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An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci

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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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Acknowledgements

We would like to thank Michelle Schaub, Hema Kasinathan, Anna Nowogrodzki, Paige Appleton, Mary Jean Welser and Jackie Lillis for their technical support phenotyping powdery mildew resistance. We thank Steve Luce and Mike Colizzi; Norma Ambriz and Jacob Andresen; and Peter Hemstad from Cornell University, USDA-ARS Parlier, and the University of Minnesota, respectively, for help maintaining the mapping families used in this study. The authors gratefully acknowledge the USDA-NIFA Specialty Crop Research Initiative (award no. 2011-51181-30635) for funding the VitisGen project (http://www.vitisgen.org/) and support for JFR, as well as the National Grape and Wine Initiative for support for SY.

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Authors and Affiliations

  1. Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, 44691, USA

    Jonathan Fresnedo-Ramírez

  2. Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA

    Shanshan Yang

  3. BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA

    Qi Sun

  4. BRC Genomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA

    Linda M. Cote & Peter A. Schweitzer

  5. Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA

    Bruce I. Reisch

  6. USDA-ARS San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA

    Craig A. Ledbetter

  7. Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA

    James J. Luby & Matthew D. Clark

  8. USDA-ARS Grape Genetics Research Unit, Geneva, NY, 14456, USA

    Jason P. Londo & Lance Cadle-Davidson

  9. Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA

    David M. Gadoury

  10. Research Institute for Viticulture and Enology, Department of Breeding, University of Pécs, Pécs, Pázmány Péter str.4, H-7634, Hungary

    Pál Kozma

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  1. Jonathan Fresnedo-Ramírez
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  2. Shanshan Yang
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  3. Qi Sun
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  4. Linda M. Cote
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  5. Peter A. Schweitzer
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  6. Bruce I. Reisch
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  8. James J. Luby
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  9. Matthew D. Clark
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  10. Jason P. Londo
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  11. David M. Gadoury
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  12. Pál Kozma
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  13. Lance Cadle-Davidson
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Contributions

JFR, SY, LCD and QS analyzed the data. LMC and PAS carried out sequencing. LCD, BIR, QS, CAL, DWR, JJL, MDC, JPL, PK and DMG developed germplasm and planned the study. JFR, SY and LCD wrote the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Lance Cadle-Davidson.

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This research does not involve human participants or animals.

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The authors declare that there are no conflicts of interest.

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Mention of trade names or commercial products is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture (USDA). USDA is an equal opportunity provider and employer.

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Fresnedo-Ramírez, J., Yang, S., Sun, Q. et al. An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci. Mol Breeding 37, 145 (2017). https://doi.org/10.1007/s11032-017-0739-0

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