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 experiments during cold acclimation and deacclimation and evaluated the impact of exogenous 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. This balancing systems potentially eliminates the long-term negative effect on grapevine growing from using ABA in the field. These findings advance our understanding about the regulation of grapevine physiology during dormancy and supports the potential of applying ABA as a cultural practice to mitigate cold injury in winter and spring.