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ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research » Research » Publications at this Location » Publication #311048

Research Project: Reducing the Impact of Diseases on Hop Production

Location: Forage Seed and Cereal Research

Title: Precision QTL mapping of downy mildew resistance in Hop (Humulus lupulus L.)

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

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2015
Publication Date: 4/30/2015
Citation: Henning, J.A., Gent, D.H., Twomey, M., Townsend, M.S., Pitra, N., Matthews, P. 2015. Precision QTL mapping of downy mildew resistance in Hop (Humulus lupulus L.). Euphytica. 202(3):487-498.

Interpretive Summary: Hop downy mildew is difficult to select for and little genetic progress has been made using traditional breeding methods. Molecular markers for downy mildew resistance would help improve selection response and speed up selection. Ninety-three offspring from a mapping population, designed to test downy mildew resistance, were screened for resistance across two states (Oregon and Washington) and in the greenhouse. All offspring and parents were partially sequenced to identify molecular markers for the test. Approximately 3350 markers were placed onto 11 different chromosomes in the correct order and distances between markers. This map was then used to help identify molecular markers linked to downy mildew resistance. This study resulted in the development of the first high-density molecular marker genetic map of hop and identified 22 molecular markers that are linked to resistance to hop downy mildew. These markers will aide in the selection for downy mildew resistance in hop breeding.

Technical Abstract: Hop Downy mildew (DM) is an obligate parasite causing severe losses in hop if not controlled. Resistance to this pathogen is a primary goal for hop breeding programs. The objective of this study was to identify QTLs linked to DM resistance. Next-generation-sequencing was performed on a mapping population segregating for downy mildew resistance levels. Cloned plants were grown in a RCD with three replicates under three environments: greenhouse, field plots in Corvallis, OR, field plots in Yakima, WA. The linkage map of 3341 SNP markers was determined with a 4-stage process using Rqtl, TMAP, Joinmap v 4.0 and MERGEMAP. QTL analysis was performed using JMP Genomics and TASSEL 5.0. SNP markers were distributed across 11 linkage groups (LG) with an average distance between markers of 0.2 cM and total distance of 745.9 cM. QTLs for all three environments were identified using multiple interval mapping (MIM). Overall heritability of the trait across the three environments varied from h2 = 0.38 (GH) to 0.57 (OR). A total of 22 QTLs across 8 LG were identified for DM resistance: Five (5) identified from OR field data, 12 using WA data and five from greenhouse DM data. No epistasis was observed. This study points out the complexity of genetic control of DM resistance in hop and identifies several markers that can be potentially be used to select for DM resistance in hop. It also provides the first linkage map suitable for helping genome sequencing due to the high density of SNP markers.