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.