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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #347559
Title: Single and multiple phenotype QTL analyses of grapevine downy mildew resistance in interspecific grapevines

Author
item DIVILOV, KONSTANTIN - Cornell University
item BARBA, PAOLA - Cornell University
item Cadle-Davidson, Lance
item REISCH, BRUCE - Cornell University

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/26/2018
Publication Date: 2/7/2018
Citation: Divilov, K., Barba, P., Cadle Davidson, L.E., Reisch, B. 2018. Single and multiple phenotype QTL analyses of grapevine downy mildew resistance in interspecific grapevines. Journal of Theoretical and Applied Genetics. 1.

Interpretive Summary: Breeding grapevines for resistance to downy mildew has traditionally focused on gene regions having major effects, which can be overcome by downy mildew evolution. In two grape breeding families, we found several resistance gene regions having small effects. Focusing on two of these regions, we identified genes with greater expression in resistant grapevines, and found that these were not the standard ‘NBS-LRR’ resistance genes. Additionally, we found three traits that related to each other: leaf hair density, hypersensitive response (plant cell death), and downy mildew sporulation. All three traits had moderate to high heritability, suggesting they are good targets for breeding. Thus, breeding for downy mildew resistance genes having small effects is an achievable goal. Combining physical (leaf hairs) and non-physical (hypersensitive response) resistance mechanisms may result in longer-lasting resistance.

Technical Abstract: Breeding grapevines for downy mildew disease resistance has traditionally relied on qualitative gene resistance, which can be overcome by pathogen evolution. Analyzing two interspecific F1 families, both having ancestry derived from Vitis vinifera and wild North American Vitis species, across two years and multiple experiments, we found multiple loci associated with downy mildew sporulation and hypersensitive response in both families using a single phenotype model, and no locus explained more than 17% of the variance for either phenotype. For two loci, we used RNA-Seq to detect differentially transcribed genes and found that the candidate genes at these loci were likely not NBS-LRR genes. Additionally, using a multiple phenotype Bayesian network analysis, we found effects between the leaf trichome density, hypersensitive response, and sporulation phenotypes. Moderate to high heritabilities were found for all three phenotypes, suggesting that selection for downy mildew resistance is an achievable goal by breeding for either physical or non-physical-based resistance mechanisms, with the combination of the two possibly providing durable resistance.