Molecular analysis of bunch architecture in grapevine

A loose grape cluster is a desired trait in grapevine breeding, since it reduces the abundance and severity of fungal infections. This is the result of better coverage of the grape bunch by antifungal spraying agents and better air exchange within the grape cluster. The reduced exposure to high humidity acts as a physical barrier against pathogens that need high moisture to proliferate, e.g., Botrytis cinerea. The aim of this study was to identify genes that influence bunch architecture and to deduce molecular markers to accelerate the selection process in grapevine breeding. Bunch compactness was characterized by phenotyping of several subtraits. The experiment comprised plants of a mapping population (‘GF.GA-47-42’ × ‘Villard blanc’) and a set of ‘Pinot noir’ clones with loose as well as compact clusters. The latter were sampled from three different wine-growing regions in Germany. A genetic mapping and quantitative trait locus (QTL) analysis approach based on the trait-segregating population of 150 F₁ individuals yielded many reproducible QTLs distributed along the genome. Some of them were concentrated in specific genomic regions. Further statistical evaluation revealed eight such QTL clusters to be of major relevance and identified flanking molecular markers for marker-assisted selection. In a transcriptional profiling approach, two loosely and two compactly clustered clones of ‘Pinot noir’ were compared. RNA from dormant winter buds and compound buds harvested during the growing period were used in differential gene expression experiments. RNA sequencing was performed at three different stages of development. Candidate genes found in these experiments were selected and re-analyzed in a more comprehensive set of ‘Pinot noir’ clones from the three different German growing locations. Finally, two genes appeared to be differentially expressed between the two groups of clones over the three locations.