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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS, GERMPLASM DEVELOPMENT AND IPM OF HOP
2011 Annual Report


1a.Objectives (from AD-416)
Identify and map molecular markers and/or genes that control the expression of specific economically important traits. Determine the loci and/or closely linked molecular markers associated with plant resistance to downy mildew using QTL analysis. Determine the loci and/or molecular markers associated with the production of beta acids in hop lupulin glands. Identify loci and/or molecular markers associated with short internode trait in hop. Develop germplasm with improved agronomic characteristics and brewing quality with combined resistance to two fungal pathogens using traditional breeding procedures. Develop predictive models for hop downy mildew and powdery mildew linked to management thresholds as components of a systems approach to pest management. Derive and validate algorithms relating weather and inoculum parameters to appearance of and infection risk by Pseudoperonospora humuli. Develop and validate PCR assays and DNA extraction protocols to monitor and detect airborne inoculum of Pseudoperonospora humuli. Develop a predictive model to estimate incidence of powdery mildew in cones and identify management threshold based on economic functions of crop loss and incorrect management decisions. Identify and develop integrated production strategies optimizing the control of both powdery mildew and biological control of arthropod pests.


1b.Approach (from AD-416)
Development and implementation of systems approaches incorporating genetic and IPM methods to reduce production costs and labor inputs. This project uses a systems approach including hop germplasm improvement for production, brewing characteristics and disease resistance through an understanding of genomics, epidemiology, and genetic mechanisms contributing to resistance to downy mildew (Pseudoperonospora humuli) and powdery mildew (Podosphaera macularis).Conventional and molecular breeding techniques will be used, PCR methodologies, GC/MS spectrophotometric, and HPLC techniques. Germplasm will be released for public use. IPM approaches will simultaneously be developed to control these diseases on cultivars with contrasting levels of genetic resistance.


3.Progress Report
Progress was made on all four objectives and their subobjectives, all of which fall under National Program 301, Component 3, Genetic Improvement of Crops. Progress on this project focuses on Problem 3.C, the need for germplasm enhancement and release of improved genetic resources and varieties. We made significant progress by partially sequencing the DNA of two genetically diverse hop accessions (one downy mildew resistant parent and one downy mildew susceptible parent). The DNA sequence information from these two individuals provides a means to select offspring with downy mildew resistance and high alpha acid levels. We also scored a segregating population of dwarf x tall hop cultivars for sex-type (male vs. female), final height (dwarf vs. full height) and level of resistance to downy mildew and powdery mildew. New crosses incorporating multiple sources of resistance to powdery mildew and downy mildew were made in 2010. Complementary studies on integrated pest management focusing on control of downy and powdery mildew were conducted. A model for downy mildew appearance was linked to site-specific weather estimates and forecasts and made publicly available via a web interface. Estimation procedures to interpolate weather data without onsite measurements were linked to risk models for downy mildew and powdery mildew and disseminated by university collaborators through the Internet along with automated text messaging, email, and voice messaging services. Risk factors for development of powdery mildew on hop cones were identified and formalized into a model and validated with new observations. Our model predicted a critical period of juvenile susceptibility to powdery mildew in cones, which was previously unknown. The experiments we conducted in the greenhouse and field using cultivars with varying levels of susceptibility to powdery mildew supported the modeling results, pointing to a rapid decline in cone susceptibility with age. Two fungicide applications targeted to this critical period were as effective at controlling powdery mildew as six regular, prophylactic applications made throughout the season.


4.Accomplishments
1. Molecular markers for downy mildew resistance and alpha acid levels in hops. Alpha acids are the primary compounds in hop that provide bitter flavor to beer. Hop producers in U.S production regions where hop downy mildew is prevalent cannot grow hop varieties that produce high levels of alpha acids because all current high alpha hop varieties are susceptible to this disease. ARS researchers at Corvallis, Oregon, utilized high throughput, next-generation DNA sequencing to identify 5,400 new molecular markers called SNPs that can be used to identify hop germplasm that has resistance to downy mildew and to select for varieties that produce high levels of alpha acids in hop cones. This research provides hop geneticists and breeders almost 10-fold the number of previously published molecular markers that can be used to select for these desirable traits, and it provides sequencing information that will be used in future research to sequence the entire hop genome.

2. Downy mildew diversity and host range. Downy mildew of cucurbits is a re-emerging disease in the U.S. that has caused millions of dollars of damage to cucurbit crops since virulent, fungicide resistant strains appeared during 2004 to 2005. Previous research indicated that the hop and cucurbit (members of the gourd family, i.e., pumpkin, squash and melons) downy mildew pathogens were the same species. Research conducted by scientists at ARS and Oregon State University in Corvallis demonstrated conclusively that populations of the cucurbit and hop pathogens are distinct both genetically and pathogenically in Europe and the U.S., but suggest a possible mixing of populations in Asia near their presumed centers of origin. This accomplishment is significant because it clarifies the relationship, naming, and host range of these organisms, which are critical for devising informed quarantine measures and management strategies.


Review Publications
Henning, J.A., Townsend, M.S., Gent, D.H., Bassil, N.V., Matthews, P., Buck, E., Beaston, R. 2011. QTL Mapping of Powdery Mildew Susceptibility in Hop (Humulus lupulus L). Euphytica. 180:411-420.

Henning, J.A., Townsend, M.S., Matthews, P. 2010. Predicting Offspring Performance in Hop (Humulus lupulus L.) Using AFLP Markers. Journal of American Society of Brewing Chemists. 68(3):125-131.

Pethybridge, S.J., Gent, D.H., Hay, F.S. 2011. Epidemics of ray blight on pyrethrum are linked to seed contamination and overwintering inoculum of Phoma ligulicola var. inoxydabilis. Phytopathology. 101:1112-1121.

Jones, S.J., Pethybridge, S.J., Gent, D.H., Hay, F.S. 2011. Sensitivity of Australian Sclerotinia sclerotiorum isolates from bean fields to boscalid. New Zealand Journal of Crop and Horticultural Science. 1:1-5.

Mitchell, M.N., Ocamb, C.M., Grunwald, N.J., Mancino, L.E., Gent, D.H. 2011. Genetic and pathogenic relatedness of Pseudoperonospora cubensis and P. humuli. Phytopathology. 101:805-818.

Gent, D.H., Farnsworth, J.L., Johnson, D.A. 2011. Spatial analysis and incidence-density relationships for downy mildew on hop. Plant Pathology. DOI:10.1111/j.1365-3059.2011.02491.x.

Jones, S.J., Gent, D.H., Pethybridge, S.J., Hay, F.S. 2011. Spatial characteristics of white mould epidemics and the development of sequential sampling plans in Australian bean fields. Plant Pathology. DOI:10.1111/j.1365-3059.2011-02466.x.

Gent, D.H., Ocamb, C.M., Farnsworth, J.L. 2010. Forecasting and management of hop downy mildew. Plant Disease. 94:425-431.

Gent, D.H., De Wolf, E., Pethybridge, S.J. 2011. Perceptions of risk, risk aversion, and barriers to adoption of decision support systems and integrated pest management: An introduction. Phytopathology. 101:640-643.

Pethybridge, S.J., Hay, F.S., Gent, D.H. 2010. Characterization of the spatiotemporal attributes of Sclerotinia flower blight epidemics in a perennial pyrethrum pathosystem. Plant Disease. 94:1305-1313.

Schwartz, H.F., Gent, D.H., Fichtner, S.M., Khosla, R., Mahaffey, L.A., Camper, M.A., Cranshaw, W.S. 2010. Spatial and temporal distribution of iris yellow spot virus and thrips in Colorado onion fields. Plant Health Progress. doi:10.1094/PHP-2010-0820-01-RS.

Last Modified: 11/25/2014
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