Graduate School of Agricultural Science, Kobe University, Nada-ku, Rokkodai 1-1, Kobe, 657-8501, Japan.
Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, Minabe, Higashi-honjo 1416-7, Wakayama, 645-0021, Japan.
Plant J. 2020 Dec;104(6):1551-1567. doi: 10.1111/tpj.15020. Epub 2020 Nov 8.
Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.
在作物的驯化和种群分化过程中，涉及到大量的表型变化。这些进化途径的记录，包括自然/人工选择，可以在当前种群的基因组中找到。然而，这些特征在树木作物中研究较少，树木作物具有特定的特征，例如长世代时间和无性繁殖，保持着高水平的杂合性。我们对李属的 129 个基因组进行了外显子靶向重测序，主要是日本杏（Prunus mume）、杏（Prunus armeniaca）、李（Prunus salicina）和桃（Prunus persica）。基于它们的全基因组单核苷酸多态性，并结合已发表的 79 个中国杏品种的重测序数据，我们推断出日本杏的完整和正在进行的种群分化。遗传分化指标的滑动窗口特征识别出日本杏与相关物种（李和杏）之间的种间片段渗入。这些区域经常表现出强烈的选择清除，形成于日本杏建立或形成亚结构的过程中，这表明日本杏经常从李属的其他物种中引入有利的基因，作为适应性进化。这些发现揭示了在经历了种间基因组片段的自然/人工选择交换的树木作物中，适应性进化的复杂性质。
