Duration: 10/01/2025 to 09/30/2030

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

Common bean (Phaseolus vulgaris L.), and other Phaseolus species, including lima (P. lunatus L.) are important crops in the United States (U.S.) with a farm-gate value $2.6 billion in 2023 (USDA-ERS, 2024). Common bean is the most important pulse crop worldwide and plays an important role in food and nutritional security (Siddiq et al., 2022). Most common and lima beans are distributed as dry seeds, canned, or in the fresh market. Demand is expected to continue rising as consumer interest in plant-based diets for health reasons continues to grow and with the expected expansion of ethnic groups in the U.S. with culinary traditions of bean consumption. More efficient use of inputs such as water and nitrogen are needed to reduce production costs, preserve scarce resources, and avoid environmental contamination. Numerous abiotic and biotic stresses threaten both dry and succulent bean production. Fungal, bacterial, and viral diseases are among the main production constraints (Beaver and Osorno, 2009; Parker et al. 2022; Schwartz et al., 2005), whereas extreme weather events (such as drought, flooding, and heat), soil mineral deficiencies, and short growing seasons reduce productivity (Beebe et al. 2011; Uebersax et al., 2022; Vandemark et al., 2014; Barrera et al. 2024).

Most common bean varieties are denser in protein, fiber, and certain essential micronutrients (Havemeier et al., 2017; Leterme, 2002; Mitchell et al., 2009; Winham et al., 2008) than commodity crops such as soybeans, maize, and wheat (Triticum aestivum L.). The nutritional benefits of common beans were recognized in the 2015 Dietary Guidelines for Americans recommendations, which state that “beans may reduce your risk of heart disease and certain cancers” and “scientists recommend that adults consume three cups of beans per week to promote health and reduce the risk of chronic diseases” (De Salvo et al., 2016). That recommendation has fluctuated between 1.5 and 3 cups per week in the past few five-year cycles.  However, in the U.S., dry beans are a minor part of the diet. From 1999 to 2002, about 8% of the population consumed beans, peas, or lentils on any given day (Mitchell et al., 2009). There is an opportunity to increase bean consumption by improving traits important to consumers, such as convenience, nutrition, and taste.

Several diseases may occur simultaneously, reducing the yield and quality of all bean classes within and across production regions. Yield losses can range from 10% to 90%, depending on the disease incidence and severity. For example, in the western United States, Beet curly top virus (BCTV), Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), Fusarium root rot (caused by Fusarium solani f.sp. phaseoli), Fusarium wilt (caused by Fusarium oxysporum f.sp. phaseoli), and white mold (caused by Sclerotinia sclerotiorum), may simultaneously infect susceptible cultivars. Many of these pathogens are highly variable in their virulence and new races or strains can appear in different regions; for example, more virulent rust races emerged in Michigan and North Dakota that overcame the widely deployed Ur-3 rust resistance gene (Markell et al., 2009; Wright et al., 2008). Many of these diseases are caused by seed-borne pathogens that are genetically variable and cannot be economically controlled with chemicals (e.g., common bacterial blight, halo blight, brown spot, bacterial wilt and BCMV). Further, the use of fungicides increases production costs and results in environmental and human health hazards if improperly used. Pyramiding host plant resistance to multiple pathogens into new bean cultivars through breeding is the most effective and sustainable solution for disease management.

As shown in several studies, the genetic base of dry and snap bean cultivars within most market classes in the U.S. is narrow (McClean et al., 1993; Miklas, 2000; Parker et al., 2022; Silbernagel and Hannan, 1992; Sonnante et al., 1994; Wallace et al., 2018) because only a very small number of wild bean ancestors were domesticated (Gepts et al., 1986; Kwak et al., 2009; Papa and Gepts, 2003). Consequently, useful traits such as resistance to bruchids (Zabrotes subfasciatus and Acanthoscelides obtectus) are not found in cultivars (van Schoonhoven et al., 1983), supporting the evidence that a large reduction in genetic diversity occurred early during domestication (Gepts et al., 1986; Koenig et al., 1990). Resistance to heat, drought, and diseases such as common bacterial blight and white mold are inadequate in most cultivars grown in the U.S. Thus, new sources of resistance are needed to broaden the genetic base of common beans in the U.S. and to provide broader resistance to highly variable pathogens. The introgression of novel traits from tropical germplasm, often from photoperiod sensitive, non-adapted materials (Porch et al., 2013), is important to make these traits available. Despite stringent requirements for visual seed quality and canning characteristics for each market class, significant progress in genetic improvement has been possible (Bassett et al., 2021; Kelly and Cichy, 2013; Singh, 1999). The recessive slow-darkening gene (sd) has been used by bean breeders in the U.S. to improve the quality of pinto bean seed (Miklas et al., 2024; Urrea et al., 2022).

Reference grade genome assemblies based on long-read genome sequence data coupled with chromosome conformation data were recently completed for eight genotypes representing wild Andean and Middle American germplasm, and representatives from each of the six races of common bean.  De novo assembly of 130 additional genotypes will capture additional genomic diversity not discovered in the eight reference genome assemblies.  Full reference genome annotations for each reference grade assembly, built with full-length mRNA data, will capture more alternatively spliced genes.  A large catalog of nucleotide-binding leucine repeat genes, the major class of disease resistance genes, will be captured across the full range of common bean diversity.  A near term goal is to develop a graph-based pan genome that incorporates the genic and non-genic diversity in common bean.

The common bean reference genome sequence; the reference grade genome assemblies based on long-read genome sequence data coupled with chromosome conformation data for eight genotypes representing wild Andean and Middle American germplasm, and representatives from each of the six races of common bean; and the reference genome for tepary bean and a wild tepary bean genome sequence, have all led to the rapid development of associated genomic technologies and accelerated the improvement of Phaseolus beans (Moghaddam et al., 2021; Schmutz et al., 2014; Vlasova et al., 2016). Through integration and collaboration with other projects, genomic resources are readily available for genotyping and genetic studies, and for developing and deploying markers for key disease (biotic) and abiotic resistance traits. The BARCBean6K_3 bead-chip with 5,398 SNPs developed through the BeanCAP project and the BARCBEAN12k_HTS chip (developed during the W-4150 project) with over 11k SNPs are broadly used by the W-4150 for the investigation of agriculturally important traits. Genotyping-by-sequencing (GBS) is also being implemented for Genome-Wide Association Studies (GWAS) in conjunction with the numerous nurseries and multi-state trials coordinated by this research group. The development of the PhaseolusGenes marker database has facilitated the design of several markers for marker assisted selection (MAS) (Miller et al., 2018). The integration of SNP markers that aid the development of dense genetic maps, their application to association and QTL mapping, and finally, their use in MAS will allow for more precise identification of regions associated with the key traits of interest mentioned above. Over 30 key SNP markers, associated with primarily with disease and insect pest resistance but also with traits such as slow seed coat darkening, have been developed and are publicly available through the Intertek KASP platform (http://www.bic.uprm.edu/wp-content/uploads/2023/12/Tm-shift-SNP-markers_List_For-BIC-11-01-23-pm2_asg2.xlsx) and are being broadly used for marker assisted selection.

Given the extensive amount of information on resistance sources, bean breeders are poised to build more selective gene pyramids of both Andean and Middle American disease resistance sources to stem the rapid evolution of new races of pathogens. However, this task remains challenging because breeders work on many traits at the same time and changes in one character can affect outcomes in another. The identification of bridging genotypes at the International Center for Tropical Agriculture (CIAT) (Barrera et al., 2022) may facilitate interspecific crosses between tepary and common beans to broaden the genetic base, and lead to improvement of both crops. A short read-based genotyping platform was also tested in a multi-state lima bean effort, and marker development for key domestication/adaptation traits is underway for limas in that same project with examination of synteny and homology with common bean.

Genetic diversity panels were established and have been used to discover regions associated with many important production traits through GWAS.  These panels include a wild bean panel, a snap bean association mapping panel (SnAP), an Andean Diversity Panel (ADP), a BeanCAP Mesoamerican Diversity Panel (MDP), a Durango Diversity Panel (DDP), a Yellow Bean Collection (YBC), and a Tepary Diversity Panel (TDP), and a subset of the USDA National Plant Germplasm System lima bean collection (most of which is thought to be photoperiod-sensitive). The ADP, for example, is a compilation of approximately 396 lines of large-seeded dry bean lines that come from breeding programs in the U.S., and varieties, landraces, and accessions from African and South American countries where Andean beans originated (Cichy et al., 2015). The ADP is proving essential in discovering useful genes for developing Andean bean varieties that are more productive, drought tolerant, and disease resistant than what is currently being grown in the U.S. (Soltani et al. 2018). Plant breeders need to narrow the gap in seed yield potential between Andean bean cultivars which often have significantly lower seed yield potential than Mesoamerican bean cultivars (Singh et al., 2002).

This interdisciplinary, multi-state, collaborative W-5150 project comprises several complementary sub-projects (see Appendix Table 1). Key collaboration among participants in these sub-projects is designed to achieve our overall goals and objectives of developing high yielding cultivars with enhanced culinary and nutritional qualities (and other aspects of seed quality) and resistance to major abiotic and biotic stresses. Extensive natural variation is being observed for multiple key nutritional traits in Phaseolus beans, which will be helpful to evaluate and dissect within and across germplasm sets and production regions. Other aspects of seed quality include visual appearance (and concordance with accepted market types) including after mechanical harvest, and seed longevity and viability. These improved cultivars will help reduce production costs and pesticide use, increase yield and competitiveness of U.S. bean growers, and sustain production for domestic consumption and export. Researchers participating in each sub-project have complementary expertise and represent two or more institutions. The inclusive group of bean researchers jointly prepared the project renewal and is committed to collaborating to achieve the overall project objectives.

Justification:

A multi-state collaborative research project for Phaseolus beans can address the many constraints that are shared among bean production regions in the U.S. Collaborative research promotes efficiency, accelerates genetic progress, avoids duplication of work, and conserves economic and physical resources. Collaborators are more likely to share information which broadens impact. Early communication integrates emerging knowledge into research. New cultivars can be selected to have superior culinary (and other aspects of seed) quality, wider adaptation, and more durable resistance to pathogen variability and environmental fluctuations that occur year to year. A multi-state collaborative research project promotes communication among dry and succulent bean researchers to address shared constraints. Ultimately, the entire bean industry (both seed and food) benefits from the knowledge and products developed by this project. Specific examples that identify the need and benefits of this multistate collaborative project are described in the following paragraphs.

Anthracnose, white mold, viruses, halo blight, rust, root rots, and other diseases caused by hyper-variable and/or emerging pathogens, require extensive and continued investigation, including developing appropriate screening methods for multi-location field and greenhouse environments. White mold, for example, involves field and greenhouse trials from multiple locations for the identification of avoidance and physiological resistance with any degree of assurance. It is, therefore, essential to continue to characterize and monitor virulence variability of bacterial, fungal, and viral pathogens causing major bean diseases in the U.S. Also, it is imperative to determine the reaction of specific resistance genes and identify potential sources of resistance in bean germplasm to pathogenic diversity so breeders can identify useful combinations of specific genes and identify additional resistance genes and mechanisms that will broaden the genetic base of new bean cultivars.

Introgression and pyramiding of favorable alleles and QTL across races, gene pools, and related wild and cultivated Phaseolus species into cultivars is often achieved only through a stepwise tiered breeding approach that often involves introgression of useful genes from wild or exotic germplasm into adapted cultivars for the temperate regions of North America (Kelly et al., 1998; Osorno et al., 2022; Singh, 2001; Singh et al., 2007; White and Singh, 1991).

The role of genomics and marker-assisted selection as an additional tool for bean breeders has become increasingly important (Miklas et al., 2006) and requires collaborations among scientists across different states or countries (Gepts et al., 2008; McClean et al., 2008). Inter-disciplinary and inter-institutional collaborative research must continue to find alternative recombination and selection methods and identify and use molecular markers to facilitate efficient introgression and pyramiding of favorable alleles and QTL into improved cultivars for diverse cropping systems. Thus, when developing improved germplasm lines and cultivars with multiple-disease resistance and tolerance to abiotic stresses and excellent culinary (and other aspects of seed) quality, researchers with limited expertise, resources and facilities can share responsibilities and exchange segregating populations and breeding lines to complement screening and selection in contrasting field environments, laboratories, and greenhouses regionally and nationally, and to form training populations for use in genomic selection that could have predictive ability across multiple projects and programs.

The use of winter nurseries in Puerto Rico (and preliminarily, the Coachella Valley of California for lima beans) accelerates the development of breeding lines in early generations and expedites the conversion of useful tropical and sub-tropical germplasm that are poorly adapted to temperate bean growing environments in the U.S. Breeding populations can be rapidly developed from crosses between adapted × exotic germplasm, followed by backcrossing in the short-day photoperiods of the tropics or in the greenhouse during the winter months. Furthermore, hybridization in the tropics is often alternated by selection for photoperiod insensitivity on the U.S. mainland during the growing season. A shuttle breeding program between Nebraska and Puerto Rico has accelerated the breeding cycle, increased genetic diversity and broadened the adaptation of bean germplasm lines (Urrea et al., 2022, Beaver et al., 2020).

Exotic germplasm is increasingly being used to broaden the genetic base of cultivated crops and develop cultivars with higher yield potential, enhanced end-use and nutritional quality, and greater resistance to abiotic and biotic stresses (Parker et al., 2022). It is essential to evaluate advanced breeding lines and cultivars developed from the conversion process across production regions, to select for broad adaptation and stability of performance. Regional and national germplasm development and testing are also important because only one growing season per year is feasible in the continental U.S. In addition, the W-5150 project will continue to conduct annual multi-location testing trials such as the National Cooperative Dry Bean Nursery (CDBN), Midwest Regional Performance Nursery (MRPN), National White Mold Monitor Nursery (WMMN), Succulent Bean Heat Stress Nursery (HSN) and Dry Bean Drought Nursery (DBDN). These nurseries are essential to identify high-yielding, broadly adapted cultivars and breeding lines with durable disease resistance, for estimating genetic progress over time, and for detecting pathogen diversity in the shortest time possible. Therefore, these nurseries will form an integral part and foundation for strong collaborative efforts within the W-5150 project. For example, data from the CDBN was key for estimating yield gains in dry beans for the four most important market classes in the U.S. since 1980 (Vandemark et al., 2014). In addition, plot tours and field days will allow W-5150 researchers, farmers, students, and other people associated with the bean industry to view and evaluate the performance of the lines under different growing conditions. These are conducted annually in Nebraska, North Dakota, Puerto Rico, California, Delaware, South Carolina and Washington. Nursery results are compiled and distributed to all project members and made available to the public via the https://cropwatch.unl.edu/Varietytest-DryBeans/2019%20CDBN%20Final.pdf  web page.

Most private and public cultivars are grown in multiple states and thus require multi-state trials for cultivar development. Each state or institution can only conduct some of the research necessary to develop improved bean cultivars for sustainable production, consumption, and export. This is especially true when most programs need more resources and personnel to carry out a relevant and efficient breeding program for their own state. In addition, funding for dry bean research is significantly less than the resources available in other major crops in which scientific networks are larger and the volume of production and price allow higher investment in research. Unique expertise is available in a few states (e.g. nutritionists and pathologists), and there are several bean-producing states (e.g., Arizona, Colorado, Florida, Idaho, Minnesota, Montana, New Mexico) that do not have public dry or succulent bean breeding programs. Due to the collaborative nature of the W-5150 project, researchers in these states will also have access to new breeding lines and cultivars of all market classes for testing and evaluation. Moreover, research and outreach efforts of agronomists, breeders, molecular geneticists, food scientists, human nutritionists, and plant pathologists must be coordinated to improve domestic consumption and export. Thus, additional resources and multi-state regional and national collaboration are essential to ameliorate the effects of major abiotic and biotic constraints, and food quality problems that currently limit the seed yield potential, domestic consumption, and export of dry and succulent beans. This comprehensive, multidisciplinary, and multi-state collaborative project is vital to maintain, monitor, and exchange pathogens, parental stocks, and improved breeding lines and cultivars, to share research data among all related areas, and to allow a more efficient use of exotic germplasm (Vandemark et al., 2014).

The accomplishments of this project during the previous funding cycles have been well documented in numerous publications and recognized by other scientists [i.e. the Western Association of Agricultural Experiment Station Directors (WAAESD) Excellence Award in March 2009]. The collaborative project offers a broad range of selection environments (from arid to humid and rainfed to fully irrigated) whereby researchers can share and complement findings and advances. Moreover, a coordinated, multidisciplinary effort will allow the efficient shared use of genetic and genomic resources, avoid duplication of research, and maximize efforts to increase bean production, consumption, and export. The W-5150 team includes early career and experienced scientists, which provides a good balance between new cutting-edge technologies, and the expertise and results gained through years of scientific work. Long-term collaboration among a multi-disciplinary group of scientists will enable the multi-state W-5150 project to conduct core research activities and to possess the ability to rapidly address new challenges identified by stakeholders. Based on this feedback from stakeholders, the W-5150 group proposes to continue to enhance genetic resistance to biotic and abiotic stresses. Exotic bean germplasm needs to be characterized and utilized to broaden the genetic base of the crop. Improved nutritional and quality traits promise to enhance the beans’ health benefits and utilization. Improved integrated pest management and agronomic/production practices should lead to more efficient and sustainable bean production systems.

Related, Current and Previous Work

Objectives

1. Increase productivity and stress tolerance for the sustainability of bean cropping systems
   
2. Enhance collaborative regional trials and winter nurseries
   
3. Develop databases and -omic tools to improve breeding efficiency
   
4. Enhance nutrition, processing, and quality traits, and develop products to increase consumption of beans
   

Methods

Measurement of Progress and Results

Outputs

Outcomes or Projected Impacts

Milestones

Projected Participation

View Appendix E: Participation

Outreach Plan

Organization/Governance

Literature Cited

Attachments

Land Grant Participating States/Institutions

DE, NY, PR, SC, WY

Non Land Grant Participating States/Institutions