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ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research » Research » Publications at this Location » Publication #299761

Research Project: Reducing the Impact of Diseases on Hop Production

Location: Forage Seed and Cereal Research

Title: Genotyping-by-sequencing of a bi-parental mapping population segregating for downy mildew resistance in hop (Humulus lupulus L.)

item Henning, John
item Gent, David - Dave
item TWOMEY, MEGAN - Oregon State University
item TOWNSEND, MICHAEL - Oregon State University
item PITRA, N - Hopsteiner
item MATTHEWS, PAUL - Hopsteiner

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/11/2015
Publication Date: 12/1/2015
Citation: Henning, J.A., Gent, D.H., Twomey, M.C., Townsend, M.S., Pitra, N.J., Matthews, P.D. 2015. Genotyping-by-sequencing of a bi-parental mapping population segregating for downy mildew resistance in hop (Humulus lupulus L.). Euphytica. 208(3):545-559. doi: 10.1007/s10681-015-1600-3.

Interpretive Summary: Hop (Humulus lupulus L.) downy mildew is a serious disease causing significant production losses in the Pacific Northwest USA. Traditional breeding methods have been unsuccessful in developing varieties with resistance to this disease due to the strong environmental impact on determining phenotype. Breeding methodologies using molecular markers would eliminate environmental impact upon selection and enable genetic improvement for resistance. We undertook a whole genome association study to identify genetic markers associated with resistance to downy mildew infection as observed under multiple environments. Thirty-nine markers were identified under this analysis with 8 markers showing significant association under field conditions in multiple environments. Validation of these markers is currently underway. We hope to develop a marker-based selection tool for hop downy mildew resistance based upon the results of this study.

Technical Abstract: Breeding for resistance to downy mildew in hop has proved difficult presumably because of the highly quantitative nature of genetic control over expression with environment playing a large role in determining phenotype. We hypothesize that eliminating environmental influences over the expression of phenotype will enable the identification and development of molecular selection tools that are both cost effective and accurate. The objective of this study was to utilize multiple environments to ascertain phenotype of downy mildew resistance and identify molecular markers linked to such resistance. A set of 9081 high quality SNP markers were identified through next generation sequencing and used for whole genome association studies looking at downy mildew resistance under field conditions in WA and OR as well as in the greenhouse. Thirty-nine markers (21 from OR, 10 from WA and 8 overlapping) were associated with response to downy mildew infection at p < 1x10-4 under field conditions. Markers associated with response to infection under greenhouse conditions were different from those identified in field experiments suggesting a different mechanism for localized versus systemic infection response. SNP markers showing overlap between field environments as well as those with strong association will be validated using high resolution melting curve analyses.