Comparative transcriptomics and metabolomics in Vitis vinifera cv. Malvasia and Vitis rupestris cv. Du Lot cultured cells provide insights in possible innate resistance against pathogens

Vitis vinifera is one of the most extensively cultivated crops with worldwide economic importance, being the only grapevine species used for the production of wine.The V. vinifera varieties are susceptible to various pathogens responsible for severe crop losses. For these reasons, the cultivation of pathogen-resistant grapevine is one of the most straightforward strategies to reduce the impact of plant infection. Despite research efforts in understanding pathogen susceptibility/resistance in grapevine, the mechanisms that regulate these processes remain unclear. In an attempt to identify the molecular and metabolic mechanisms associated with putative different susceptibility to pathogens, a transcriptome and metabolome profile were carried out in cultured cells of V. vinifera cv. Malvasia and V. rupetris cv. du Lot.Comparative transcriptomic analysis revealed a higher enrichment of genes involved in biosynthesis of cell wall proteins, PR protein, ROS activation, phenylpropanoid pathway, TIR-NBS-LRR proteins and WRKY transcription factors in V. rupestris compared to V. vinifera. 1H-NMR based metabolomic analysis highlighted that leucine, isoleucine, valine, threonine, alanine, gamma-aminobutyric acid (GABA), glutamine, phenylalanine and pyruvate significantly increased in V. rupestris compared to V. vinifera. Conversely, glucose, sucrose, and fumarate significantly decreased in V. rupestris compared to V. vinifera. Our findings reveal distinct pre-constitutive defense systems in two species consisting in an up-regulation of genes and primary metabolites involved in plant defense responses. These responses could be constitutively activated in V. rupestris opening new perspectives for sustainable viticulture through improved breeding programs. The number of up-regulated loci as well as the fold change values were greater in V. rupestris than V. vinifera.

葡萄（Vitis vinifera）是全球种植范围最广、经济价值举足轻重的栽培作物之一，同时也是唯一可用于酿酒的葡萄品种。该种葡萄的多数栽培品种易受多种病原菌侵染，进而引发严重的作物减产。基于上述背景，培育抗病葡萄品种是减轻植物病害危害最直接有效的策略之一。尽管学界已针对葡萄的病原菌易感性与抗病性开展了大量研究，但调控这些过程的分子与代谢机制仍未明确。
为解析与病原菌潜在差异易感性相关的分子与代谢机制，本研究针对两个葡萄品种的培养细胞开展了转录组与代谢组谱分析，供试材料分别为葡萄（Vitis vinifera）cv. Malvasia与河岸葡萄（Vitis rupestris）cv. du Lot。
比较转录组分析结果显示，相较于葡萄（Vitis vinifera），河岸葡萄（Vitis rupestris）中参与细胞壁蛋白合成、病程相关蛋白（Pathogenesis-related protein, PR）表达、活性氧（Reactive Oxygen Species, ROS）激活、苯丙烷途径、TIR-NBS-LRR蛋白调控以及WRKY转录因子调控的基因富集程度显著更高。基于核磁共振氢谱（Proton Nuclear Magnetic Resonance, ¹H-NMR）的代谢组分析显示，相较于葡萄（Vitis vinifera），河岸葡萄（Vitis rupestris）中亮氨酸、异亮氨酸、缬氨酸、苏氨酸、丙氨酸、γ-氨基丁酸（gamma-aminobutyric acid, GABA）、谷氨酰胺、苯丙氨酸及丙酮酸的含量显著升高；与之相反，该物种中葡萄糖、蔗糖及延胡索酸的含量显著降低。
本研究结果揭示了两个葡萄物种间存在截然不同的组成型固有防御系统，其核心特征为参与植物防御反应的基因与初级代谢产物的上调表达。河岸葡萄中的这类防御反应可被组成型激活，这为通过优化育种程序实现可持续葡萄栽培提供了全新的研究视角。此外，河岸葡萄中上调表达的基因座数量及其表达倍数变化值均显著高于葡萄（Vitis vinifera）。