Similarities and differences in alternative splicing profiles of two grapevine (Vitis vinifera L.) varieties during berry ripening.

Alternative splicing (AS) can produce transcript variants from multiexon genes, with potential roles in proteome diversification and gene expression regulation. Splicing modulation is therefore thought essential for transcriptome reprofiling in response to developmental needs or environmental stimuli. In grapevine, a better understanding of the processes involved in berry development is a major issue for the adaptation of variety selection and viticulture practices to climate warming. Profound changes in gene expression have been shown to occur in developing berries at the transcriptional level, but no detailed study on AS modifications during this period has been published so far. We report here on the regulation of AS in developing berries of two white Vitis vinifera L. varieties, Gewuztraminer (Gw) and Riesling (Ri), with phenological and metabolic specificities. Replicate RNAseq data obtained for four developmental stages, from the green stage, six weeks post-flowering, to mid-ripening, were analyzed in pairwise comparisons between stages and varieties. A total of 305 differential AS (DAS) events were found to affect 258 genes. Among the genes undergoing the most significant splicing variations, a number showed similar stage-associated regulation in the two varieties, some of them being related to putative developmental functions. Moreover, numerous genes exhibited variety-dependent splicing patterns, and the loss or gain of a splice site characterized several variety-specific AS events. The identification of stage-regulated AS events should contribute towards a better knowledge of the process of grape berry ripening. Additionally, the many differential splicing events detected between the two varieties could be explored for explaining phenotypic specificities. The weak overlap observed between splicing and transcriptional modulation identifies AS regulation as an independent way for transcriptome reprofiling during the course of berry ripening.