Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

Pascale Maillot,Didier Merdinoglu,Camille Rustenholz,Amandine Velt,Gisèle Butterlin,Eric Duchêne

doi:10.1186/s12870-021-03266-1

Abstract

BackgroundAlternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties.ResultsA total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome.ConclusionsThe analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.

Highlights

Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation
Total differential AS events detected in stage‐ and variety‐comparisons The comparisons between consecutive stages in Gw and Ri, and between the two varieties at each stage, were performed using replicates of RNAseq data obtained from berries harvested at four developmental stages, i.e. green berry, 6 weeks after flowering (S1), hard berry and soft berry at the mid-véraison stage, and mid-ripening (S4)
In order to minimize the amount of the false positives, we selected the AS events supported by a minimum number of 15 reads of the rarest of the two isoforms, and presenting an inclusion level (IL) between 10 and 90%, under at least one condition

Summary

Introduction

Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. A better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Transcriptional and proteomic profiling of developing berries have highlighted extensive changes in gene expression at different developmental stages [4,5,6]. Previous transcriptomic analyses have shown that berry growth and maturation involve important changes in the transcription rate of genes related to primary and secondary metabolism (amino-acids, organic acids, sugars, flavonoids), molecular transport, cell wall modification, and to the synthesis of phytohormones and signaling [4,5,6,7]. The development of this non-climacteric fruit is dependent on auxins and abscisic acid (ABA), which can be partly imported from the seeds to play complementary roles in the control of ripening [8,9,10]. The decrease in the level of auxin concomitant with the increase in the level of ABA in the pericarp, at the end of seed growth, seem to determine the ripening initiation of the fruit [8]

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