Molecular Breeding

, 37:145 | Cite as

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

  • 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


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.


Marker-assisted breeding Erysiphe necator Uncinula necator Vitis Disease resistance Marker-assisted seedling selection 



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 ( and support for JFR, as well as the National Grape and Wine Initiative for support for SY.

Author contribution statements

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.

Compliance with ethical standards

This research does not involve human participants or animals.

Conflict of interest

The authors declare that there are no conflicts of interest.

Supplementary material

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11032_2017_739_MOESM2_ESM.txt (4 kb)
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Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2017

Authors and Affiliations

  • Jonathan Fresnedo-Ramírez
    • 1
  • Shanshan Yang
    • 2
  • Qi Sun
    • 3
  • Linda M. Cote
    • 4
  • Peter A. Schweitzer
    • 4
  • Bruce I. Reisch
    • 5
  • Craig A. Ledbetter
    • 6
  • James J. Luby
    • 7
  • Matthew D. Clark
    • 7
  • Jason P. Londo
    • 8
  • David M. Gadoury
    • 9
  • Pál Kozma
    • 10
  • Lance Cadle-Davidson
    • 8
  1. 1.Department of Horticulture and Crop ScienceThe Ohio State University/OARDCWoosterUSA
  2. 2.Virginia G. Piper Center for Personalized Diagnostics, Biodesign InstituteArizona State UniversityTempeUSA
  3. 3.BRC Bioinformatics Facility, Institute of BiotechnologyCornell UniversityIthacaUSA
  4. 4.BRC Genomics Facility, Institute of BiotechnologyCornell UniversityIthacaUSA
  5. 5.Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaUSA
  6. 6.USDA-ARS San Joaquin Valley Agricultural Sciences CenterParlierUSA
  7. 7.Department of Horticultural ScienceUniversity of MinnesotaSt. PaulUSA
  8. 8.USDA-ARS Grape Genetics Research UnitGenevaUSA
  9. 9.Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant ScienceCornell UniversityGenevaUSA
  10. 10.Research Institute for Viticulture and Enology, Department of BreedingUniversity of PécsPécsHungary

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