Location: Grain Legume Genetics Physiology Research
2025 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 2025 progress for project 2090-21220-003-000D, titled “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 were generated and greenhouse and field trials were used to evaluate them for disease and stress resistance. Three common bean diversity populations representing 950 individual accessions were used to identify genes conferring resistance to major yield-limiting potyvirus diseases: Bean common mosaic virus and Bean common mosaic necrosis virus. The specific R-gene underpinning the dominant I gene conferring broad resistance to potyviruses was identified amongst a cluster of 33 similar genes by finding mutations which knocked out the gene’s function. The Snap bean diversity population of 378 accessions, inoculated with different viral strains, identified 30 snap bean accessions with superior resistance to potyviruses and revealed four new resistance alleles for previously established genes. Another dry bean population, inoculated with seven races of the Anthracnose pathogen, identified six genes conditioning quantitative resistance to this fungus, one of which was novel. There were 37 bean genotypes screened in separate trials for field tolerance to low fertility and terminal drought stress, and 12 select bean genotypes from two inbred mapping populations are currently being screened for elite resistance to Sclerotinia white mold disease under field conditions. The single pea plant core collection located in Pullman, Washington, consisting of 285 lines was screened twice for resistance to Fusarium redolens under greenhouse conditions. Plants were scored for root rot severity, root and shoot dry weight, and plant height. The results from this study will be used to genetically characterize resistance genes to this prominent pathogen.
In support of Objective 2, 66 dry bean hybridizations generated new breeding populations for germplasm release and cultivar development. The breeding program for germplasm development of pinto, pink, and red bean market classes selected 350 single plants with superior performance from 42 F2 populations. There were 115 advanced breeding lines grown in replicated field trials in Washington State. Twenty-two superior breeding lines including pinto, pink, red, great northern, cranberry, and yellow bean market classes are in advanced testing for yield and agronomic performance in trials across the country (Colorado, Michigan, North Dakota, and Nebraska).
Accomplishments
1. Determining the function of the ‘I’ gene that confers durable and broad-spectrum resistance to viral diseases of bean. Viral diseases, particularly those caused by potyviruses, severely constrain bean production worldwide. The dominant I gene has provided durable and broad-spectrum resistance to potyviruses for nearly a century, yet its molecular identity remained unknown. ARS researchers in Prosser, Washington, cloned the I gene and determined it codes for a Toll/interleukin-1 receptor-like NLR protein, which promotes the death of infected cells to restrict infection. This finding has led to specific markers that enable precise selection for the I gene during selective breeding, thereby accelerating the development of more disease resistant varieties.
Review Publications
McClean, P., Roy, J., Colbert, C., Osborne, C., Lee, R., Miklas, P.N., Osorno, J. 2024. T and Z, two partial seed coat patterning genes in common bean, provide insight into the structure and protein interactions of a plant MBW complex. G3: Genes, Genomes, Genetics. 14(10). Article jkae184. https://doi.org/10.1093/g3journal/jkae184.
Sadohara, R., Cichy, K.A., Fourie, D., Nchimbi Msolla, S., Song, Q., Miklas, P.N., Porch, T.G. 2024. Andean common bean bulk breeding lines selected on multiple continents exhibit broad genetic diversity and stress adaptation. Crop Science. 64:2801-2822. https://doi.org/10.1002/csc2.21309.
Soler-Garzon, A., Mulube, M., Kamfwa, K., Lungu, D., Hamabwe, S., Roy, J., Salegua, V., Fourie, D., Porch, T.G., McClean, P., Miklas, P.N. 2024. GWAS of resistance to three bacterial diseases in the Andean common bean diversity panel. Frontiers in Plant Science. 15. Article 1469381. https://doi.org/10.3389/fpls.2024.1469381.
Soler-Garzon, A., Lopes, F.S., Roy, J., Clevenger, J., Myers, Z., Korani, W., Pereira, W.A., Song, Q., Porch, T.G., McClean, P., Miklas, P.N. 2024. Mapping resistance to Sclerotinia white mold in two pinto bean recombinant inbred line populations. The Plant Genome. 18(1). Article e20538. https://doi.org/10.1002/tpg2.20538.
Kachapulula, J., Kuwabo, K., Hamabwe, S., Nkandela, M., Mukuma, C., Soler-Garzon, A., Miklas, P.N., Kamfwa, K. 2025. Quantitative trait loci analysis for anthracnose resistance in a population derived from Andean varieties Bukoba and Kijivu of common bean (Phaseolus vulgaris L.). Plant Breeding. 144(3):432-439. https://doi.org/10.1111/pbr.13264.
Fu, M., Qu, Z., Pierre-Pierre, N.N., Jiang, D., Souza, F.L., Miklas, P.N., Porter, L.D., Vandemark, G.J., Chen, W. 2024. Exploring the mycovirus Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 as a biocontrol agent of white mold caused by Sclerotinia sclerotiorum. Plant Disease. 108(3):624-634. https://doi.org/10.1094/PDIS-07-23-1458-RE.
Das, S., Rahman, T., Rahman, M., Porter, L.D., Rahman, M., Dash, P.K., Kamal, M.M. 2024. Characterization of fall armyworm (Spodoptera frugiperda J. E. Smith) resistance in maize. Crop Protection. 57(11-12):823-847. https://doi.org/10.1080/03235408.2024.2415150.
Porter, L.D. 2024. Managing Fusarium root rots in pea. Legume Perspectives. 25:4-5. Available: https://www.legumesociety.org/2019/12/02/legume-perspectives/.
Soler-Garzon, A., Miklas, P.N. 2025. An RNase H-Like gene complements resistance to Bean common mosaic necrosis virus in Phaseolus vulgaris. The Plant Genome. 18(2). e70046. https://doi.org/10.1002/tpg2.70046.