Location: Grain Legume Genetics Physiology Research
2022 Annual Report
Objectives
Dry peas, lentils, and chickpeas are integral components of dryland agriculture systems throughout the U.S. and have served as globally important nutrition sources of protein, fiber, and minerals for millennia. These crops form symbiotic associations with rhizobacteria that results in biological nitrogen fixation that contributes to productivity and profitability of cropping systems. Peas, lentils, and chickpeas are typically sown in the spring, and the development of autumn sown legumes may provide alternatives to winter wheat. Diseases cause considerable losses in these crops every year and are primarily managed by the use of resistant varieties. However, resistance is lacking to several important diseases, including root rots caused by Aphanomyces and Fusarium, Ascochyta blight, Pythium seed rot, and Sclerotinia white mold. Improved understanding of fungicide resistance and mechanisms of pathogenicity and virulence will accelerate the development of effective and efficient practices for managing diseases of these crops. Over the next five years this research project has the following objectives.
Objective 1: Develop and release improved germplasm and cultivars of peas, lentils, and chickpeas that have desirable agronomic traits coupled with enhancements in nutritional characteristics and the ability to form symbiotic effective relationships with nitrogen-fixing rhizobacteria.
Subobjective 1A: Develop improved germplasm and cultivars of peas, lentils, and chickpeas that have enhanced field performance and nutritional quality.
Subobjective 1B: Characterize factors that influence biological nitrogen fixation resulting from symbiosis between autumn sown pea and Rhizobium leguminosarum.
Sub-objective 1C: Work with the Pulse quality lab at Fargo, North Dakota, and other pulse breeders to identify, evaluate, and screen the intrinsic end-use quality of peas, chickpea, and lentil and evaluate nutritional and industrial properties to enable development of improved cultivars needed by the pulse industry to expand the uses of peas, chickpeas, and lentils as food ingredients and other by-products and meat and milk substitutes.
Objective 2: Develop increased understanding of the population structure of selected pathogens, host resistance, and mechanisms of virulence and pathogenicity, and use the knowledge to improve integrated disease management practices and methods for identifying resistant plants.
Subobjective 2A: Characterize fungicide resistant populations of Pythium ultimum and Ascochyta rabiei and develop management strategies for fungicide resistance.
Subobjective 2B: Identify sources of resistance in pea, lentil, and chickpea to Fusarium root rot, Pythium seed rot, and Aphanomyces root rot, respectively.
Subobjective 2C: Increase understanding of factors conditioning virulence and pathogenicity of Sclerotinia sclerotiorum.
The advances resulting from these studies will provide comprehensive technology platforms for developing new and improved cultivars of cool season food legumes and effective integrated disease control strategies for these crops.
Approach
1A. Research Goal: Develop and release new cultivars of peas, lentils and chickpeas that have superior agronomic performance and nutritional qualities.
Crossing blocks will be established for peas, lentils, and chickpeas. Families and lines will be selected for plant height, disease resistance, tolerance to lodging, early flowering, and seed traits. Remote sensing will be used to estimate canopy vigor of field plots. Correlations will be determined between remote sensing and ground truth data. Promising breeding lines will be released as either germplasm or cultivars. Molecular markers will be detected that are associated with disease resistance and desirable seed nutritional qualities. If desirable traits such as disease resistance are linked to undesirable commercial traits then large population sizes and backcross breeding approaches may be necessary to introduce traits into adapted backgrounds.
1B. Hypothesis: Biological nitrogen fixation in elite winter pea genotypes is conditioned by effects of plant genotype, genotype of the Rhizobium leguminosarum strain, the environment, and interaction effects between these sources of variance.
Tests will be performed in growth chambers to evaluate plant and rhizobia genotype effects on biological nitrogen (N) fixation. 15N/14N ratios will be estimated from ground pea tissues to determine %Ndfa. Winter pea lines will be tested in the field for ability to be colonized by endemic rhizobacteria. Plots will be mechanically harvested and the contribution of biological nitrogen fixation to total seed N will be determined. If results based on field studies do not support growth chamber results, the growth chamber conditions will be changed to better reflect field conditions.
2A. Hypothesis: Characterizing and understanding fungicide-resistant pathogen populations will improve efficacy of management of fungicide resistance.
The stability of metalaxyl resistance (MR) in MR isolates of Pythium ultimum will be determined, as will the fitness of MR isolates of the pathogen. Microsatelllite DNA markers will be used to survey genetic variation in P. ultimum. Isolates of Ascochyta rabiei will be evaluated for sensitivity to Qol fungicides.
2B. Research Goal: Improve resistance to Pythium seed rot in chickpea and Aphanomyces root rot in lentil.
The chickpea single plant core collection will be tested for resistance to Pythium seed rot using a recently developed growth chamber assay. More than 300 accessions from the National Plant Germplasm System (NPGS) lentil core collection will be evaluated for resistance to Aphanomyces root rot using a greenhouse screening assay. Sources of resistance in lentil to Aphanomyces root rot may only be detected in the secondary gene pool.
2C. Research Goal: Increase our understanding of virulence mechanisms of Sclerotinia sclerotiorum by investigating and validating roles of pathogenicity effectors of the pathogen.
Seventeen mRNA transcripts of the fungus will be targets of gene-knockout (KO) experiments and the virulence of the KO mutants will be determined. Yeast two-hybrid systems will be used to identify host receptors targeted by pathogen effectors.
Progress Report
In support of Objective 1, research continued to develop new pulse cultivars with improved agronomic performance and enhanced nutritional qualities. In Fall 2021, chickpea yield trials conducted at four locations (Colton, Fairfield, Pullman, and Walla Walla) in Washington were harvested. Entries included 20 ARS breeding lines and four cultivars (Sierra, Billy Beans, Nash, and USDA-Quinn). The grand mean of all entries across all locations was 1079 kg/ha. Mean yields of entries across all locations ranged from 692 kg/ha to 1520 kg/ha. The mean yield of Sierra was 1175 kg/ha. Seven breeding lines and Billy Beans had mean yields equal or greater than Sierra. The highest yielding breeding line was CA17900016C (1313 kg/ha), which was 11% greater than Sierra.
Similarly, lentil yield trials conducted at three locations (Fairfield, Garfield, and Pullman) in Washington were harvested in Fall 2021. Entries included 13 ARS Richlea-type breeding lines and two cultivars (Avondale and Richlea). The grand mean of all entries across all locations was 797 kg/ha. Mean yields of entries across all locations ranged from 628 kg/ha to 977 kg/ha. The mean yield of Richlea was 878 kg/ha. Three breeding lines and Avondale had mean yields greater than Richlea. The highest yielding breeding line was LC11600370R (939 kg/ha), which was 7% greater than Richlea.
Spring-sown pea yield trials were harvested from three locations (Colton, Fairfield, and Pullman) in Washington. Entries included 23 ARS green pea breeding lines and three cultivars (Banner, Columbian, and Hampton). The grand mean of all entries across all locations was 1262 kg/ha. Mean yields of entries across all locations ranged from 1040 kg/ha to 1461 kg/ha. The mean yield of Banner was 1291 kg/ha. Eight breeding lines had mean yields greater than Banner. The highest yielding breeding line was PS1410B0065 (1461 kg/ha), which was 13% greater than Richlea.
Fall-sown pea yield trials were harvested from three locations (Garfield, Pullman, and St. John) in Washington. Entries included 18 ARS Fall-sown green pea breeding lines and three cultivars (Lakota, Lynx, and Windham). The grand mean of all entries across all locations was 1931 kg/ha. Mean yields of entries across all locations ranged from 1399 kg/ha to 2288 kg/ha. The mean yield of Windham was 2040 kg/ha. Eight breeding lines had mean yields greater than Windham. The highest yielding breeding line was PS1430NZ001W (2288 kg/ha), which was 12% greater than Windham.
Improving nutritional qualities of chickpea has emerging as an area of increased focus for breeding programs. In 2022 we evaluated chickpea breeding lines and cultivars grown at four locations in 2021 for seed protein concentration. A total of 24 entries were evaluated including four check cultivars (Sierra, Nash, Billy Bean, and USDA Quinn) and 18 breeding lines. The grand mean of all entries across all locations was 19.1%. Mean protein concentrations of entries across all locations ranged from 17.1% to 20.8% (USDA Quinn). The mean protein concentration of Sierra was 20.6%. One ARS breeding line (CA17900026C) and USDA Quinn had higher protein concentrations than Sierra.
In support of Objective 2, we continued research to define genetic and biochemical factors involved in virulence and pathogenicity of Sclerotinia sclerotiorum (Ss), which causes white mold disease of more than 400 different crop species. Fatty acid hydroxylases (FAH) are produced by plants to control cell death associated with mechanisms of disease resistance. We identified a peptide, temporarily named SsE3, which is produced by Sclerotinia and specifically interacts with plant FAHs. Sclerotinia mutants that had the SsE3 gene deleted did not cause as severe disease as isolates of the pathogen with a normal SsE3 gene. We suspect SsE3 plays an important role in disease development by interacting with plant FAHs, however this role has not been experimentally demonstrated.
Accomplishments
1. Discovery of new fungal effector protein that contributes to Sclerotinia white mold disease. More than 400 different crop species across the world are susceptible to white mold disease caused by the fungus Sclerotinia sclerotiorum. White mold is clearly one of the most globally destructive plant diseases and how Sclerotinia can cause disease across such a wide range of crops has been poorly understood. ARS researchers in Pullman, Washington, discovered the fungus produces a protein named polygalacturonase inhibiting protein effector (SsPINE1) that inactivates polygalacturonase inhibiting proteins (PGIPs) produced by plants to resist diseases. Sclerotinia mutants with a defective SsPINE1 gene caused less disease than isolates of the pathogen with the normal gene. This is the first example of a new class of fungal effectors that can inactivate plant defense mechanisms. This discovery has stimulated new approaches for improving disease resistance by identifying plant PGIPs that cannot be inactivated by fungal effector proteins.
