The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.

中文翻译：

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对美国农业部核心大豆收藏的测序揭示了驯化和育种过程中的基因丢失


由于基因存在/不存在的差异，植物的基因含量在同一物种的个体之间存在差异，并且选择可以改变群体中特定基因的频率。驯化和育种过程中的选择将改变基因组景观，尽管这些修饰的性质仅针对特定基因或更一般的水平（例如，通过遗传多样性的丧失）来了解。在这里，我们组装并分析了大豆 ( Glycine spp.) 全基因组，代表来自美国农业部大豆种质保藏的 1,000 多个大豆种质，包括野生和栽培谱系，以评估驯化和育种过程中基因和等位基因频率的全基因组变化。我们鉴定了 Lee 参考基因组组装中缺失的 3,765 个基因，并评估了该群体中所有基因的存在/缺失。除了遗传多样性的丧失之外，我们发现在驯化和随后的育种过程中，每个个体的蛋白质编码基因的平均数量显着减少，尽管一些基因和等位基因变异的频率与农艺性状的选择相关。该分析提供了这种重要油料作物驯化和育种的基因组视角。