits in M. amblycephala, contributing to the conservation of germplasm resources and supporting ongoing selective breeding efforts.
摘要：
对遗传变异的特征化对于理解所选性状背后的分子机制以及通过人工选择提高遗传增益的速度至关重要。本研究探讨了中国水产养殖中关键淡水鱼——团头鲂（Megalobrama amblycephala）的遗传多样性和种群结构。研究对来自六个种群的个体进行了全基因组重测序，这些种群包括三个自然种群和三个基因改良品系，以评估遗传多样性、种群结构以及选择育种的影响。研究识别出17,009,590个高质量的双等位基因单核苷酸多态性（SNP）位点。遗传多样性评估显示，各种群的多态性水平较低，而基因改良品系与其源种群之间表现出中等到高度的遗传分化。研究还强调了同源性区间（ROH）并分析了连锁不平衡（LD）衰减，表明最近的近交程度较低，各种群之间存在多样的重组事件。选择扫除分析揭示了与生长和缺氧耐受性性状相关的重要选择位点。富集分析识别出参与嗅觉信号转导、免疫反应和代谢途径的基因，这些基因与这些选择性状密切相关。这些发现为平头鲢关键性状的遗传基础提供了见解，有助于保护种质资源并支持持续的选择育种工作。