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Additional file 5: Figure S4. Genetic maps marker order and distances compared to marker physical position on grape reference genome.

Additional file 5. Genes regulated between consecutive stages of berry development at both transcriptional and splicing level. Gene IDs correspond to the VCost.v3 genome annotation.

Additional file 3: Figure S2. Pairwise correlations between phenotypic data recorded for the cross populations during the E. necator infections.

Additional file 2: Figure S1. Distributions of the phenotypic data related to E. necator resistance of the cross populations.

Additional file 3. Functional classification of the genes affected by differential AS in stage and variety comparisons. The classification was performed using the PANTHER GO-slim tool ( www.pantherdb.org/ ). GO terms are split in the three usual categories a Biological Process (BP). b Molecular Function (MF). c Cellular Component (CC). The percent of genes belonging to each category is given on the x-axis.

Additional file 4: Figure S3. Parental genetic maps.

Additional file 1. Total number of AS events and DAS events in comparisons between consecutive stages or varieties. Retained events were supported by a minimum number of 15 reads of the rarest isoform under at least one condition, and a minimum inclusion level (IL) of 10%.

Additional file 4. Differential isoform ratios between Gw and Ri, for fifteen AS events regulated between véraison and mid-ripening in only one variety.