Tornielli Giovanni Battista, Sandri Marco, Fasoli Marianna, Amato Alessandra, Pezzotti Mario, Zuccolotto Paola, Zenoni Sara
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
Big & Open Data Innovation Laboratory, University of Brescia, C.da S. Chiara 50, 25122 Brescia, Italy.
Hortic Res. 2023 Mar 15;10(5):uhad048. doi: 10.1093/hr/uhad048. eCollection 2023 May.
Fruit growth and development consist of a continuous succession of physical, biochemical, and physiological changes driven by a genetic program that dynamically responds to environmental cues. Establishing recognizable stages over the whole fruit lifetime represents a fundamental requirement for research and fruit crop cultivation. This is especially relevant in perennial crops like grapevine ( L.) to scale the development of its fruit across genotypes and growing conditions. In this work, molecular-based information from several grape berry transcriptomic datasets was exploited to build a molecular phenology scale (MPhS) and to map the ontogenic development of the fruit. The proposed statistical pipeline consisted of an unsupervised learning procedure yielding an innovative combination of semiparametric, smoothing, and dimensionality reduction tools. The transcriptomic distance between fruit samples was precisely quantified by means of the MPhS that also enabled to highlight the complex dynamics of the transcriptional program over berry development through the calculation of the rate of variation of MPhS stages by time. The MPhS allowed the alignment of time-series fruit samples proving to be a complementary method for mapping the progression of grape berry development with higher detail compared to classic time- or phenotype-based approaches.
果实的生长和发育由一系列连续的物理、生化和生理变化组成，这些变化由一个遗传程序驱动，该程序能动态响应环境信号。在果实的整个生命周期中确定可识别的阶段是果实研究和作物栽培的一项基本要求。这在多年生作物如葡萄（Vitis vinifera L.）中尤为重要，以便在不同基因型和生长条件下衡量其果实的发育情况。在这项工作中，利用来自多个葡萄浆果转录组数据集的分子信息构建了一个分子物候量表（MPhS），并绘制了果实的个体发育过程。所提出的统计流程包括一个无监督学习程序，产生了半参数、平滑和降维工具的创新组合。通过MPhS精确量化了果实样本之间的转录组距离，该量表还能够通过计算MPhS阶段随时间的变化率，突出转录程序在浆果发育过程中的复杂动态。MPhS允许对时间序列果实样本进行比对，事实证明，与基于经典时间或表型的方法相比，它是一种更详细地绘制葡萄浆果发育进程的补充方法。
