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United States Department of Agriculture

Agricultural Research Service

Research Project: Enhancing Resistance to Diseases and Abiotic Stresses Alfalfa
2008 Annual Report


1a.Objectives (from AD-416)
Objective 1: Develop molecular markers to screen alfalfa for resistance to environmental stresses and identify different physiological races of pathogens responsible for soilborne diseases of alfalfa. Sub-objective 1.1: Identify markers linked to tolerance to lodging in commercial alfalfa populations. Sub-objective 1.2: Develop molecular markers that discriminate unambiguously between Race 1 and Race 2 of Aphanomyces euteiches. Objective 2: Identify and develop sources of disease resistance in alfalfa and common bean. Sub-objective 2.1: Identify bean germplasm with resistance to Clover Yellow Vein Virus.


1b.Approach (from AD-416)
Two alfalfa clones have been identified that differ in resistance to lodging. The lodging susceptible and lodging resistant clones and the F1 resulting from this cross was crossed with each parent to produce two different backcross populations. Replicated clones of each parent, F1 and backcross plants will be produced in the greenhouse. The replicated clones will be transplanted into three different field locations, two in WA and one in WI. DNA from the parents, F1 and BC1s will be screened for the presence of sequence related amplified polymorphisms (SRAPs) using protocols optimized for amplifying SRAP markers from alfalfa. Resistant and susceptible bulk DNA extracts will be subjected to bulk segregant analysis with SRAP primers to identify candidate polymorphic loci associated with resistance to lodging. Candidate markers will be clustered into a linkage group map. Molecular markers will be developed that discriminate unambiguously between Race 1 and Race 2 of Aphanomyces euteiches that cause root rot in alfalfa. Markers specific to each race will be converted into SCAR markers and will then be evaluated for their robustness using a test profile of DNA samples extracted from known race 1 and race 2 isolates of A. euteiches. All candidate markers will be screened across a collection of other isolates A. euteiches collected from other states in the U.S. The assay will be validated on total DNA extracts from alfalfa tissue infected with each race of the pathogen. If a SCAR marker is successfully developed early in the research plan, collaboration will be sought with industry or university breeding programs to identify sources of tolerance and eventually DNA markers linked to tolerance to this pathogen. Sources of resistance will be identified in common bean germplasm with resistance to Clover yellow vein virus (ClYVV). Included in the screening assays will be four sets of bean germplasm: one set representative of each of 12 host groups used in the identification of strains of Bean common mosaic virus and Bean common mosaic necrosis virus; a second set of differential cultivars for identification of Bean yellow mosaic virus strains obtained from the Plant Introduction Station, Pullman, WA.; the third group will consist of reported sources of resistance to ClYVV which include US1140, UI-31, and Jolanda; and lastly, cultivars and breeding lines will be screened to identify sources of resistance already deployed in a snap bean background because this market class is currently at the greatest risk from this disease. A recombinant inbred line (RIL) population segregating for the resistance gene(s) also will be evaluated against strains of ClYVV. Segregation ratios for numbers of resistant and susceptible plants observed within the RIL population(s) and chi-square tests will be used to determine if the genes between sources are allelic, independent, or linked. Formerly 5354-21000-014-00D (3/08).


3.Progress Report
Developing resistance to lodging in alfalfa. An advanced population of alfalfa clones has been developed for improved lodging resistance response. Replicated clones of each parent, F1 and backcross plants were produced in the greenhouse. The replicated clones were then transplanted into three different field locations, two in Washington and one in Wisconsin. Six clones of each genotype (parents, F1s, and all backcross progeny) were planted at each location. Plants will be evaluated for resistance to lodging using a widely accepted standard test protocol Results will be tabulated on lodging characteristics using same seed of the parental breeding lines as planted in seed cages.

This project addresses components of National Program 215, Component 3, (Sustainable Harvested Forage Systems for Livestock, Bioenergy and Bioproducts), Problem Statement H, Obj H.1. and NP 303 (Plant Diseases), particularly Component 1 (Disease diagnosis: Detection, identification and characterization of plant pathogens), and Component 3 (Plant disease resistance).


4.Accomplishments
1. Identify molecular markers linked to lodging resistance in alfalfa.

Lodging of alfalfa reduces alfalfa yields because the collapsed stems often cannot be cut, and also adversely impacts the quality of harvested forage because of leaf decay and senescence associated with lodging. Six alfalfa clones have been identified by ARS scientists in the Vegetable and Forrage Crops Production Research Unit in Prosser, WA that differ in resistance to lodging. The replicated clones were transplanted into three different field locations where they have established for later evaluation. Data of plants both highly resistant and highly susceptible to lodging will be used to develop molecular markers linked to resistance to lodging in commercial alfalfa populations. Identification of markers associated with lodging resistance will allow breeders to easily follow the resistance trait in new breeding lines, thus potentially eliminating years of costly and time-consuming field trials.

This accomplishment aligns with National Program 215 Component 3, (Sustainable Harvested Forage Systems for Livestock, Bioenergy and Bioproducts), Problem Statement H, Obj H.1.

2. Evaluate bean germplasm for resistance to Clover yellow vein virus (ClYVV).

ClYVV continues to plague snap bean crops in the upper Midwest States where the soybean aphid is the common vector of the virus that causes severe pod necrosis resulting in beans that are unmarketable. Nine dry bean lines were identified by ARS scientists in the Vegetable and Forrage Crops Production Research Unit in Prosser, WA with good resistance to ClYVV. Over 60 commercial snap bean cultivars were screened for resistance to ClYVV and only one was shown to have a high level of tolerance to the virus. Because insecticides are not effective against ClYVV in bean, identification of resistance genes and development of resistant breeding lines will be significant in reducing future losses in snap bean.

This accomplishment addresses components of NP 303 (Plant Diseases), particularly Component 1, Problem area b; and Component 3, Problem area b .


5.Significant Activities that Support Special Target Populations
None.


6.Technology Transfer

Number of Active CRADAs1
Number of Non-Peer Reviewed Presentations and Proceedings1

Review Publications
Larsen, R. C., Miklas, P. N., Eastwell, K. C., and Grau, C. R. 2008. A strain of Clover yellow vein virus that causes severe pod necrosis disease in snap bean. Plant Dis. 92:1026-1032.

Last Modified: 12/19/2014
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