title: Lessons from a Phenotyping Center Revealed by the Genome-Guided Mapping of Powdery Mildew Resistance Loci.
abstract: The genomics era brought unprecedented opportunities for genetic analysis of host resistance, but it came with the challenge that accurate and reproducible phenotypes are needed 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, 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 grapevine progeny per F1family. We applied these methodologies to F1families segregating for REN1- or REN2-mediated resistance and validated that some but not all bioassays identified the REN1 or REN2 locus. A point-intercept method (hyphal transects) to quantify colony density objectively at 8 or 9 days postinoculation proved to be the phenotypic response most reproducibly predicted by these resistance loci. Quantitative trait locus (QTL) mapping with genotyping-by-sequencing maps defined the REN1 and REN2 loci at relatively high resolution. In the reference PN40024 genome under each QTL, nucleotide-binding site-leucine-rich repeat candidate resistance genes were identified-one gene for REN1 and two genes for REN2. 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.
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Lance
authors.initials: L
authors.lastname: Cadle-Davidson
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: David
authors.initials: D
authors.lastname: Gadoury
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Fresnedo-Ramírez
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Yang
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Paola
authors.initials: P
authors.lastname: Barba
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Qi
authors.initials: Q
authors.lastname: Sun
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Demmings
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Robert
authors.initials: R
authors.lastname: Seem
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Michelle
authors.initials: M
authors.lastname: Schaub
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Anna
authors.initials: A
authors.lastname: Nowogrodzki
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Hema
authors.initials: H
authors.lastname: Kasinathan
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Craig
authors.initials: C
authors.lastname: Ledbetter
authors.affiliation: First and ninth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Grape Genetics Research Unit, Geneva, NY 14456; second, fourth, fifth, seventh, eighth, tenth, eleventh, and thirteenth authors: School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva 14456; third and sixth authors: Bioinformatics Facility, Cornell University, Ithaca, NY 14853; and twelfth author: USDA-ARS, Crop Disease, Pests and Genetics Unit, Parlier, CA 93648.
authors.forename: Bruce I
authors.initials: BI
authors.lastname: Reisch
mesh_terms: D001203:Ascomycota / Q000502:physiology*; D001947:Breeding; D002874:Chromosome Mapping / Q000379:methods*; D060467:Disease Resistance / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D060005:Genotyping Techniques; D010641:Phenotype; D010935:Plant Diseases / Q000276:immunology* / Q000382:microbiology; D018515:Plant Leaves / Q000235:genetics / Q000276:immunology / Q000382:microbiology; D040641:Quantitative Trait Loci / Q000235:genetics*; D027843:Vitis / Q000235:genetics* / Q000276:immunology / Q000382:microbiology