Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
Mol Biol Evol. 2023 Aug 3;40(8). doi: 10.1093/molbev/msad170.
Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.
未来的育种可能涉及有害等位基因的检测和去除，这些等位基因是指对作物适应性产生负面影响的突变。然而，对于现代作物育种中此类突变的普遍性及其对表型特征的影响，我们知之甚少。为了解决这个问题，我们检测了过去几十年间在中国和美国开发的 350 个玉米优良自交系中有害突变的数量和频率。我们的研究结果揭示了弱有害突变的积累和强有害突变的减少，这表明遗传漂变和纯化选择分别对这两种类型的突变起主导作用。我们还发现，在开发的杂种中，当较低频率的轻度有害突变呈杂合状态时，更有可能是杂合状态。这与杂种优势的互补作用解释一致。随后，我们发现有害突变比具有匹配的次要等位基因频率的非有害突变对表型特征的变异有更大的影响，尤其是与叶角和开花时间相关的特征。此外，我们在不同的表达基因的启动子和基因体区域中检测到的有害突变比在非差异表达基因中少。总的来说，我们的研究结果全面评估了现代玉米育种中有害突变的普遍性和影响，并为未来的玉米改良工作建立了一个有用的基准。
