Transcriptomic analysis of grapevine in response to ABA application reveals its diverse regulations during cold acclimation and deacclimation. Transcriptomic analysis of grapevine in response to ABA application reveals its diverse regulations during cold acclimation and deacclimation

Abscisic acid (ABA) plays crucial regulatory roles in cold acclimation and deacclimation of grapevine, making it a potential tool to be utilized in vineyards for the acquisition of preferred phenotypes in winter and spring. To understand the function of ABA , we conducted two experiments during cold acclimation and deacclimation and evaluated the impact of exogenous abscisic acid (ABA) on the grapevine transcriptome. RNA-seq data were collected periodically hours or days after ABA treatment. Transcriptomic data were analyzed using principal component analysis (PCA) , hierarchical clustering, unsupervised weighed gene co-expression network analysis (WGCNA), contrast-based differentially expressed genes (DEGs) identification and pre-ranked gene set enrichment analysis (GSEA). Our results suggest that ABA functions differently during cold acclimation and deacclimation by selectively regulating key pathways including auxin/indole acetic acid (IAA) metabolism, galactose metabolism and ribosome biogenesis. We also identified the activation of several apparent negative feedback systems that regulated ABA-induced transcriptomic changes, suggesting the existence of a balancing system in response to excessive ABA. Overall design: In the acclimation experiment, 40 leaf samples were analyzed in a time serie. These samples include eight replicates of control samples at pre-treatment and four replicates of control and ABA-treated samples at 2 h, 4 h, 24 h and 48 h post-treatment. In the deacclimation experiment, 34 bud samples were analyzed in a time serie. These samples include three replicates of control samples at pre-treatment and three replicates of control and ABA-treated samples at 6 h, 12 h, 24 h, 48 h (one more control sample at 48 h) and 72 h post-treatment.

脱落酸（Abscisic acid, ABA）在葡萄的冷驯化与脱冷驯化过程中发挥关键调控作用，使其成为葡萄园冬季与春季获取目标表型的潜在应用工具。为解析ABA的功能，我们在冷驯化与脱冷驯化阶段开展了两组实验，评估外源脱落酸（ABA）对葡萄转录组的影响。在ABA处理后的数小时或数天内定期采集RNA测序（RNA-seq）数据。转录组数据分析采用主成分分析（Principal Component Analysis, PCA）、层级聚类、无监督加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis, WGCNA）、基于对照的差异表达基因（Differentially Expressed Genes, DEGs）鉴定，以及预排名基因集富集分析（Gene Set Enrichment Analysis, GSEA）。本研究结果表明，ABA在冷驯化与脱冷驯化阶段的功能存在显著差异，通过选择性调控生长素/吲哚乙酸（Auxin/Indole Acetic Acid, IAA）代谢、半乳糖代谢以及核糖体生物发生等关键通路实现功能分化。我们还鉴定到若干可调控ABA诱导转录组变化的潜在负反馈系统，提示植物存在响应过量ABA的平衡调控体系。总体实验设计：冷驯化实验共分析40份叶片样本，以时间序列开展分析，该批样本涵盖处理前对照组的8次生物学重复，以及处理后2 h、4 h、24 h、48 h时的对照组与ABA处理组各4次生物学重复。脱冷驯化实验共分析34份芽组织样本，以时间序列开展分析，该批样本涵盖处理前对照组的3次生物学重复，以及处理后6 h、12 h、24 h、48 h（含1份额外对照组样本）与72 h时的对照组与ABA处理组各3次生物学重复。