RNA-seq based analysis of transcriptomic changes associated with ABA-induced postharvest cold tolerance in zucchini fruit

Given that external treatments with ABA had been proved to alleviate chilling injury in the immature zucchini fruit, an RNAseq analysis was conducted to gain insight into the molecular mechanisms that are involved in ABA-induced postharvest cold tolerance. Fruit from the cold sensitive cultivar Sinatra were treated with ABA and then stored for 14 d at 4 ºC. Exocarp samples from control and ABA-treated fruit were taken at 1, 5 and 14 d of cold storage, assessing the transcriptional changes during postharvest storage relative to freshly harvested fruit. The RNAseq analysis produced 229 million high-quality reads from a total of about 23,000 unigenes. Pairwise comparisons of differentially expressed genes (DEGs) in treated and untreated samples at each cold storage time resulted in 852, 793 and 1120 DEGs that were specifically found in the ABA-treated but not in the control fruit at either 1, 5 or 14 d of cold storage. This ABA-specific DEG list was subjected to a GO and KEGG enrichment analysis, as well as to a clusterization of gene expression profiles. This revealed the significance of certain metabolic and signaling pathways participating in ABA-induced postharvest cold tolerance, highlighting the relevance of the Ca2+ signaling pathway, as well as the positive regulation mediated by certain hormones such as ethylene and jasmonate, and the negative regulation mediated by others like auxins and brassinosteroids. A number of DEGs were also found in the ABA-treated fruit that code for transcription factors, as well as for genes involved in oxidative stress response and in membrane and cell wall metabolism. Data indicates that ABA-induced cold tolerance is not mediated by CBF-like genes but involve the up- and down-regulation of several transcription factors in the BZIP, GRAS, MYB, MYC, NAC and ZAT families that are known to participate as positive and negative regulators in the cold defensive response. Moreover, ABA regulates different genes responsible for reducing oxidative stress damage, inducing the biosynthesis of cuticular wax and repressing the biosynthesis of lignin, as well as protecting membrane and cell wall integrity in fruit cells during postharvest cold storage. •ABA induces postharvest cold tolerance in zucchini fruit independently of CBF pathway.•Specific roles of TFs and membrane and cell wall enzymes in postharvest cold response.•Ethylene, jasmonate, auxin and brassinosteroid mediate the ABA-induced cold tolerance.•Signaling genes for Ca2+