Data_Sheet_1_Transcriptomics of Differential Ripening in ‘d’Anjou’ Pear (Pyrus communis L.).ZIP

Estimating maturity in pome fruits is a critical task that directs virtually all postharvest supply chain decisions. This is especially important for European pear (Pyrus communis) cultivars because losses due to spoilage and senescence must be minimized while ensuring proper ripening capacity is achieved (in part by satisfying a fruit chilling requirement). Reliable methods are lacking for accurate estimation of pear fruit maturity, and because ripening is maturity dependent it makes predicting ripening capacity a challenge. In this study of the European pear cultivar ‘d’Anjou’, we sorted fruit at harvest based upon on-tree fruit position to build contrasts of maturity. Our sorting scheme showed clear contrasts of maturity between canopy positions, yet there was substantial overlap in the distribution of values for the index of absorbance difference (IAD), a non-destructive spectroscopic measurement that has been used as a proxy for pome fruit maturity. This presented an opportunity to explore a contrast of maturity that was more subtle than IAD could differentiate, and thus guided our subsequent transcriptome analysis of tissue samples taken at harvest and during storage. Using a novel approach that tests for condition-specific differences of co-expressed genes, we discovered genes with a phased character that mirrored our sorting scheme. The expression patterns of these genes are associated with fruit quality and ripening differences across the experiment. Functional profiles of these co-expressed genes are concordant with previous findings, and also offer new clues, and thus hypotheses, about genes involved in pear fruit quality, maturity, and ripening. This work may lead to new tools for enhanced postharvest management based on activity of gene co-expression modules, rather than individual genes. Further, our results indicate that modules may have utility within specific windows of time during postharvest management of ‘d’Anjou’ pear.

评估仁果类果实（pome fruits）的成熟度，是指导几乎所有采后供应链决策的核心任务。这一点对于西洋梨（Pyrus communis）栽培品种尤为关键：需在保证果实获得正常成熟能力（部分需满足需冷量要求）的同时，最大限度降低因腐烂与衰老带来的损耗。目前尚缺乏能够准确评估梨果成熟度的可靠方法，且由于果实成熟依赖于成熟度，因此预测成熟能力成为一项难题。在本研究针对西洋梨栽培品种‘安茹’（d’Anjou）开展的实验中，我们基于果实挂树位置对采收期的果实进行分级，以构建成熟度梯度差异。我们的分级方案清晰展现了不同冠层位置间的成熟度差异，但吸光差指数（IAD，index of absorbance difference）——一种被用作仁果类果实成熟度替代指标的无损光谱检测指标——的数值分布存在大量重叠。这为我们探索IAD无法区分的细微成熟度差异提供了契机，也为后续针对采收期及贮藏期组织样本的转录组分析指明了方向。我们采用一种检测共表达基因条件特异性差异的创新方法，发现了一批呈现阶段性特征的基因，其表达模式与我们的分级方案相契合。实验中，这些基因的表达模式与果实品质及成熟差异密切相关。这些共表达基因的功能特征谱与既往研究结果一致，同时也为参与梨果品质、成熟度及成熟过程的相关基因提供了全新线索与研究假说。本研究有望基于基因共表达模块（而非单个基因）的表达活性，开发出用于优化采后管理的全新工具。此外，我们的研究结果表明，在‘安茹’西洋梨的采后管理过程中，共表达模块在特定时间窗口内具有应用价值。