Bayer Philipp E, Valliyodan Babu, Hu Haifei, Marsh Jacob I, Yuan Yuxuan, Vuong Tri D, Patil Gunvant, Song Qijian, Batley Jacqueline, Varshney Rajeev K, Lam Hon-Ming, Edwards David, Nguyen Henry T
School of Biological Sciences and Inst. of Agriculture, The Univ. of Western Australia, Crawley, WA, Australia.
Dep. of Agriculture and Environmental Sciences, Lincoln Univ., Jefferson, City, MO, 65101, USA.
Plant Genome. 2022 Mar;15(1):e20109. doi: 10.1002/tpg2.20109. Epub 2021 Jun 24.
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.
由于基因存在/缺失变异，同一物种个体之间的植物基因含量存在差异，而且选择能够改变种群中特定基因的频率。驯化和育种过程中的选择会改变基因组格局，不过这些改变的本质仅在特定基因层面或更普遍层面上得到了解（例如，通过遗传多样性的丧失）。在这里，我们组装并分析了一个大豆泛基因组，该泛基因组代表了来自美国农业部大豆种质资源库的1000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全基因组范围内基因和等位基因频率的变化。我们鉴定出了3765个在Lee参考基因组组装中不存在的基因，并评估了该群体中所有基因的存在/缺失情况。除了遗传多样性的丧失，我们还发现驯化和后续育种过程中每个个体的蛋白质编码基因平均数量显著减少，不过一些与农艺性状选择相关的基因和等位基因变体频率增加。该分析为这种重要油料作物的驯化和育种提供了基因组视角。
