Zhu Min, Cheng Yingyu, Wu Sanling, Huang Xuehui, Qiu Jie
Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University, Hangzhou, China.
Genomics. 2022 Mar;114(2):110290. doi: 10.1016/j.ygeno.2022.110290. Epub 2022 Feb 4.
Deleterious mutations can reduce the fitness of crop varieties, which limits the plant breeding efficacy. While crop deleterious mutations have been extensively examined, most studies focused on one specific crop with different analyzing methods, which hinders unveiling shared genomic characteristics of deleterious mutations across diverse crops. Here we used standardized approaches to characterize the deleterious mutations in genomes of domesticated inbreeding (i.e., rice, soybean, and tomato) and clonally propagated crops (i.e., grape and pineapple). We found that deleterious mutations are commonly targeted by purifying selection, and are over-presented in a nearly fixed derived allele frequency in the course of plant domestication. Further, a generally negative correlation between genetic load and the artificial selection strength is observed. Importantly, we consistently uncovered the higher derived genomic heterozygosity for deleterious mutations compared to other genic variants. This study broadens our understanding of the evolution of deleterious mutations in plant genomes.
有害突变会降低作物品种的适应性，这限制了植物育种的效率。虽然对作物有害突变已进行了广泛研究，但大多数研究集中于一种特定作物且采用不同分析方法，这阻碍了揭示不同作物间有害突变的共同基因组特征。在此，我们使用标准化方法来表征驯化自交作物（即水稻、大豆和番茄）以及克隆繁殖作物（即葡萄和菠萝）基因组中的有害突变。我们发现有害突变通常受到纯化选择的靶向作用，并且在植物驯化过程中以接近固定的衍生等位基因频率过度呈现。此外，观察到遗传负荷与人工选择强度之间普遍呈负相关。重要的是，与其他基因变异相比，我们一致发现有害突变具有更高的衍生基因组杂合性。这项研究拓宽了我们对植物基因组中有害突变进化的理解。
