Location: Grape Genetics Research Unit (GGRU)Title: Lessons from a phenotyping center revealed by the genome-guided mapping of powdery mildew resistance loci
|GADOURY, DAVID - Cornell University - New York|
|FRESNEDO, JONATHAN - Cornell University - New York|
|YANG, SHANSHAN - Cornell University - New York|
|BARBA, PAOLA - Cornell University - New York|
|SUN, QI - Cornell University - New York|
|SEEM, ROBERT - Cornell University - New York|
|NOWOGRODZKI, ANNA - Cornell University - New York|
|KASINATHAN, HEMA - Cornell University - New York|
|REISCH, BRUCE - Cornell University - New York|
Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2016
Publication Date: 10/1/2016
Citation: Cadle Davidson, L.E., Gadoury, D., Fresnedo, J., Yang, S., Barba, P., Sun, Q., Seem, R., Schaub, M.L., Nowogrodzki, A., Kasinathan, H., Ledbetter, C.A., Reisch, B. 2016. Lessons from a phenotyping center revealed by the genome-guided mapping of powdery mildew resistance loci. Phytopathology. 106:1159-1169.
Interpretive Summary: Evaluating disease resistance in the field can produce variable results due to many uncontrollable factors. Therefore, we developed highly controlled methods for evaluating powdery mildew resistance in a service laboratory. We received samples of full-sibling progeny shipped from grape breeding vineyards, and used families with two known resistance genes to determine which methods work best. Genetic analysis identified both resistance gene regions at relatively high-resolution, each having a single candidate resistance gene. The methods described here can guide strategies for breeding resistance to powdery mildews and other pathogens on diverse crops.
Technical Abstract: The genomics era brought unprecedented tools for genetic analysis of host resistance, but careful attention is needed on obtaining accurate and reproducible phenotypes so that genomic results appropriately reflect biology. Phenotyping host resistance by natural infection in the field can produce variable results due to the uncontrolled environment, uneven distribution and genetics of the pathogen, stress-induced disease resistance, and developmentally regulated resistance among other factors. To address these challenges, we developed highly controlled, standardized methodologies for phenotyping powdery mildew resistance in the context of a phenotyping center, receiving samples of up to 140 progeny per F1 family shipped from distant breeding vineyards. We applied these methodologies to F1 families segregating for REN1- or REN2-mediated resistance and validated that some but not all bioassays identified the REN1 or REN2 locus. Quantitative trait locus (QTL) mapping with genotyping-by-sequencing (GBS) maps defined the REN1 and REN2 loci at relatively high-resolution, with an average distance of 94kb between markers. Under each QTL, a single NB-LRR candidate resistance gene was identified in the reference PN40024 genome. The methods described here for centralized resistance phenotyping and high-resolution genetic mapping can inform strategies for breeding resistance to powdery mildews and other pathogens on diverse, highly heterozygous hosts.