The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.
The New Zealand Institute for Plant & Food Research Limited (PFR), Mount Albert Research Centre, Auckland, New Zealand.
Plant Biotechnol J. 2019 Oct;17(10):1954-1970. doi: 10.1111/pbi.13112. Epub 2019 Apr 16.
Crop evolution is a long-term process involving selection by natural evolutionary forces and anthropogenic influences; however, the genetic mechanisms underlying the domestication and improvement of fruit crops have not been well studied to date. Here, we performed a population structure analysis in peach (Prunus persica) based on the genome-wide resequencing of 418 accessions and confirmed the presence of an obvious domestication event during evolution. We identified 132 and 106 selective sweeps associated with domestication and improvement, respectively. Analysis of their tissue-specific expression patterns indicated that the up-regulation of selection genes during domestication occurred mostly in fruit and seeds as opposed to other organs. However, during the improvement stage, more up-regulated selection genes were identified in leaves and seeds than in the other organs. Genome-wide association studies (GWAS) using 4.24 million single nucleotide polymorphisms (SNPs) revealed 171 loci associated with 26 fruit domestication traits. Among these loci, three candidate genes were highly associated with fruit weight and the sorbitol and catechin content in fruit. We demonstrated that as the allele frequency of the SNPs associated with high polyphenol composition decreased during peach evolution, alleles associated with high sugar content increased significantly. This indicates that there is genetic potential for the breeding of more nutritious fruit with enhanced bioactive polyphenols without disturbing a harmonious sugar and acid balance by crossing with wild species. This study also describes the development of the genomic resources necessary for evolutionary research in peach and provides the large-scale characterization of key agronomic traits in this crop species.
作物进化是一个长期的过程，涉及自然进化力量和人为影响的选择；然而，迄今为止，水果作物驯化和改良的遗传机制尚未得到很好的研究。在这里，我们基于 418 个品种的全基因组重测序，对桃（Prunus persica）进行了群体结构分析，并证实了进化过程中存在明显的驯化事件。我们分别鉴定了 132 个和 106 个与驯化和改良相关的选择清除。对其组织特异性表达模式的分析表明，驯化过程中选择基因的上调主要发生在果实和种子中，而不是其他器官。然而，在改良阶段，叶片和种子中的上调选择基因比其他器官更多。利用 424 万个单核苷酸多态性（SNP）进行的全基因组关联研究（GWAS）揭示了 171 个与 26 个果实驯化性状相关的位点。在这些位点中，有 3 个候选基因与果实重量以及果实中的山梨醇和儿茶素含量高度相关。我们证明，随着与高多酚组成相关的 SNPs 等位基因频率在桃进化过程中降低，与高糖含量相关的等位基因显著增加。这表明，通过与野生种杂交，培育具有更高营养价值、增强生物活性多酚的水果，而不破坏糖酸平衡的和谐，具有遗传潜力。本研究还描述了桃进化研究所需的基因组资源的开发，并为该作物物种的关键农艺性状提供了大规模的特征描述。
