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ARS Home » Pacific West Area » Pullman, Washington » Grain Legume Genetics Physiology Research » Research » Research Project #423174

Research Project: Genetic Improvement of Cool Season Food Legumes

Location: Grain Legume Genetics Physiology Research

2015 Annual Report


Objectives
In the United States, pea, lentils and chickpeas are grown primarily in the Pacific Northwest and Northern Plains. Over the past five crop seasons (2007-2012), these crops have been grown on an average of 1,260,000 acres in the US with an average harvest value of over $320 million. These crops also contribute to the success of the US wheat and barley industry by serving as useful rotation crops in small grain production systems. This research project has three objectives that focus on developing new and improved varieties of cool season food legumes (peas, lentils, and chickpeas) and effective integrated disease control strategies for these crops. 1) Develop and release new varieties and germplasm of peas, lentils, and chickpea that have higher seed mineral concentrations; improved host-plant resistance to Aphanomyces root rot, Sclerotinia wilt and Ascochyta blight; and higher yields than existing commercial varieties. 2) Identify genetic markers closely associated with superior yield, optimal plant height for harvest, seed mineral concentration, resistance to Aphanomyces root rot, and improved cold tolerance for autumn-sown peas, and validate their utility for marker-assisted plant breeding. Sub-objective 2A: Identify molecular markers in adapted pea populations that are associated with important traits including concentrations of minerals in seed, resistance to Aphanomyces root rot, and winter hardiness. Sub-objective 2B: Identify molecular markers in adapted chickpea populations that are associated with seed size and early maturity. 3) Develop efficient techniques to screen peas, lentils, and chickpeas for host-plant resistance to Ascochyta blight and Sclerotinia wilt, and characterize genetic and physiological factors responsible for the virulence of these pathogens. Sub-objective 3A: Develop efficient techniques to screen peas, lentils and chickpeas for resistance to Ascochyta blight and Sclerotinia white mold. Sub-objective 3B: Determine genetic factors responsible for pathogenicity of Sclerotinia sclerotiorum using a variety of genetic and genomic tools. Sub-objective 3C: Determine the role of solanapyrone phytotoxins produced by A. rabiei during the development of Ascochyta blight disease in chickpea. This research will result in several products, including new varieties of peas, lentils, and chickpeas along with improved methods for controlling diseases of these crops.


Approach
New varieties and germplasm will be developed from pure lines selected from among segregating populations of peas, lentils, and chickpeas. Cyclical hybridization will be conducted to combine favorable alleles for traits of interest. Parental lines will include adapted germplasm, commercial cultivars and accessions from the various international breeding programs. Promising breeding lines will be released as either germplasm or varieties based on a rigorous comparison of their performance relative to that of commercial check varieties. Linkage analysis and the detection of associations between markers and different traits will be done using simple sequence repeats (SSRs), expressed sequence tagged- SSRs, and single nucleotide polymorphisms (SNPs). Pea recombinant inbred line (RIL) populations will be developed from a cross between Aragorn and Kiflica to identify markers associated with seed mineral concentrations. RILs from a cross between the pea cultivars Medora and Melrose will be used to identify markers associated with cold tolerance. Molecular markers associated with seed size and early maturity in chickpea will be detected using a RIL population developed from an interspecific cross between C. arientinum line Flip 90-27 and PI599072 (C. reticulatum). Associations between markers and quantitative trait loci (QTL) conditioning traits of interest will be detected by composite interval mapping. Improved methods will be developed to screen chickpea for reaction to Ascochyta blight. Toxins will be purified from liquid cultures of A. rabiei. Toxins will be adjusted to various concentrations and applied to detached chickpea leaflets. Leaflets treated with water will be used as controls. The speed of lesion development and final lesion size will be used to compare the reactions of different chickpea genotypes. The relationship between field disease scores of the chickpea genotypes and their sensitivity to the toxin will be determined. Studies to develop more efficient methods to screen peas and lentils for reaction to Sclerotinia white mold will initially examine resistant and susceptible materials reported in prior studies. Plants will be grown in the greenhouse and inoculated with agar plugs containing mycelia of S. sclerotiorum. Disease reaction will be scored by measuring the length of the lesion produced by the fungus over different time points. Two approaches will be taken to investigate the genetic factors responsible for pathogenicity and virulence of S. sclerotiorum. One approach will be to use Agrobacterium mediated transformation (AMT) to generate random mutations that will be screened to detect mutants with reduced virulence. The other approach will be to identify genes of S. sclerotiorum that are differentially expressed during the processes of infection and disease development.


Progress Report
This research project is focused on developing improved germplasms and varieties of peas, lentils, and chickpeas that are adapted to existing and emerging areas of production in the U.S., advancing basic knowledge of plant-pathogen interactions, and improving methods to control diseases of these crops. Research projects are addressed through a combinatorial approach that includes plant breeding and genetics, plant pathology, and molecular biology. Advanced yield trials for peas, lentils, and chickpeas are in progress at several locations in Washington and Idaho. Breeding lines, commercial varieties, and populations are also being evaluated in field nurseries for reaction to several diseases including Ascochyta blight, Fusarium wilt, Aphanomyces root rot, and several aphid-transmitted viruses including bean leafroll virus and pea enation mosaic virus. Our most elite breeding lines are also being evaluated in independent yield trials conducted by collaborators from university extension and industry in Washington, Idaho, Montana, and North Dakota. Breeding lines that demonstrate superior performance over multiple years and locations and have desirable market qualities are released as new varieties provided that commercial interest exists for the new variety. Intellectual property protection of new varieties is pursued when requested by the ARS Plant Variety Protection (PVP) Committee. The USDA entered into two license agreements this year for varieties developed by the research unit (USDA License 1630-001: Nash chickpea and License 1632-001: Royal chickpea). Four Plant Variety Protection (PVP) certificates were issued this year for varieties developed by the research unit: PVP 20140092 (Lynx pea), PVP 20140093 (Avondale lentil), PVP 201400311 (Royal chickpea) and PVP 201400311 (Nash chickpea). Foundation seed is currently being produced of Avondale lentil, Hampton pea, Nash chickpea and Royal chickpea by the Washington State Crop Improvement Association. Commercial seed sales of these varieties will begin later this year. The ability of legumes to produce their own nitrogen fertilizer through interactions with beneficial rhizobacteria is one of the primary factors that make legumes very desirable crops for use in rotations with small cereal grains including wheat and barley. Despite the importance of biological nitrogen fixation to sustainable crop production, there are considerable gaps in the understanding of how legumes and these bacteria interact with each other and the surrounding environment. This year we screened chickpea breeding lines and varieties for their ability to be colonized by beneficial rhizobacteria. Breeding lines were identified that supported significantly more beneficial bacteria than several chickpea varieties that are currently grown commercially. We also collected over 50 isolates of indigenous rhizobacteria from chickpea and have begun to examine differences among these isolate in their ability to colonize chickpea roots.


Accomplishments
1. Identifying a method to control chickpea seed rot. During this year a new disease of chickpea has significantly increased in severity and distribution throughout the U.S. Pacific Northwest. The disease is caused by the soilborne plant pathogen Pythium, specifically isolates of Pythium that are resistant to the fungicide metalaxyl, which has historically been applied to chickpea seeds to protect them from several diseases. The development of metalaxyl resistant Pythium has resulted in an acute need to identify alternative methods to control this disease. ARS scientists with the Grain Legume Genetics and Physiology Research Unit, located in Pullman, Washington, tested several different compounds under field conditions for their ability to control this disease. They identified a compound named Ethoboxam that could be applied to chickpea seeds and successfully protected the seeds from rot caused by metalaxyl-resistant Pythium. Chickpeas are grown on over 200,000 acres annually in the U.S. and this new method for controlling an important emerging disease will promote increases in production and enhancement of rural communities where chickpeas are grown and processed.


Review Publications
Rubiales, D., Fondevilla, S., Chen, W., Gentzbittel, L., Higgins, T.J., Castillejo, M.A., Singh, K.B., Rispail, N. 2015. Achievements and challenges in legume breeding for pest and disease resistance. Critical Reviews in Plant Sciences. 34:195-236.
Vandemark, G.J., Guy, S.O., Chen, W., Mcphee, K., Pfaff, J.S., Lauver, M., Muehlbauer, F.J. 2015. Registration of 'Nash' Chickpea. Journal of Plant Registrations. doi: 10.3198/jpr2014.07.0047crc.
Zhang, Q., Yang, L., Zhang, J., Wu, M., Chen, W., Jiang, D., Li, G. 2015. Production of anti-fungal volatiles by non-pathogenic Fusarium oxysporum and its efficacy in suppression of verticillium wilt of cotton. Plant and Soil. 392:101-114.
Zeng, L., Zhang, J., Han, Y., Yang, L., Wu, M., Jiang, D., Chen, W., Li, G. 2014. Degradation of oxalic acid by the mycoparasite Coniothyrium minitans plays an important role in interacting with Sclerotinia sclerotiorum. Environmental Microbiology. 16(8):2591–2610.
Yu, L., Sang, W., Wu, M., Zhang, J., Yang, L., Zhou, Y., Chen, W., Li, G. 2015. Novel hypovirulence-associated RNA mycovirus in the plant pathogenic fungus botrytis cinerea: molecular and biological characterization. Applied and Environmental Microbiology. 81:2299-2310.
Kim, W., Park, C., Park, J., Akamatsu, H.O., Peever, T., Xian, M., Gang, D.R., Vandemark, G.J., Chen, W. 2015. Functional analyses of the Diels-Alderase gene sol5 of Ascochyta rabiei and Alternaria solani indicate that the Solanapyrone phytotoxins are not required for pathogenicity. Molecular Plant-Microbe Interactions. 28:482-496.
Coyne, C.J., Pilet-Nayel, M., McGee, R.J., Porter, L., Smykal, P., Grunwald, N.J., Inglis, D. 2015. Identification of QTL controlling high levels of partial resistance to Fusarium solani f. sp. pisi in pea. Plant Breeding. 134:446-453.
Fan, X., Zhang, J., Yang, L., Wu, M., Chen, W., Li, G. 2015. Development of PCR-based assays for detecting and differentiating three species of botrytis infecting broad bean. Plant Disease. 99:691-698.