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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #341206
Title: An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci

Author
item FRESNEDO, JONATHAN - Cornell University
item YANG, SHANSHAN - Cornell University
item SUN, QI - Cornell University
item COTE, LINDA - Cornell University
item SCHWEITZER, PETER - Cornell University
item REISCH, BRUCE - Cornell University
item Ledbetter, Craig
item LUBY, JAMES - University Of Minnesota
item CLARK, MATTHEW - University Of Minnesota
item Londo, Jason
item GADOURY, DAVID - Cornell University
item KOZMA, PAL - University Of Pecs
item Cadle-Davidson, Lance

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2017
Publication Date: 12/7/2017
Citation: Fresnedo, J., Yang, S., Sun, Q., Cote, L., Schweitzer, P., Reisch, B., Ledbetter, C.A., Luby, J., Clark, M., Londo, J.P., Gadoury, D., Kozma, P., Cadle Davidson, L.E. 2017. An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci. Molecular Breeding. 37(145). https://doi.org/10.1007/s11032-017-0739-0.
DOI: https://doi.org/10.1007/s11032-017-0739-0

Interpretive Summary: Breeding disease resistant grapes often requires cross-hybridizing resistant wild grapes with commercially desirable grapes. Breeders can use DNA markers to detect the presence of resistance genes in new grapevines resulting from cross-hybridization, and then to identify grapes with multiple disease resistance genes. DNA marker technologies change quickly, which can complicate marker-assisted breeding strategies. Here, amplicon sequencing (AmpSeq) technology was used to integrate several DNA marker technologies, for the simultaneous tracking of five genes for resistance to grape powdery mildew. These AmpSeq markers were successfully applied in diverse grape breeding programs, and provide a high-throughput, cost-effective tool for marker-assisted grape breeding.

Technical 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 (P/A) markers derived from genotyping-by-sequencing and other genotyping platforms, 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. P/A markers for RUN1 and REN4 were validated to predict qualitative resistance phenotypes and corresponded with previous P/A 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 P/A 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.