Integrating systems biology with marker assisted selection to guide the stacking of powdery mildew resistance genes

The long-term goal of this project is to develop grape varieties that possess effective and durable resistance to powdery mildew (PM). Stacking resistance genes from multiple resistant genetic backgrounds and with the least functional redundancy is a proven breeding strategy to improve both durability and level of resistance. This strategy requires (a) the identification of multiple sources of resistance, (b) the functional characterization of the mechanisms of resistance to prioritize optimal genetic combination, and, finally, (c) marker assisted breeding to introduce the selected genes into elite varieties.

In continuation of our multi-year breeding effort, with the awarded budget in the 2017-2018 funding period we have continued the functional characterization of resistance responses activated in presence of known PM resistance loci. Analysis of the data generated by the experiments for the functional characterization of Ren2, Ren3, Ren4, Ren6, Ren7, Run1, Run1.1, Run2.1 and Run2.2 showed differences of gene expression between accessions in response to PM. Deep-learning analysis to predict the best R gene combination for gene stacking by marker assisted breeding is