Lyndon Porter, Research Plant Pathologist

Objectives:

Objective 1: Develop molecular markers tightly linked with economically important disease resistance traits and use them to develop bean germplasm with enhanced levels of disease resistance.

Subobjective 1A: Develop molecular markers with application for marker-assisted selection (MAS) of disease resistance to Sclerotinia white mold, halo blight, and bean rust.

Subobjective 1B: Develop bean germplasm with enhanced resistance to Sclerotinia white mold, common bacterial blight, and bean anthracnose using MAS in combination with traditional breeding approaches.

Objective 2: Develop improved disease management practices for several soilborne diseases of edible legumes.

Subobjective 2A: Characterize specific aspects of the epidemiology and population structure of Aphanomyces euteiches, Fusarium solani, and Sclerotinia sclerotiorum on bean, chickpea, lentil and pea using molecular and traditional approaches to improve disease management.

Subobjective 2B: Identify novel sources of resistance and improve resistance of pea and lentil germplasm to soilborne diseases.

Potential Benefits:

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Inheritance of disease resistance, gene mapping, and tightly linked markers with utility for MAS of disease resistance will provide breeders with a knowledge base and new tools useful for facilitating development of enhanced bean germplasm and cultivars. Enhanced bean germplasm released by this program will contribute to the development of cultivars with improved disease resistance. Cultivars with improved disease resistance will increase income to growers through improved yield and quality, enhance overall effectiveness of integrated disease management strategies, and reduce dependency on expensive chemicals.

Improved knowledge of the ecology, epidemiology and population structure of soilborne plant pathogens will form the basis for development of novel methods to manage plant diseases of edible legumes. This will result in increased production efficiency, while preserving the environment and promoting sustainability.

Anticipated Products:

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New marker-assisted selection assays, technologies and expertise for implementing MAS for multiple disease resistance into traditional plant breeding programs will be developed. Germplasm with resistance genes in adapted phenotypes for rapid deployment into elite breeding lines and cultivars to combat emerging (anthracnose, halo blight) and entrenched (white mold, rust, common bacterial blight) disease problems will be developed. Positional mapping, QTL discovery, and visualization of gene clusters will be generated for important disease resistance traits in bean.

A better understanding of the ecology, epidemiology and population genetics of soilborne pathogens of edible legumes will lay the foundation for improved disease management strategies. Microsatellite and other molecular markers for studying systematics and population genetics of Aphanomyces and Sclerotinia pathogens will be developed and/or applied. Pea and lentil accessions and breeding lines with resistance to white mold, Fusarium root rot and other soilborne diseases will be identified.

Collaborations:

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Subobjective 1A: (within ARS) Dr. Talo Pastor-Corrales, USDA-ARS, Beltsville, MD.

(external to ARS) Dr. Ken Grafton, North Dakota State University, Fargo, ND; Dr. Ron Riley, Syngenta Seed, Inc., Nampa, ID; Dr. Deidre Fourie, Agriculture Research Center, Grain Crops Institute, Potchefstroom, South Africa.

Subobjective 1B: (within ARS) None. (external to ARS) Dr. Ron Riley, Syngenta Seed, Inc., Nampa, ID; Dr. James D. Kelly, Michigan State University, East Lansing, MI; Dr. Shree Singh, University of Idaho, Kimberly, ID.

Subobjective 2A: (within ARS) Dr. Weidong Chen, USDA-ARS, Pullman, WA. Dr. George Vandemark, USDA-ARS, Prosser, WA. (External to ARS) Dr. Craig R. Grau, University of Wisconsin, Madison; Dr. Linda M. Kohn, University of Toronto, Toronto, Canada.

Subobjective 2B: (within ARS) Drs. Weidong Chen, Kevin McPhee, Fred Muehlbauer, USDA-ARS, Pullman, WA. Dr. Tim Paulitz, USDA-ARS, Pullman. (External to ARS) None.

Customers:

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Public and private plant breeders and geneticists, commercial seed companies, extension agents, and growers will benefit from new germplasm/cultivars with enhanced disease resistance, new markers and assays useful for MAS, QTL discovery and improved genetic maps, new insights into epidemiology and population structure of diseases, new/improved molecular markers for pathogen detection, as well as improved disease management strategies. The general public will benefit from a more sustainable production of a healthy and affordable food product, reduced chemical use, and improved food quality that will result from improved resistance and disease management strategies contributed by this program

MAJOR RESEARCH ACCOMPLISHMENTS

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• White Mold Resistance in Common Bean: Sclerotinia white mold is the most important disease limiting common bean production in the U.S. Genetic resistance as a component of integrated management strategies for control of white mold in bean is generally lacking because resistance is extremely complex and difficult to breed for. We identified, characterized, and mapped three genes from two exotic sources that combat white mold disease of common bean. Linked markers have been refined to facilitate marker-assisted selection of the genes across laboratories. Detection of resistance genes via pathogen screening is unpredictable because adequate and uniform disease epidemics rarely occur, and greenhouse screening does not always correlate well with field reaction. Thus, development of white mold resistant cultivars is an arduous, laborious, and time-consuming enterprise. Marker-assisted selection for the three genes identified and tagged by Dr. Miklas will expedite development of dry bean and snap bean cultivars with improved levels of resistance to white mold. Breeders will be to develop resistant cultivars in 4 to 5 years versus 8 to 10 years time using only traditional breeding methods. The availability of white mold resistant cultivars will increase the effectiveness of integrated disease control strategies saving growers millions of dollars via improved yields and reduced input costs.

• Pea - Integrated Pest Management: Common root rot is the most devastating disease of pea in the U.S. and world-wide. A new recommendation for control of the disease was developed on a cooperative (Oregon State University) integrated pest management study at two field sites in Oregon. Better control of common root rot offered by our recommendation will save growers and processors millions of dollars by minimizing yield losses and improving quality.

We have combined an array of minor genes for virtually every economically important soilborne fungal pathogen of peas together with resistance to several viruses and fungal pathogens of the foliage. Specifically, lines with resistance or tolerance to Fusarium and Aphanomyces root rot, Fusarium wilt races 1, 2, 3, and 6, powdery mildew, pea seedborne mosaic virus and pea enation mosaic virus. The breeding lines of peas released from this program have become the mainstay of pea variety development by seed companies in the U.S. and overseas.

Screening techniques have been developed to evaluate pea cultivars, germplasm and plant introduction accessions for resistance to several soilborne pathogens. Thirty-three enhanced pea germplasm lines have been officially released from this program since 1971.

• Techniques to detect a severe root rot pathogen of peas in growers’ fields and seedling pea plants were developed and used to determine that this pathogen (Aphanomyces euteiches) is widespread in northern Idaho, Oregon, and Washington.

• Bean Improvement: New bean market classes are needed to expand export markets and enhance global competitiveness of the U.S. dry edible bean industry. Germplasm introduced from the Center for Tropical Agriculture, in Cali, Colombia, representing bean market classes grown and consumed in Latin America and elsewhere were evaluated for adaptation to U.S. production by ARS (Prosser, WA) in collaboration with Colorado State University and University of Idaho. Adapted germplasm identified in at least nine market classes will provide breeders with a starting point from which to develop cultivars suitable for U.S. production of new Latin American market types. It is envisioned that most of the beans would be exported, however, domestic markets could emerge in the future. In addition, the foreign germplasm will help breeders to improve traditional market classes grown here by providing novel genes for improving disease resistance and other traits.

Our cooperative studies with ARS, East Lansing, MI, and Washington State University resulted in the release of a small red dry edible bean cultivar ‘LeBaron’ which is virus resistant and has excellent canning quality. This cultivar provides bean growers an opportunity and short season r for double cropping after peas or late planting due to spring rains.

• Prosser ARS Unit leads regional cooperative efforts on release of dry bean germplasms resistant to bacterial blight. Five years of research and plant breeding efforts led by Dr. Phil Miklas of the ARS Vegetable and Forage Crop Research Unit in Prosser, WA, resulted in the August through October 2000 release of 14 dry bean germplasm lines with enhanced disease resistance. These lines include one black, one great northern, one cranberry, four kidney, four navy, and three pinto beans. The cooperating institutions in this research included the ARS Tropical Agricultural Research Station, in Mayaguez, PR; the ARS Microbiology and Plant Pathology Lab in Beltsville, MD; and the Colorado, Michigan, Nebraska, North Dakota, and Washington Agricultural Experiment Stations. These lines address the immediate need expressed by private and public breeders for dry beans with improved resistance to common bacterial blight, a disease of increasing importance in the major bean production regions of the United States. This work is a fine example of ARS leadership and effectiveness of excellent cooperation between the ARS units and land grant universities in achieving a common goal of assisting the industry to overcome the negative impacts of this complex disease problem.

• A virus disease epidemic of snap bean occurring in the Great Lakes region of the United States: A virus epidemic of snap bean in the Great Lakes region of the US and Ontario, Canada, occurred in the 2001 growing season that resulted in typical losses of 60-90% and up to 100% in many fields. We identified seven different viruses that were associated with pod necrosis and twisting, mosaic symptoms, leaf blistering, severe stunting and plant death. Many samples were infected with multiple viruses. For example fifteen strains of alfalfa mosaic virus were isolated from two individual bean plants. We were able to demonstrate by ELISA and polymerase chain reaction that in samples collected in Wisconsin, plants were infected with cucumber mosaic virus (90%), alfalfa mosaic (AMV) (82%), tobacco streak (24%), viruses belonging to the potyvirus group (30%), white clover mosaic (15%), and clover yellow mosaic virus (12%).

• Bean research at Prosser has made valuable contributions to the bean industry by improving our understanding of the biology and pathogenic variability of bean common mosaic virus, curly top virus, Sclerotinia white mold, and the root rot complex of pathogens plaguing bean production across the U.S.

• Numerous beans with resistance to virus and root rot pathogens have been released, and some cultivars continue to dominate the pink and small red bean acreage (70,000 acres) across the U.S. today. Othello pinto bean (released by USDA-ARS at Prosser) is grown on about 30% of the acreage in the Pacific Northwest and has generated 68 million dollars revenue in the state of Idaho alone in the last 5 years. Other successful cultivar releases include Viva and Roza pinks, NW-63 and Rufus small reds, Nodak and NW 410 pintos, and Kardinal and Kamiakin light red kidneys.

• Two recent cultivar releases Burke pinto (1998) and LeBaron small red (2000) show promise for improving bean yields in the Pacific Northwest. LeBaron was specifically developed with early maturity for use in double cropping systems following peas and other early season vegetables.

• Potential sources of novel resistance to white mold were identified recently in a germplasm core collection representing bean accessions from Central and South America. Crosses have been initiated to transfer the white mold resistance from the more promising Plant Introductions (PI accessions) into U.S. dry and snap bean market types. This research was the first to document for any crop the use of core collections to target ranges of useful germplasm in a base collection.

• Interspecific crosses were used to transfer resistance fromscarlet runner bean to black, red, and pink dry bean lines that were officially released as sources of white mold resistance. The black bean I9365-31 yields extremely well in addition to having exceptional physiological resistance to white mold. Genetic populations for studying the inheritance of this source of white mold resistance have been developed.

• Genetic and genomic analysis of white mold tolerance in accession PI 163120 revealed that resistance was conditioned by a combination of mechanisms, physiological resistance on linkage group 7 and avoidance on linkage group 1. The gene for physiological resistance was expressed in both field and greenhouse disease screening trials. Currently we are searching for markers linked with these genes to facilitate future breeding efforts for the improvement of white mold resistance in bean.

• We identified and synthesized DNA markers that are instrumental in accelerating the development of bean golden mosaic resistant varieties. The markers are very closely associated with the most effective resistance genes available to date for combating the disease. Private snap bean breeders are using the markers to quickly obtain snap bean varieties with bean golden mosaic resistance for southern Floria production. The International Center for Tropical Agriculture (CIAT), Cali, Colombia currently uses the markers for developing varieties of dry edible beans for Central America, Brazil, Mexico, and the Caribbean Basin, and in the course of a year have screened 8000 plants and 600 advanced lines for presence of the markers.

• A DNA marker diagnostic for the bc-12 gene conditioning resistance to bean common mosaic virus was developed. Selection for this marker obviates the need for test crosses to obtain valuable combinations of genes for durable and broad spectrum resistance to a wide array of virus strains.

• We described a new isolate of bean common mosaic necrosis virus and its interaction with the bc-3 gene for resistance. It is the most virulent strain of BCMNV found to date, as it was observed to overcome the most effective resistance gene (bc-3) in certain genetic backgrounds. Results direct breeders to proceed with caution while deploying the bc-3 gene in their programs.

• We have demonstrated the utility of marker-assisted selection for combining genes conferring quantitative resistance to common bacterial blight. This disease is a major production constraint in the Midwest and High Plains regions. This research has led directly to the development and planned release of germplasm lines with exceptional resistance to common bacterial blight for all the major U.S. dry and snap bean market classes. This work also represents the first actual applied use of markers to breed for a complex inherited disease resistance trait in bean.

• We identified new dry edible bean market classes with potential for U.S. production. Several dozen market classes of dry edible bean are grown and consumed in tropical and sub-tropical Latin America and elsewhere. Over the last few years, promising breeding lines and germplasm representing a wide range of market classes have been introduced from the International Center for Tropical Agriculture (CIAT), Cali, Colombia. With the primary objective of establishing new export markets in mind, these lines will provide breeders with a starting point from which to develop cultivars suitable for U.S. production of new Latin American dry bean market types.

• We developed a genetic linkage map of common bean which locates genes conditioning resistance to two viral, three fungal, and one bacterial pathogen. Genomic relationships among the resistance traits indicate that recombination between disease resistance loci on two separate linkage groups would be required to obtain lines with multiple disease resistance against rust, common bacterial blight, ashy stem blight, and bean golden mosaic virus. Thus, breeding multiple disease resistant cultivars is complicated initially by these trans-linkages, and subsequently simplified once the linked genes are recombined in cis-orientation.

• Conducted the first in-depth look at the exploitation of dominant DNA marker (RAPD) orientation for specific breeding objectives. Information gained led to development of the “recombinant-facilitated marker-assisted selection” strategy as the most effective way to overcome gene pool specificity exhibited by many genetic markers. Furthermore, this strategy can change linkage orientation of a dominant marker to that with the greatest selection efficiency for a particular breeding program, and diagnose homology between same-sized markers.

• We developed multiple root disease resistant pea germplasm lines, with acceptable horticultural characteristics which have been used by public and private breeders in the United States, New Zealand, France, and Australia to improve germplasm and cultivars.

• Screening techniques have been developed whereby prospective germplasm and Plant Introduction lines can be quickly evaluated for resistance to root rot and wilt in the seedling stage. Techniques have been developed whereby large numbers of progeny can be evaluated quickly and accurately.

• We conducted two IPM studies in the Blue Mountain area of Northeastern Oregon and Southeastern Washington. Data on the use of reduced tillage, green manure plowdowns, residue management and seed treatments to control Aphanomyces and Fusarium root rot of peas were collected and presented as an Extension Bulletin which is being utilized by growers in the above area.