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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS, GERMPLASM DEVELOPMENT AND IPM OF HOP

Location: Forage Seed and Cereal Research

2012 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 Integrated Pest Management (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, Polymerase Chain Reaction (PCR) methodologies, Gas Chromatography/Mass spectrometry (GC)/(MS) spectrophotometric, and High Pressure Liquid Chromatography (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:
Powdery mildew and downy mildew diseases continue to impact U.S. hop production resulting in substantial input costs and crop losses for producers. In addition to continued focus upon development of resistance to downy mildew, the U.S. hop industry requires renewed focus on powdery mildew biology and management due to development of new races capable of overcoming previously resistant varieties. Due to the scope of problems to be solved, a systems approach is required that integrates genetics, plant pathology, and integrated pest management approaches to ensure the continued economic sustainability of U.S. agriculture. Focused development of disease resistant varieties would be greatly accelerated by the identification and application of molecular markers associated with disease resistance. In support of this effort, partial genome sequencing of individual offspring (~100) and parents from a downy mildew resistance mapping population was completed and these same offspring were screened for downy mildew resistance under greenhouse conditions. The second year of screening this same population for downy mildew resistance under field conditions was completed in Washington and Oregon. DNA sequence differences among these offspring were analyzed to determine whether specific sequences correlated with disease resistance in order to identify genetic markers linked to downy mildew resistance. Sequence data from approximately 1500 genetic markers were deposited with National Center for Bioinformatics Information for public dissemination. Approximately 150 out of 300 genetic markers have been validated and are being added to a previously developed genetic map of powdery mildew resistance to identify the most effective genetic indicators of resistance to this disease. New crosses incorporating multiple sources of resistance to powdery mildew and downy mildew were made in 2011. The offspring from crosses were screened for powdery mildew resistance and the most resistant selections transplanted to the field. Crosses made in 2010 were screened for powdery mildew resistance and superior selections were transplanted into growers’ fields for observations under regular farming regimes. To ensure successful long-term production of disease resistant varieties, complementary studies on integrated pest management focusing on control of downy and powdery mildew were continued. Predictive models for powdery mildew and downy mildew were evaluated using weather data estimated from nearby weather stations, a so-called “virtual weather station”. Both predictive models were found to be insensitive to estimation errors in virtual weather stations, which will free stakeholders from the burden of recording weather data. Spatialized risk maps for powdery mildew are being evaluated and disseminated to stakeholders via a web interface for beta testing.


4.Accomplishments
1. Powdery mildew damage function and management. Powdery mildew of hop became epidemic into the Pacific Northwestern United States in 1997, with estimated economic impacts at over $15,000,000 annually. Optimal management of the disease is constrained by lack of means to predict when powdery mildew will occur at damaging levels and basic information on when the crop is susceptible. Research conducted by ARS scientists at Corvallis, Oregon, and Washington State University quantified the relationships between powdery mildew severity, yield, and on crop quality factors, and identified periods of juvenile susceptibility to the disease. This accomplishment is significant because it defines periods of greatest susceptibility of the host to the disease and thus defines when control measures are of greatest importance to maximize yield and quality. Management tactics to reduce crop loss and rationalize use of purchased inputs have been identified which will enhance the economic sustainability and security of production of this crop.

2. Development of high throughput molecular markers for downy mildew resistance. Hop producers in United States' production regions where hop downy mildew is prevalent cannot grow hop varieties expressing high levels of alpha acids due to the susceptibility of all current high alpha hop varieties to this disease. Selection for resistance to downy mildew has proven difficult due to the highly quantitative nature of genetic resistance to this pathogen. ARS researchers at Corvallis, Oregon, led an international effort with scientists from Germany, Slovenia, Czech Republic, New Zealand and Australia to utilize high throughput, next-generation DNA sequencing to identify genetic markers that are linked to downy mildew resistance. Sequencing data will be used to develop a map of the hop genome saturated with over 10,000 markers. This research provides geneticists and breeders almost 100-fold the number of previously published sequences that can be used to identify markers linked to downy mildew resistance, and it provides sequencing information crucial to mapping the entire hop genome.


Review Publications
Kropf, S.M., Twomey, M.C., Woods, J.L., Gent, D.H., Putnam, M.L., Serdani, M. 2012. Sclerotinia wilt of Hop (Humulus lupulus) caused by Sclerotinia sclerotiorum in the Pacific Northwest U.S. Plant Disease. 96: 583.

Last Modified: 8/27/2014
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