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ARS Home » Pacific West Area » Pullman, Washington » Grain Legume Genetics Physiology Research » Research » Research Project #434605

Research Project: Enhanced Agronomic Performance and Disease Resistance in Edible Legumes

Location: Grain Legume Genetics Physiology Research

2020 Annual Report


1a. Objectives (from AD-416):
Development and release of novel edible legume germplasm lines and cultivars with enhanced traits that benefit breeders, growers, consumers, and the environment, represent the long-term goals for this project. Given favorable outcomes, breeders will benefit from germplasm releases, growers from increased yield potential and nitrogen fixation, consumers from healthy low cost food with improved quality, and the environment from reduced pesticide use. Germplasm lines which incorporate novel traits from exotic sources into near-commercial seed market types will provide public and private breeders with useful traits for cultivar development. Moving traits from exotic sources into adapted commercial cultivars is an otherwise arduous task for most breeding programs. Thus, these germplasm releases will facilitate adoption of new traits by breeders and increase genetic diversity in their programs which is crucial for advancing yield potential and for sustainability in the long term. It is expected that some breeding lines with exceptional performance generated by this project will be released as cultivars. Another long-term goal is to better understand the genetics underpinning complex traits and leverage this knowledge to improve breeding strategies. High-throughput next generation sequencing combined with optical mapping and updated reference genomes will significantly facilitate genetic studies geared toward advancing our breeding efforts. We will seek better markers for indirect selection of economically important traits in pea and common bean and examine new marker-assisted breeding strategies. 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: Develop genomic analysis populations, and use them to improve genetic understanding of complex traits as well as to accelerate breeding for improved agronomic traits, including biological nitrogen fixation, drought tolerance, tolerance to low soil fertility, and resistance to problematic bacterial, fungal, and viral diseases. Objective 2: Develop, evaluate, and release fresh green pea and dry bean (kidney, pinto, black) germplasm with improved agronomic performance combined with durable disease resistance.


1b. Approach (from AD-416):
1. Research Goal: Genetic factors which condition complex stress resistance traits will be positioned on physical maps, with associated genomic sequences leveraged for marker-assisted breeding. Select populations will be evaluated for response to abiotic stresses (drought, low fertility) and diseases (Bean Common Mosaic Virus [BCMV], common bacterial blight [CBB], Fusarium root rot, Pea Seed-borne Mosaic Virus [PSbMV] and white mold) and genotyped with genomic markers (single-nucleotide polymorphisms [SNPs]). Linkage maps will be developed and quantitative trait loci (QTL) detected. SNPs with potential marker-assisted selection applications will be detected by melting temperature Tm-shift analysis. Reference genome data bases will be used for physical mapping, validating genetic map positions, and candidate gene discovery. If the BARCBean6K_3 BeadChip SNP array we intend to use for bean studies provides inadequate marker coverage then it may be necessary to generate additional SNPs through genotyping-by sequencing (GBS). 2. Research Goal: Combining independent QTL and major resistant genes will improve genetic resistance to abiotic stresses and contribute to durable disease resistance in pea and dry bean, and be combinable with quality attributes and enhanced agronomic performance. Bean improvement efforts will be based on the use of F4 bulk breeding populations. These populations derive from Andean Diversity Panel accessions selected to combine resistance to both biotic and abiotic stresses. All materials in the F4 generation and later must perform well under multiple stresses in the white mold nursery, terminal drought trial, low nitrogen (N)trial, purgatory plot (drought, soil compaction, low fertility, and root rots), and in the non-stress trial used to determine maximum yield potential, in order to be advanced for subsequent testing. Measured traits recorded for each plot in each trial will include grain yield, seed weight, early plant vigor, plant height, growth habit, flowering date and maturity, days to seed fill, biomass, pod wall ratio, Normalized Difference Vegetation Index (NDVI), and canopy temperature. Individual populations will be chosen for use in the Genome Wide Association Study (GWAS) to detect genomic regions under selection in different stress environments. Resistance to halo blight in beans will be improved by combining HB4.2 and HB5.1 QTL with major genes Pse-2 and Pse-3, which can produce lines that have durable resistance to all nine differential races of the pathogen Pseudomonas syringae. Seed quality and yield potential will be improved in pinto beans by developing lines through crosses between the new pinto germplasm releases USPT-WM-12 and PRP 153 and commercial pinto varieties. If no useful QTLs for abiotic stress resistance in beans are detected then these traits will be improved by phenotypic selection. Pea germplasm from the NPGS Pea Core Collection, commercial pea cultivars and advanced breeding lines will be screened for resistance to Bean Leaf Roll Virus (BLRV). Germplasm with resistance to BLRV will be identified that can be used in breeding programs to develop resistant cultivars.


3. Progress Report:
Substantial progress was made across all project objectives, all of which address Problem Statement 1A (Trait discovery, analysis, and superior breeding methods) of Component 1 (Crop Genetic Improvement) of the National Program 301, Plant Genetic Resources, Genomics, and Genetic Improvement Action Plan (2018-2022). In support of Objective 1, there were 17 dry bean populations evaluated for economically important traits including tolerance to drought and durable resistance to fungal and viral diseases. Two inbred populations were advanced two generations to study drought tolerance. Two large inbred populations with 360 accessions between them were characterized for resistance to white mold disease in the greenhouse. Genomic and genetic analyses revealed two major genes for resistance to white mold, one in each population. Genomic analyses of 800 accessions across six populations revealed a mutation that knocks out a gene (NAC domain) in beans that is involved in plant development. The Bean golden yellow mosaic virus (BGYMV) needs this gene to fully infect dry bean plants. The NAC domain mutation is now the selectable marker for the virus resistance gene bgm-1. This is the first reported discovery of a gene in bean that possibly confers resistance to BGYMV. Also in support of Objective 1, two genetic markers were used to rapidly screen 382 pea lines for genes conferring resistance to Pea seedborne mosaic virus (PSbMV). Marker results were confirmed by screening each line in a greenhouse with PSbMV. We detected 39 pea lines that had resistance genes. One pea line was identified that appears to have a novel gene associated with PSbMV resistance. Dry bean breeding nurseries, drought and disease trials, and preliminary and advanced yield trials, comprising 300 lines and 1400 research plots were planted in 2020 in support of Objective 2. Ten superior advanced lines including four pinto, two great northern, one pink, one red, one yellow, and one red-mottled bean, were increased and distributed to collaborators for independent testing to determine their potential for release as new cultivars. A new “environmentally friendly” pinto bean cultivar “USDA-Rattler” with tolerance to drought and low soil fertility stresses was released by the Office of Technology Transfer, and a plant variety protection patent is pending.


4. Accomplishments
1. Molecular test developed to detect virus resistance genes in pea. Pea Seedborne Mosaic virus (PSbMV) is the most destructive viral disease of pea worldwide. It is difficult to screen for virus resistance in the field because aphids are required to transmit the virus, and it is also challenging to develop reliable greenhouse screening methods using specially reared aphids that transmit the virus. Researchers in Prosser, Washington, developed a DNA-based molecular test that was 100% accurate at identifying pea lines with resistance to PSbMV. Pea breeders can use these markers to rapidly and reliably select pea seedlings with virus resistance instead of conducting field or greenhouse screenings that can take several months. This test is currently being used by a company that is providing commercial molecular testing to pea breeders.

2. New environmentally friendly pinto bean cultivar developed. Pinto beans are the most widely grown dry bean market class in the United States. Researchers in Prosser, Washington, released a new pinto bean cultivar “USDA-Rattler”, which was developed for superior performance under both low and high input production systems. USDA-Rattler exhibits tolerance to drought and low soil fertility that allows it to be grown with less water and fertilizer inputs. It also has excellent disease resistance to Bean common mosaic virus and bean rust that expands its range of production across the United States. A major seed company has expressed interest in licensing this versatile pinto bean cultivar that has excellent yield potential under less favorable growing conditions.


5. Record of Any Impact of Maximized Teleworking Requirement:
The maximized telework requirement prevented the testing of inoculated pea lines for the presence or absence of the Bean leafroll virus in our greenhouse screening tests that were conducted. The tissue was frozen at -80 C for future testing. Maximized telework also prevented at least four greenhouse Fusarium root rot screening trials from being conducted to assess the resistance of pea lines to Fusarium avenaceum.


Review Publications
Coyne, C.J., Porter, L.D., Boutet, G., Ma, Y., McGee, R.J., Lesné, A., Baranger, A., Pilet-Nayal, M. 2019. Confirmation of Fusarium root rot resistance QTL Fsp-Ps 2.1 of pea under controlled conditions. Biomed Central (BMC) Plant Biology. 19:98(2019). https://doi.org/10.1186/s12870-019-1699-9.
Ma, Y., Coyne, C.J., Sankaran, S., Main, D., Porter, L.D., Mugabe, D., Smitchger, J., Zhang, C., Amin, M., Fasheed, N., Ficklin, S., McGee, R.J. 2020. Dissecting genetic architecture of Aphanomyces root rot resistance in lentil by QTL mapping and genome-wide association. International Journal of Molecular Sciences. 21(6):2129. https://doi.org/10.3390/ijms21062129.
Cichy, K.A., Wiesinger, J.A., Berry, M., Nchimbi-Msolla, S., Fourie, D., Porch, T.G., Ambechew, D., Miklas, P.N. 2019. The role of genotype and production environment in determining the cooking time of dry beans (Phaseolus vulgaris L.). Legume Science. 1(1):e13. https://doi.org/10.1002/leg3.13.
Mndolwa, Msolla, S.N., Porch, T.G., Miklas, P.N. 2019. CGE biplot analysis of yield stability for andean dry bean accessions grown under different abiotic stress regimes in Tanzania. African Crop Science Journal. 27:413-425.
MacQueen, A., White, J.W., Lee, R., Osorno, J., Schmutz, J., Miklas, P., Myers, J.R., McClean, P., Juenger, T. 2020. Genetic associations in four decades of multienvironment trials reveal agronomic trait evolution in common bean. Genetics. 215:267-284. https://doi.org/10.1534/genetics.120.303038.