Developmental and metabolic plasticity of ripe Sémillon grape berries in response to Botrytis cinerea during noble rot

Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of Sémillon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at véraison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma. Overall design: The experimental design consists of 4 treatments, berries at 3 distinct stages of noble rot and berries without apparent symptoms of infection. From each treatment a total of 4 biological replicates were sequenced with RNAseq, each replicate corresponded to independent pools of 10-15 berries harvested from adjacent grapevines.

贵腐病（noble rot）由灰葡萄孢（Botrytis cinerea）对成熟葡萄浆果的非典型侵染引发。与葡萄串腐病（bunch rot）不同，贵腐病可促使葡萄浆果产生有益变化，并积累提升酿酒葡萄品质的次生代谢产物。研究人员于三年间，在同一商业化葡萄园采集了受贵腐病侵染的赛美蓉（Sémillon）浆果——该品种为白果皮葡萄品种，采集时机与该园用于酿制贵腐葡萄酒（botrytized wine）的果实采收时间完全同步。通过整合转录组学（transcriptomic）与代谢组学（metabolomic）数据，研究人员鉴定出与贵腐病不同侵染阶段相关的代谢通路。灰葡萄孢可诱导与浆果成熟相关的次生代谢通路的已知关键调控因子的表达。通过与红果皮品种转色期（véraison）的转录组数据进行对比，进一步验证了贵腐病进程中灰葡萄孢对与浆果成熟相关的代谢通路的激活作用。贵腐病与浆果成熟过程中一个显著且共通的变化是苯丙烷代谢（phenylpropanoid metabolism）的增强。转录组与代谢物分析均证实，芪类物质（stilbenes）、黄酮类物质（flavonoids）及花青素（anthocyanins）的合成受到诱导上调。针对三年采集的样本开展的酶活测定与靶向基因表达分析证实，核心及旁支苯丙烷通路的激活是贵腐病的一贯标志性特征。最后，本研究证实贵腐病对葡萄代谢的影响在贵腐葡萄酒中仍可被检测到。上述结果表明，尽管植物器官已处于衰老末期，生物胁迫仍可引发植物代谢的大规模重编程；在贵腐病案例中，这种重编程可合成对葡萄浆果风味与香气至关重要的代谢产物。实验设计：本实验共设置4组处理，分别为处于贵腐病3个不同侵染阶段的浆果，以及无明显侵染症状的健康浆果。每组处理均设置4个生物学重复，每个重复均为从相邻葡萄植株上采集的10~15颗浆果的混合样本，所有样本均通过RNA测序（RNAseq）完成测序。