Research Project: Enhancing Yield, Disease Resistance, and Agronomic Performance in Edible Legumes

Location: Grain Legume Genetics Physiology Research

2024 Annual Report

Objectives
Germplasm enhancement and improved genetic understanding of complex traits, including resistance to problematic bacterial, fungal, and viral diseases, and tolerance to drought and to low soil fertility stresses, represent long-term goals of this project. The new genetic information, breeding tools, and breeding strategies will benefit development and release of novel dry bean germplasm and cultivars with enhanced disease resistance, abiotic stress tolerance, and agronomic performance. Breeders will benefit from new germplasm and marker-assisted selection tools, growers from cultivars with improved yield performance and nitrogen fixation, consumers from healthy nutritious food with improved quality, and the environment from reduced fertilizer, pesticide, and water use. Another long-term goal is to identify the genes underpinning important traits and to leverage that information to develop trait-linked DNA markers to facilitate germplasm and cultivar development. Next generation sequencing technologies, new genomic software, and improved long-read assemblies for reference genomes will contribute to identification of candidate genes underlying economically important traits in common bean and pea. Genetic populations will validate efficient markers for indirect selection of targeted genes in breeding applications. These same populations generated for genetic analyses will be used for breeding and vice versa. Such dual-purpose populations facilitate simultaneous advancement toward our long-term goals (germplasm development and genetic knowledge from genomic analyses). For the next five years this project will focus on the following objectives. Objective 1: Conduct research to generate breeding populations for improving genetic understanding of complex traits, including resistance to problematic bacterial, fungal, and viral diseases, and tolerance to drought and to low soil fertility. Objective 2: Develop, evaluate, and release dry bean germplasm and cultivars with enhanced disease resistance and agronomic performance.

Approach
1. Research Goal: Place genetic factors which control complex stress resistance traits onto physical maps to leverage associated genomic sequences for marker-assisted breeding. Specific populations (diversity panels, recombinant inbred lines (RIL) will be phenotyped for response to diseases (BCMV, Fusarium root rot, Fusarium wilt, and white mold) and abiotic stresses (drought, low fertility) and genotyped with genomic markers primarily in the form of single nucleotide polymorphisms (SNPs). Genome wide association studies and quantitative trait (QTL) analyses will identify genes conferring resistance to targeted stresses. Putative candidate genes will be sequenced across contrasting genotypes for discovery of SNP markers within the resistance genes. Select SNPs with potential for marker-assisted selection will be assayed by melting temperature Tm-shift analysis. To broaden utilization, Tm-shift assays shown to be effective for marker-assisted selection will be converted to Kompetitive Allele Specific PCR (KASP) markers. 2: Research Goal: Combine QTL and major resistant genes that contribute to durable disease resistance and improved genetic resistance to abiotic stresses in dry bean with quality attributes and enhanced agronomic performance. Dry bean suffers from diseases and abiotic stresses. QTL and major genes conditioning existing, new, and novel resistance traits can be combined with agronomic performance traits in enhanced germplasm lines and improved cultivars to limit production losses caused by biotic and abiotic stresses. Bi-parental, 3-way, and 4-way crosses and some backcrosses are conducted in the greenhouse to combine parents with complimentary traits or to further advance traits identified in Objective 1 into commercially adapted backgrounds. Parents are selected from advanced breeding lines, released germplasm and cultivars from other programs, and elite performing inbred lines (RILs, other) often with major genes and QTL (and linked markers) incorporated from the genetic studies in Objective 1. The F1 generation is advanced in the greenhouse. Marker-assisted selection is applied to select individual plants in segregating F1 populations for traits identified in Objective 1. Harvested F2 populations are planted in nonstress field sites at the WSU-Othello research station. Selected F2:3 progeny rows are planted under nonstress at WSU-Othello. Advanced F2:4 lines are planted in replicated trials in stress and nonstress trials at WSU-Prosser and Othello stations. Often individual F4:5 plants are selected from the better performing lines in these preliminary yield trials. Marker-assisted selection will be used to track traits from the F3 generation on. Materials from the F4 generation and later must perform well (above the trial means) in the purgatory plot under multiple stresses (drought, soil compaction, low fertility, and root rots) and in the non-stress trial used to determine maximum yield potential, to advance for subsequent testing. The advanced F5 and later generation lines will be evaluated in terminal drought and low N trials to further characterize tolerance to specific abiotic stresses.

Progress Report
This report documents FY 2024 progress for project 2090-21220-003-000D, “Enhancing Yield, Disease Resistance, and Agronomic Performance in Edible Legumes”, which began in April 2023. In support of Objective 1, common bean and pea populations and field trials were used to evaluate disease and stress resistance and root rot pathogens in pea production fields were monitored. The Andean diversity panel of common bean which includes large kidney, yellow, and cranberry beans was used in genome wide association analyses to study genetic resistance to bacterial brown spot, common bacterial blight, and halo bacterial blight, which severely impact common bean yields. Overall, there were 24 quantitative trait loci (QTL) detected which conditioned resistance to these major bacterial diseases. Five QTL possessed resistance to multiple bacterial pathogens. Several bean populations that were evaluated for virus resistance revealed new genetic markers in candidate genes underpinning resistances to bean common mosaic virus and bean pod mottle virus. There were 220 bean genotypes screened for field tolerance to terminal drought stress, and there are 70 bean genotypes from two inbred mapping populations currently being screened for resistance to Sclerotinia white mold disease. Pea roots were collected from several pea production areas in Washington state to obtain different Fusarium root rot species to screen pea mapping populations for resistance to Fusarium oxysporum, F. redolens, and F. acuminatum. Isolates of F. oxysporum (four isolates), F. redolens (six isolates), and F. acuminatum (two isolates), were obtained and genetically characterized based on internal transcribed spacer (ITS) region and elF1a genes. The F. redolens and F. acuminatum isolates were tested for pathogenicity and aggressiveness, and all isolates were determined to be useful to screen pea mapping populations for resistance to these pathogens. In support of Objective 2, 36 dry bean hybridizations were conducted to generate genetic populations for studying the inheritance of resistance to bean common mosaic virus. Five crosses were conducted to generate genetic stocks of host differentials for genetic resistance to bean common mosaic virus. One hundred seven hybridizations generated breeding populations for the improvement of pinto bean for germplasm release and cultivar development. The breeding program for germplasm development of cranberry, kidney, pinto, pink, and red bean market classes selected 550 single plants from 70 F2 populations. There were 145 advanced lines grown in replicated field trials in Washington state. Two previously developed dry bean cultivars “USDA Cody” pinto and “USDA Lava” small red bean were licensed to a private seed company for seed increase and distribution across the United States.

Accomplishments
1. Use of Komada’s medium to detect Fusarium oxysporum infecting pea seeds. Fusarium wilt of pea caused by Fusarium oxysporum results in considerable losses in pea production across the U.S. Japan requires imported U.S. pea seed to be harvested from plants that do not show symptoms of the disease. In the absence of field certification, regulatory officials in Japan have demanded the use of an alternative protocol to certify seeds are free of F. oxysporum. ARS researchers in Prosser, Washington, determined Komada’s medium could be used under controlled conditions to detect seeds that were infested with F. oxysporum. This method will assist with the exportation of U.S. pea seed to foreign markets.

2. Two dry bean cultivars with high yield potential. Pinto bean and small red bean are two important dry bean market classes grown in the United States. ARS researchers in Prosser, Washington, issued exclusive licenses to a seed company for the increase and distribution of “USDA Cody” pinto bean and “USDA Lava” small red bean. These cultivars, developed by ARS researchers in Prosser, Washington, possess high yield potential, multiple disease resistance and tolerance to drought and low soil fertility. These cultivars provide growers with new options for increasing yield potential while reducing input costs.

Review Publications
Soler-Garzon, A., Goldoff, D., Thornton, A., Swisher Grimm, K.D., Hart, J.P., Song, Q., Strausbaugh, C.A., Miklas, P.N. 2023. A robust SNP-haplotype assay for Bct gene region conferring resistance to beet curly top virus in common bean (Phaseolus vulgaris L.). Frontiers in Plant Science. 14. Article 1215950. https://doi.org/10.3389/fpls.2023.1215950.
Zaleski-Cox, M., Miklas, P.N., Soler-Gaarzon, A., Hoyos-Villegas, V. 2023. Automating high-throughput screening for anthracnose resistance in common bean using allele specific PCR. Plant Methods. 19. Article 102. https://doi.org/10.1186/s13007-023-01071-5.
Roy, J., Soler-Garzon, A., Miklas, P.N., Lee, R., Clevenger, J., Myers, Z., Korani, W., McClean, P. 2023. Integrating de novo QTL-seq and linkage mapping to identify quantitative trait loci conditioning physiological resistance and avoidance to white mold disease in dry bean. The Plant Genome. 16(4). Article e20380. https://doi.org/10.1002/tpg2.20380.
Soler-Garzon, A., McClean, P., Miklas, P.N. 2023. The alleles bc-ud and bc-ur (previously bc-4 gene), representing coding mutations within Vps4 AAA+ ATPase ESCRT protein, interact with other genes to condition resistance to BCMV and BCMNV in common bean. The Plant Genome. 17(1). Article e20421. https://doi.org/10.1002/tpg2.20421.
Miklas, P.N., Soler-Garzon, A., Pastor Corrales, M.A., Cichy, K.A. 2024. Registration of ‘USDA Diamondback’ slow-darkening pinto bean. Journal of Plant Registrations. 18(1):52-60. https://doi.org/10.1002/plr2.20334.
Meziadi, C., Alvarez Diaz, J., Thareau, V., Gratias, A., Marande, W., Soler Garzon, A., Miklas, P.N., Pflieger, S., Geffroy, V. 2023. Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L. Theoretical and Applied Genetics. 137. Article 8. https://doi.org/10.1007/s00122-023-04513-9.
Mwense, B., Hamabwe, S., Kuwabo, K., Mataa, M., Miklas, P.N., Mukuma, C., Kamfwa, K. 2024. Evaluation of pinto genotypes of common bean for resistance to anthracnose. Legume Science. 6(2). Article e228. https://doi.org/10.1002/leg3.228.
Miklas, P.N., Soler-Garzon, A., Valentini, G., Pastor-Corrales, M.A. 2023. Registration of ‘USDA Rattler’ pinto bean. Journal of Plant Registrations. 17(2):271-279. https://doi.org/10.1002/plr2.20289.
Parker, T.A., Gallegos, J.A., Beaver, J., Brick, M., Brown, J.K., Cichy, K.A., Debouck, D., Delgado-Salinas, A., Dohle, S., Ernest, E., Estevez de Jensen, C., Gomez, F., Hellier, B.C., Karasev, A.V., Kelly, J.D., McClean, P., Miklas, P.N., Myers, J.R., Osorno, J., Pasche, J.S., Pastor-Corrales, M.A., Porch, T.G., Steadman, J.R., Urrea, C., Wallace, L.T., Diepenbrock, C.H., Gepts, P. 2022. Genetic resources and breeding priorities in Phaseolus beans: Vulnerability, resilience, and future challenges. Plant Breeding Reviews. Volume 46. Somerset, New Jersey: John Wiley & Sons, Inc. p. 289-420. https://doi.org/10.1002/9781119874157.ch6.
Hamabwe, S., Otiento, N., Soler-Garzon, A., Miklas, P.N., Parker, T., Kramer, D., Chattopadhyay, A., Cheelo, P., Kuwabo, K., Kamfwa, K. 2023. Identification of quantitative trait loci for drought tolerance in Bukoba/Kijivu Andean mapping population of common bean. Journal of Theoretical and Applied Genetics. 136. Article 222. https://doi.org/10.1007/s00122-023-04463-2.
Rahman, M.M., Porter, L.D., Ma, Y., Coyne, C.J., Zheng, P., Chaves-Cordoba, B., Naidu, R.A. 2023. Resistance in pea (Pisum sativum) genetic resources to the pea aphid, Acyrthosiphon pisum. Entomologia Experimentalis et Applicata. 171(6):435-448. https://doi.org/10.1111/eea.13296.