Candidate genes and signatures of directional selection on fruit quality traits during apple domestication

PREMISE OF THE STUDY: During plant domestication, traits can be subject to a variety of types of selection, ranging from strong directional selection for traits such as seed or fruit size to diversifying selection for traits like color or flavor. These types of selection interact with other evolutionary processes including genetic bottlenecks and interspecific gene flow to generate different levels of genetic diversity across the genome and at target genes in domesticated lineages, but little is known about the impacts of these processes in perennial fruit crops. METHODS: We used sequence-capture by hybridization to examine patterns of diversity at a suite of candidate domestication and anonymous background genes in domesticated apple (Malus x domestica) in comparison to its wild relatives Malus sieversii and Malus orientalis. KEY RESULTS: We found no change in average diversity at these candidate domestication genes across the three species. However, a subset of the genes did exhibit patterns of very high or very low diversity in M. x domestica compared to its progenitor, M. sieversii. Of the genes with characterized function, the low diversity genes mainly contributed to fruit quality traits like color and flavor, predicted to be under conscious, directional selection relatively late in the domestication process, while the high diversity genes included a variety of functions. CONCLUSIONS: Overall, these results are consistent with predictions based on the likely timing and nature of selection during domestication, and open new avenues for understanding genes with high diversity in a perennial crop compared to its wild relatives.

研究背景：在植物驯化进程中，性状会受到多种类型的选择压作用——从针对种子或果实大小等性状的强定向选择，到针对色泽、风味等性状的多样化选择。这类选择作用会与遗传瓶颈、种间基因流等其他进化过程相互作用，在驯化谱系的全基因组及靶标基因区域催生差异化的遗传多样性水平，但目前学界对多年生果树中这些演化过程的影响仍知之甚少。
研究方法：本研究采用杂交序列捕获技术（sequence-capture by hybridization），以栽培苹果（Malus × domestica）及其野生近缘种新疆野苹果（Malus sieversii）和东方苹果（Malus orientalis）为研究材料，分析了一组候选驯化基因与匿名背景基因的多样性分布模式。
主要研究结果：本研究未在这三个物种的候选驯化基因中观察到平均多样性水平存在显著差异。然而，相较于其野生祖先种新疆野苹果，栽培苹果中有部分基因呈现出极高或极低的多样性特征。在功能已被注释的基因中，低多样性基因主要参与调控色泽、风味等果实品质性状，这类性状被推测在驯化过程后期受到了有意识的定向选择；而高多样性基因则涵盖了多种功能类别。
研究结论：总体而言，本研究结果与基于驯化过程中选择作用的时序与本质所提出的预测相一致，同时为解析多年生作物相较于其野生近缘种中高多样性基因的演化机制与功能开辟了全新的研究路径。