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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #315688
Title: Application of genotyping-by-sequencing for mapping disease resistance in grapevine breeding families

Author
item Cadle-Davidson, Lance
item PAOLA, BARBA - Cornell University
item SUN, QI - Cornell University
item HYMA, KATIE - Cornell University
item TAKACS, ELIZABETH - Cornell University
item Lillis, Jacquelyn
item Ledbetter, Craig
item Ramming, David
item REISCH, BRUCE - Cornell University

Submitted to: American Phytopathological Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 4/30/2015
Publication Date: 8/1/2015
Citation: Cadle Davidson, L.E., Paola, B., Sun, Q., Hyma, K., Takacs, E., Lillis, J.A., Ledbetter, C.A., Ramming, D.W., Reisch, B. 2015. Application of genotyping-by-sequencing for mapping disease resistance in grapevine breeding families. American Phytopathological Society Annual Meeting. 104(11):152.

Interpretive Summary:

Technical Abstract: Genotyping-by-Sequencing (GBS) is a low-cost, high-throughput, method for genome-wide polymorphism discovery and genotyping adjacent to restriction sites. Since 2010, GBS has been applied for the genotyping of over 12,000 grape breeding lines, with a primary focus on identifying markers predictive of disease resistance. Using standard SNP calling pipelines in TASSEL with the Vitis vinifera ‘PN40024’ reference genome, 20,000 to 50,000 SNPs per family remain after moderately stringent filtering based on genotype quality, allele frequency, and missing data. For linkage mapping, more stringent filters are applied to obtain about 5,000 robust markers, which is sufficient for typical population sizes in grape breeding programs. Qualitative marker-trait associations were identified for resistance to foliar powdery mildew or to Phomopsis cankers on canes. In addition, a quantitative locus underlying powdery mildew susceptibility from V. vinifera ‘Chardonnay’ was identified (Sen1), explaining about 22% of the variation in disease severity. Because disease resistance is often an introgressed trait from wild Vitis into domesticated V. vinifera genetic backgrounds, GBS provides the opportunity to select for resistance loci (and/or against susceptibility) simultaneous to genome-wide selection for V. vinifera alleles to accelerate trait introgression.