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

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


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.

Original languageEnglish (US)
Article number145
JournalMolecular Breeding
Issue number12
StatePublished - Dec 1 2017

Bibliographical note

Funding Information:
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. and support for JFR, as well as the National Grape and Wine Initiative for support for SY.

Publisher Copyright:
© 2017, This is a U.S. government work.


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


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