An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci |
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| Authors: | Jonathan Fresnedo-Ramírez Shanshan Yang Qi Sun Linda M. Cote Peter A. Schweitzer Bruce I. Reisch Craig A. Ledbetter James J. Luby Matthew D. Clark Jason P. Londo David M. Gadoury Pál Kozma Lance Cadle-Davidson |
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| Affiliation: | 1.Department of Horticulture and Crop Science,The Ohio State University/OARDC,Wooster,USA;2.Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute,Arizona State University,Tempe,USA;3.BRC Bioinformatics Facility, Institute of Biotechnology,Cornell University,Ithaca,USA;4.BRC Genomics Facility, Institute of Biotechnology,Cornell University,Ithaca,USA;5.Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station,Cornell University,Geneva,USA;6.USDA-ARS San Joaquin Valley Agricultural Sciences Center,Parlier,USA;7.Department of Horticultural Science,University of Minnesota,St. Paul,USA;8.USDA-ARS Grape Genetics Research Unit,Geneva,USA;9.Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science,Cornell University,Geneva,USA;10.Research Institute for Viticulture and Enology, Department of Breeding,University of Pécs,Pécs,Hungary |
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| Abstract: | ![]()
Resistance breeding often requires the introgression and tracking of resistance loci from wild species into domesticated backgrounds, typically with the goal of pyramiding multiple resistance genes, to provide durable disease resistance to breeding selections and ultimately cultivars. While molecular markers are commonly used to facilitate these efforts, high genetic diversity and divergent marker technologies can complicate marker-assisted breeding strategies. Here, amplicon sequencing (AmpSeq) was used to integrate SNP markers with dominant presence/absence markers derived from genotyping-by-sequencing and other genotyping technologies, for the simultaneous tracking of five loci for resistance to grapevine powdery mildew. SNP haploblocks defined the loci for REN1, REN2 and REN3, which confer quantitative resistance phenotypes that are challenging to measure via field ratings of natural infections. Presence/absence markers for RUN1 and REN4 were validated to predict qualitative resistance phenotypes and corresponded with previous presence/absence fluorescent electrophoretic assays. Thus, 37 AmpSeq-derived markers were identified for the five loci, and markers for REN1, REN2, REN4 and RUN1 were used for multiplexed screening and selection within diverse breeding germplasm. Poor transferability of SNP markers indicated imperfect marker-trait association in some families. Together, AmpSeq SNP haploblocks and presence/absence markers provide a high-throughput, cost-effective tool to integrate divergent technologies for marker-assisted selection and genetic analysis of introgressed disease resistance loci in grapevine. |
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