RNA-seq and WGBS analyses during fruit ripening and in response to ABA in sweet cherry (Prunus avium) reveal genetic and epigenetic modulation of auxin and cytokinin genes

Abscisic acid (ABA) is a plant hormone that plays a key role in the ripening process of non-climacteric fruits, triggering pigment production, fruit softening, and sugar accumulation. Transcriptional studies show that ABA modifies the expression of several ripening-related genes, but epigenetic effects of ABA during this process are lacking. Therefore, this work aimed to perform transcriptomic and DNA methylation analyses of fruit samples treated with ABA during the fruit ripening process in the non-climacteric sweet cherry model. RNA-seq analyses revealed an overrepresentation of transcripts annotated in functional categories related to ABA response, secondary metabolism, and sugar synthesis during fruit ripening. In contrast, Whole Genome Bisulfite Sequencing (WGBS) analyses revealed DNA hypomethylation in the 5′UTR region of genes related to carotene catabolism. Transcriptional and epigenetic regulation of genes encoding xyloglucan enzymes, associated with cell wall modifications, were also detected. ABA treatment enhanced fruit color development and the accumulation of ripening markers, including carotenoids and several anthocyanins. Gene Ontology analysis in the RNA-seq of ABA-treated fruits revealed expression variations in genes encoding members of the Aux/IAA and ARF families. In the WGBS analysis, genes encoding enzymes for cytokinin biosynthesis had differential DNA methylation after the ABA treatment. Our work identified ABA-modulated factors at the genetic and epigenetic levels, suggesting complex hormone networks controlling non-climacteric sweet cherry fruit ripening