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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

2016 Annual Report

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.

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
A primary objective of the research project is to develop improved germplasm and varieties of grain legumes. In light of this objective, advanced yield trials for peas, lentils, and chickpeas are in progress at several locations in Washington and Idaho. The majority of these trials are conducted on private land in collaboration with commercial grain legume producers. Breeding lines and comparative check commercial varieties 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 universities and industry in Washington, Idaho, Montana, and North Dakota. Washington State Crop Improvement Association is producing Foundation seed of several varieties recently released by the ARS including Avondale lentil, Hampton pea, Nash chickpea and Royal chickpea. Rapid and accurate methods for identifying disease resistant plants can accelerate the process of developing improved varieties. The most globally destructive disease of chickpea is Ascochyta blight, and it is difficult to get reliable results based on screening in the field. Disease reaction results from field nurseries were compared with results based on a method that uses a growth chamber and it was found that the growth chamber method gave much more reliable and accurate results based on the performance of chickpea varieties with known levels of disease resistance. This will allow us to accurately determine levels of resistance to this important disease even if field conditions are not conducive to disease expression. 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 over 150 isolates of rhizobacteria that were collected from pea and chickpea root for DNA polymorphisms. This work has identified different lineages of bacteria that can be subjected to more rigorous cultural and genetic analysis to identify host-rhizobia combinations that promote more biological nitrogen fixation.

1. Identification of DNA markers associated with seed mineral nutrient concentration in pea. Mineral nutrient deficiency is a major global health concern with over two-thirds of the world’s population estimated to lack one or more mineral nutrients, particularly iron, zinc, and calcium. Biofortification through breeding is a powerful and sustainable approach to significantly increase nutrient concentration in plants, and grain legumes are nutrient dense crops that are consumed throughout the world. ARS scientists at Pullman, Washington, and Houston, Texas, in collaboration with researchers at Washington State University, conducted field and laboratory tests and identified five DNA markers that explained over 30% of the differences between pea lines for seed concentrations of boron, calcium, potassium, magnesium and molybdenum. These DNA markers are being added to a “genomic tool box” that plant breeders can use to develop new pea cultivars with increased concentrations of mineral nutrients, which will help improve global nutrition.

An ARS scientist in Pullman, Washington, delivered a presentation to summer interns that participated in the Washington State University (WSU) Upward Bound Bridge Internship Program, which is a program that supports internships for primarily Latino and Native American high school graduates from Washington. A summer intern student was hired through the Upward Bound Program and trained in several laboratory techniques and methods of data analysis. The intern participated in a project to evaluate chickpeas for resistance to seed rot caused by Pythium ultimum. We assisted the intern in developing, practicing and presenting a short seminar describing the project to other interns and faculty. ARS scientists in Pullman, Washington, served as mentors throughout the year to two Latino undergraduate students of Washington State University. In this role we provided these students with research training in microbiology, genetics and molecular biology. We also provided general guidance to the students for career and academic development and individual instruction as needed to facilitate success in Science, Technology, Engineering and Mathematics (STEM) courses. One of these students was accepted into the McNair Scholars Program in 2016.

Review Publications
Kim, W., Park, J., Gang, D.R., Peever, T., Chen, W. 2015. Genomic analysis of Ascochyta rabiei identifies dynamic genome environments of solanapyrone biosynthesis gene cluster and a novel type of pathway-specific regulator. Eukaryotic Cell. 14: 1102-1113.
Li, M., Zhang, Y.Y., Wang, K., Hou, Y.G., Zhou, H.Y., Jin, L., Chen, W., Zhao, J. 2016. First report of sunflower white mold caused by Sclerotinia minor Jagger in Inner Mongolia region, China. Plant Disease. 100:211.
Kim, W., Peever, T., Park, J., Park, C., Gang, D., Xian, M., Davidson, J.A., Infantino, A., Chen, W. 2016. Use of metabolomics for the chemotaxonomy of legume-associated Ascochyta and allied genera. Scientific Reports. 6:20192 doi: 10.1038/srep20192.
Vandemark, G.J., Muehlbauer, F.J., Mihov, M., Chen, W., Mcphee, K., Chengci, C. 2014. Registration of CA0469C025C chickpea germplasm. Journal of Plant Registrations. 8:303-307. doi: 10.3198/jpr2013.09.0057crg.
Bourret, T., Grove, G., Vandemark, G.J., Henick-Kling, T., Glawe, D. 2013. Diversity and molecular determination of wild yeasts in a central Washington vineyard. North American Fungi. 8:1-32. doi: 10.2509/naf2013.008.015.
Oss, R.P., Sherman, A., Zhang, H., Vandemark, G.J., Coyne, C.J., Abbo, S. 2015. Vernalization response of domesticated× wild chickpea progeny is subject to strong genotype by environment interaction. Plant Breeding. 135:102-110.
Khot, L., Zuniga, C., Jarolmasjed, S., Sathuvalli, V., Vandemark, G.J., Miklas, P.N., Carter, A., Pumphrey, M., Knowles, R., Pavek, M. 2015. Low-altitude, high-resolution aerial imaging systems for row and field crop phenotyping: A review. European Journal of Agronomy. 70:112-123.
Van Oss, R., Abbo, S., Eshed, R., Sherman, A., Coyne, C.J., Vandemark, G.J., Zhang, H., Peleg, Z. 2015. Genetic relationship in Cicer Sp. expose evidence for geneflow between the cultigen and its wild progenitor. PLoS One. doi: 10.1371/journal.pone.0139789.
Chen, W. 2011. Lentil diseases: A threat to lentil production worldwide. Grain Legumes. 57:35-36.
Chen, W., Castro, P., Cobos, M. 2014. Resistance to Fusarium wilt in chickpea. Grain Legumes. 3:23-24.
Xu, L., Chen, W. 2013. Random T-DNA mutagenesis identifies a Cu-Zn-superoxide dismutase gene as a virulence factor of Sclerotinia sclerotiorum. Molecular Plant-Microbe Interactions. 26:431-441.
Porter, L., Pasche, J.S., Chen, W., Harveson, R.M. 2015. A diagnostic guide for Fusarium Root Rot of pea. Plant Health Progress. doi: 10.1094/PHP-DG-15-0013.
Xu, L., Xiang, M., White, D., Chen, W. 2015. pH Dependency of sclerotial development and pathogenicity revealed by using genetically defined oxalate-minus mutants of Sclerotinia sclerotiorum. Environmental Microbiology. 17:2896-2909.
Habibi, A., Tobin, P., Wonyong, K., Chilvers, M., Chen, W., Kaiser Jr, W.J., Muehlbauer, F.J. 2015. First report of Ascochyta blight of Spotted Locoweed (Astragalus lentiginosus) caused by Ascochyta sp. in Idaho. Plant Disease. 99:1446.
Attanayake, R., Tennekoon, V., Johnson, D., Porter, L., Del Río-Mendoza, L., Jiang, D., Chen, W. 2014. Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay. Heredity. 113:353-363. doi: 10.1038/hdy.2014.37.
Ali, L., Azam, S., Rubio, J., Kudapa, H., Madrid, E., Varshney, R.K., Castro, P., Chen, W., Gil, J., Milan, T. 2015. Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses. Euphytica. 204:473-485.
Landry, E.J., Coyne, C.J., Mcgee, R.J., Hu, J. 2016. Adaptation of autumn-sown faba bean germplasm to southeastern Washington. Agronomy Journal. 108:301–308.
Ekanayake, L.J., Thavarajah, D., Vial, E., Mcgee, R.J., Thavarajah, P. 2015. Selenium fertilization on lentil (Lens culinaris Medikus) grain yield, seed selenium concentration, and antioxidant activity. Field Crops Research. 177:9-14.
Johnson, C., Thavarajah, D., Fenlason, A., Thavarajah, P., Mcgee, R.J., Agrawal, S., Combs, G.F. 2015. A global survey of low-molecular weight carbohydrates in lentils. Journal of Food Composition and Analysis. 44:178-185.
Cheng, P., Holdsworth, W., Ma, Y., Coyne, C.J., Mazourek, M., Grusak, M.A., Fuchs, S., Mcgee, R.J. 2015. Phylogenetic analysis and association mapping for agronomic and quality traits in the USDA pea single-plant collection. Molecular Breeding. 35:75. doi: 10.1007/s11032-015-0277-6.
Desgroux, A., L'Anthoene, V., Roux-Duparque, M., Riviere, J., Aubert, G., Tayeh, N., Moussart, A., Mangin, P., Vetel, P., Pirio, C., Mcgee, R.J., Coyne, C.J., Burstin, J., Baranger, A., Manzanares-Dauleux, M., Bourion, V., Pilet-Nayel, M. 2016. Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea. BMC Genomics. 17:124.
Idrissi, O., Udupa, S.M., De Keyser, E., Mcgee, R.J., Coyne, C.J., Saha, G., Muehlbauer, F., Van Damme, P., De Riek, J. 2016. Identification of quantitative trait loci controlling root and shoot traits associated to drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population. Frontiers in Plant Science. doi: 10.3389/fpls.2016.01174.
Ma, Y., Hu, J., Myers, J., Mazourek, M., Coyne, C.J., Main, D., Wang, M., Humann, J., Mcgee, R.J. 2016. Development of SCAR markers linked to sin-2, the stringless pod locus in pea (Pisum sativum L.). Molecular Breeding. doi: 10.1007/s11032-016-0525-4.