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

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Phaseolus beans, including common bean (dry and snap beans) and lima bean, are economically important crops in the U.S., with a combined farm-gate value of $2.6 billion. Fungal, bacterial, and viral diseases are among the main production constraints, whereas extreme weather events (drought, flooding, and heat), soil mineral deficiencies, and short growing seasons reduce productivity. Phaseolus dry beans are a rich source of many essential shortfall nutrients in the U.S., but their domestic consumption falls well below recommended dietary guidelines. However, this is rapidly changing because of consumer’s interest in eating healthier and more sustainable foods (e.g. plant-based protein). This project aims to form a collaborative network of researchers working on improving Phaseolus beans to address constraints on bean production and consumption synergistically. Namely, our objectives are to (1) increase productivity and stress tolerance, (2) enhance collaborative regional trials and winter nurseries, (3) develop databases and -omic tools to improve breeding efficiency, and (4) enhance nutrition, processing, and quality traits, and develop products to increase consumption of beans. Key collaboration among participants is designed to achieve our goals and objectives of developing high-yielding cultivars with enhanced culinary and nutritional qualities and resistance to major abiotic and biotic stresses. These improved cultivars will help reduce production costs and pesticide use, increase U.S. bean growers' yield and competitiveness, and increase domestic consumption and export productivity. 

Statement of Issues and Justification

Common bean (Phaseolus vulgaris L.) and other Phaseolus species including lima bean (P. lunatus L.) are important crops in the United States (U.S.) with a farm-gate value of $2.6 billion in 2023 (USDA-ERS, 2024). Common bean is the most important pulse crop for human consumption worldwide and plays an important role in food and nutritional security (Broughton et al., 2003; 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 sustainable and efficient use of inputs such as water and nitrogen are needed to reduce production costs, preserve scarce resources, and avoid negative environmental impacts. Numerous biotic (living or viral) and abiotic (non-living) stresses threaten both dry and succulent bean production. Fungal, bacterial, and viral diseases are among the main production constraints (Beaver and Osorno, 2009; 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 cultivars have higher grain concentrations of 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 3 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, nutritional quality, 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 U.S., 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. In the U.S. Midwest and the Great Plains, diseases such as white mold, bacterial blights, and root rot fungal complexes are the main biotic problems. 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 (Uromyces appendiculatus) emerged in Michigan and North Dakota that overcame the widely deployed Ur-3 rust resistance gene (Markell et al., 2009; Monclova-Santana, 2019; Wright et al., 2008). This required the prompt action of bean breeders to deploy additional resistance genes such as Ur-5 and Ur-11 (Osorno et al., 2020a). Many of these diseases are caused by seed-borne pathogens that are genetically variable and cannot be economically controlled with chemicals. Further, the use of fungicides increases production costs and results in both 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 allele (sd) has been used by bean breeders in the U.S. to improve the quality of pinto bean seed (Miklas et al., 2024; Osorno et al., 2018; Osorno et al., 2024a; Urrea et al., 2022a).

The common bean reference genome sequence 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; Schroder et al., 2016) 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 integration of SNP markers that aid the development of dense genetic maps, their application to association and QTL mapping, and finally, their use in marker-assisted selection (MAS) will allow for more precise identification and monitoring of regions associated with the key traits of interest mentioned above. Over 30 key SNP-based markers associated 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 MAS. 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 pangenome that incorporates the genic and non-genic diversity in common bean.

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 (and phenotypic) 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), white mold MAGIC population, black bean MAGIC population, common bean MAGIC population with a focus on drought tolerance, 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., 2015a). 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. (Sadohara et al., 2024a; Soler-Garzón et al., 2024a). 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., 2001).

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 increase productivity for domestic consumption and export. Researchers participating in each sub-project have complementary expertise and represent two or more institutions across states. 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 provides a collaborative platform that allows researchers to synergistically 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 strengthens and 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.

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. The mode of resistance of many of these pathogens is multigenic, which makes breeding progress even more difficult. 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; 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., 2022b, 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 the 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), 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), and to identify genomic regions associated with traits of interest and local adaptation (MacQueen et al., 2020 and 2022). In addition, plot tours and field days will allow W-5150 researchers, farmers, students, and other bean stakeholders/ 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. Even more concerning is the fact that at least 2 public dry bean breeding programs (e.g. Idaho and Colorado) have been eliminated during the last ~10-15 years. 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, Wisconsin) 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 (Parker et al., 2022; 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 from 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 both 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. Variety development is a multi-year process and therefore, 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, processing, 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

The following is a list of the most important accomplishments and current research activities of the W4150.

Biotic Stresses:

Viruses (AZ, PR, WA):

Potyvirus: Bean common mosaic virus (BCMV) and related Bean common mosaic necrosis virus (BCMNV), are seed-borne potyviruses that plague common bean production worldwide. Major host-pathogen updates reveal that bc-1 and bc-2 resistance genes interact with different bc-u alleles to condition differential effects across viral pathogroups (Soler-Garzón et al., 2021a,b; 2024b). An affinity for recombination among potyviruses has led to more virulent strains and a new pathogroup which threatens effectiveness of host resistance genes (Feng et al., 2015). Markers for the causal mutations within candidate genes have been useful for selecting combinations among I, bc-u, bc-1, bc-2, and bc-3 for enhanced resistance to BCMV and BCMNV in new cultivars (Miklas et al., 2023). More effective gene combinations and introgression of new resistance genes into common bean from tepary bean (Bornowski et al., 2023) will facilitate breeding for sustainable resistance to BCMV and BCMNV.

Geminivirus: Beet curly top virus (BCTV), and related curtoviruses, transmitted by the beet leaf hopper, is a cyclic disease that threatens common bean production in the western U.S. (Creamer, 2020). Whitefly-transmitted geminiviruses, transmitted by the Bemisia tabaci cryptic species (Brown et al., 2023), such as Bean golden yellow mosaic virus (BGYMV) and Macroptilium mosaic virus (Brown, 2010; Brown et al., 1986; 1999; Brown and Idris, 2009; Idris et al., 2003) infect common bean in the subtropical/tropical Americas, including Florida and/or Puerto Rico.  Screening is difficult, in part, because natural epidemics are infrequent and agro-inoculation with available infectious clones for specific strains is tedious and/or infectious clones are not available. Therefore, many breeders rely on marker-assisted selection for the major Bct gene which is effective against all BCTV strains.  Three unique resistance haplotypes based on three SNP markers were recently discovered for the Bct region (Soler-Garzón et al., 2023). The markers are being used by breeders to select the most resistant Bct haplotype Haplo3-1 from race Durango.  A new candidate gene marker for bgm-1, which conditions resistance to Bean golden yellow mosaic virus (BGYMV), a Begomovirus vectored by whiteflies, was recently identified (Soler-Garzón et al., 2021c) and is being used by breeders to develop BGYMV-resistant cultivars for the Caribbean Basin (Beaver et al., 2024a). The presence of QTL BGY8.1 enhances the effect of bgm-1 conditioned resistance.

Bacterial Diseases (CA, MN, NE, ND, PR, WA, WI, WY):

Common bacterial blight (CBB): caused by Xanthomonas axonopodis pv. phaseoli (Xap), continues to limit common bean production east of the Continental Divide.  Breeding for CBB resistance continues to rely on using parental materials possessing major QTL, namely SU91 and SAP6 (Singh and Miklas, 2015). Recovering seed size when deploying SU91 had been a challenge in large-seeded beans (Kelly et al., 2018) until recent development of ‘Red Barn’ kidney bean which possesses CBB resistance and large seed size (Osorno et al., 2024b). Minor QTL conditioning resistance have been detected as well (Simons et al., 2021), but few have been validated. Breeders continue to use MAS for major QTL in combination with pathogen testing to develop CBB resistant cultivars. 

Halo bacterial blight (HBB): caused by Pseudomonas syringae pv. phaseolicola (Psp), is similarly prevalent east of the Continental Divide. The Pse-2 gene protects against 7 of 9 differential Psp races but not against the globally prevalent Race 6. HB4.2 and HB5.1 QTL provide resistance to Race 6 (Tock et al., 2017) and have been used to deploy HBB resistance in snap beans (Rietman, PC 2024). Four QTL intervals on Pv01, Pv03, Pv05, and Pv08 overlapped with bacterial brown spot and HBB resistance (Soler-Garzón et al., 2024a). Continued severe outbreaks of HBB in some major production areas (MN, ND, WI, WY) emphasize the need to continue pathogen variability surveys and breeding efforts to deploy and enhance resistance to this disease.  

Bacterial wilt (BW): caused by Curtobacterium flaccumfaciens pv. flaccumfaciens, has reemerged throughout the irrigated High Plains in 2006 and has been detected in more than 500 fields in NE, CO, and WY since 2004 (Harveson and Schwartz, 2007; Harveson et al., 2015). This pathogen is subject to phytosanitary regulations in some states and countries and is considered an A2 quarantine pest in Europe (EEPO/CABI, 1997). Recent focus has been on evaluating a wide array of bean accessions against local isolates of the BW pathogen from NE and CO. Results reflect differences in pathogenic isolates, environmental conditions, inoculation methodology, etc. For CIAT’s Core Collection, 1,685 accessions were susceptible (99.12%), and 15 accessions showed resistance (0.88%) to multiple BW isolates. Resistant accessions included eight wild beans, four P. coccineus, one P. acutifolius, and two cultivated beans (Urrea and Harveson, personal communication). The bacterial wilt resistance in the G18829/Raven showed a 13:3 (susceptible: resistant) F2 ratio and in the RIL population a major quantitative trait loci (QTL) was detected on chromosome 8 at position 42.7 cM which accounted for 35% of the variation in resistant response. This QTL was named  BW8.1GR, according to the QTL nomenclature guidelines for P. vulgaris (Miklas and Porch, 2010).

Fungal Diseases (CA, DE, MD, MI, NE, ND, PR, SC):

Anthracnose: caused by Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib., is a major seed-transmitted fungal disease that can cause significant yield loss. Planting seed from a field where anthracnose was present, even if those seeds are asymptomatic, will result in yield and quality losses (Halvorson et al., 2021). In addition to using certified seed, genetic resistance conditioned by major genes (Ferreira et al., 2013) and QTL (Shafi et al., 2022) provide useful disease control. The pathogen is hypervariable with 100’s of races identified, so resistance genes deployed must be effective against endemic and emerging races such as the 105/109 race complex in Manitoba, MI, and ND.  There have been many recent genomic studies (GWAS, classical mapping) conducted to identify novel and useful resistance available in different backgrounds such as in yellow (Kuwabo et al., 2023), pinto (Mwense et al., 2024), and climbing beans (Maldonado-Mota et al., 2021). Fine mapping and candidate gene analysis of the Co-1 (Richard et al., 2021) and Co-4² loci (Burt et al., 2015) has been a priority because they confer broad resistance. MAS for anthracnose resistance in common bean has experienced successes (Zaleski-Cox et al., 2023), but improvements are needed. For instance, the markers for Co-1 do not distinguish the series of five alleles for the locus (Co-1 to Co-1⁵), and markers for other loci (Co-2, Co-5, Co-6) need updating.  Adult Plant Resistance (APR), also known as Age-Related Resistance (ARR), has also been shown to have some effect in partial levels of tolerance to this fungal disease (Simons et al., 2022).

In lima beans, anthracnose is caused by Colletotrichum truncatum (Schwein). As with anthracnose in common bean, this fungal pathogen is seed-transmitted and often yield-limiting. However, much less is known about genetic resistance in this pathosystem than with anthracnose of common bean. The last United States-based study on lima bean anthracnose was published over seventy years ago (Cox, 1950). Putative resistance has been observed in the field in South Carolina, but additional investigation is needed to identify pathogen races and sources of resistance in lima bean germplasm.

Root rots: Root rot disease is caused by a complex of soil-borne fungal pathogens, including Fusarium solani f. sp. phaseoli, Rhizoctonia solani, Pythium spp. and in some cases, Aphanomyces euteiches. These pathogens attack roots and the crown of bean plants, mostly at early stages and 60% yield losses have been reported (Hall, 1996; Keenan et al., 1974). Infected plants are more vulnerable to abiotic stresses, such as drought, because they lack a healthy root system. F. solani is the most common causal agent of root rot in NE, ND, and MN, and is followed by R. solani in importance (Bradley and Luecke, 2004; Venette and Lamey, 1998). Seed treatments are somewhat effective, at early stages (emergence), but quantitative genetic resistance is needed to control root rots. Several genomic regions associated with root rot resistance have been reported and are being selected in breeding programs (Hagerty et al., 2015; Oladzad et al., 2019a; Soltani et al., 2017; Wang et al., 2018). Genotypes belonging to the Andean gene pool are generally more susceptible to the root rot pathogens. Several cultivars have been released with intermediate levels of resistance/tolerance.

Rust: caused by Uromyces appendiculatus (Pers.) Unger, and with many different pathogen races reported, infects common bean worldwide. The rapid rise of new races underscores the need for new resistance genes.  For instance, a new race 20-3 in ND overcomes Ur-3, Ur-4, Ur-5, Ur-9, and Ur-13 resistance genes (Monclova-Santana, 2019). The broad resistances in common bean landraces PI 310762 (Hurtado-Gonzales et al., 2016), G19833 (Chaucha Chuga), and PI 260418, and in tepary bean TARS-Tep 22 and -Tep 23 (Porch et al., 2024a) are under investigation for effectiveness against new strains in the U.S. New SNP based markers have been developed for MAS of Ur-3, Ur-4, Ur-5, and Ur-11 genes and have revealed epistatic interactions (Hurtado and Pastor-Corrales, 2019). The Ur-11 gene in common bean accession PI 181996 was recently associated with candidate genes and narrowed genomic intervals on Pv11 (Erfatpour et al., 2025; Valentini et al., 2025) which will yield improved markers. However, the markers for Ur-11 from PI 181996, are not completely diagnostic for Ur-11 derived from other landraces (PI 151388, PI 190078). Recent dry bean cultivar releases characterize the rust resistance present using gene-linked SNP markers (Miklas et al., 2023, 2024; Osorno et al., 2020a and 2021; Urrea et al., 2019). 

White mold: is caused by Sclerotinia sclerotiorum. Integrated management, including genetic resistance, is used to reduce losses. The multi-state bean white mold nursery (BWMN) supported by the National Sclerotinia Initiative (NSI - https://www.ars.usda.gov/plains-area/fargo-nd/etsarc/docs/national-sclerotinia-initiative/), is used to verify resistance in bean lines in multiple field nurseries and greenhouse straw tests. Several new cultivars were recently identified with white mold tolerance in the BWMN (Kelly et al., 2021). To develop MAS for WM resistance, breeders have focused on identifying, validating, and refining major QTL intervals with stable expression across populations and environments (Escobar et al., 2022; Oladzad et al., 2023; Roy et al., 2023). GWAS of the SnAP snap bean diversity panel has revealed that resistance to white mold is a function of many genes, generally with small effect and strongly influenced by the environment (Arkwazee et al., 2022). Resistance QTL identified in snap beans appears to be different from those QTL found in dry beans and may constitute a unique source for introgression into dry beans. Genomic selection can provide a means to capturing high levels of resistance to white mold given the existing genetic architecture (Escobar et al., 2022). Genotyping and multivariate analysis indicate that geographical region of origin is the strongest determinant of pathogen population structure and aggressiveness (Kamvar et al., 2017; Pannullo et al., 2019), underscoring the importance of the BWMN for screening for resistance. The level of aggressiveness of isolates in laboratory screening must be standardized for consistent results (Miorini et al., 2019), and simple pairing of isolates to determine mycelial compatibility is no longer considered sufficient for population characterization (Kamvar and Everhart, 2019).

Pythium pod rot: Pythium spp. are a major constraint to bean production causing disease below ground as Pythium root rot and above ground as Pythium pot rot. Pythium pod rot infects pods, leaves and stems with profuse growth of fluffy, white mycelium leading to wet rot of the tissues. Infection can spread in transit leading to additional losses post-harvest (Harter and Whitney, 1927).  Pythium pod rot has been reported as the most problematic pod decay disease in Oklahoma, Arkansas, and Missouri, predominantly caused by P. ultimum and P. aphanidermatum (Damicone et al., 2012; Olson et al. 2016). Extension visits to commercial bean production fields have identified Pythium pod rot as one of the most common disease issues in South Carolina and Delaware. Disease control through fungicide application was inconsistent between years and limited to 40% control in field trials (Damicone et al., 2012). Identification of host plant resistance and the underlying causal loci has focused on Pythium root rot resistance (Campa et al., 2010; Dramadri et al., 2020). Germplasm screening for resistance to Pythium pod rot has been limited to fewer than 20 snap bean cultivars (Damicone et al., 2012), which found only partial resistance, and no genetic analyses have been reported to date.

Nematodes (CA, DE, MN, ND, SC):

Soybean cyst nematode (Heterodera glycines; SCN): is the most devastating pathogen of soybean (Glycine max L.), resulting in over $1 billion in annual losses in the US alone (Wrather et al.,1997). Dry bean is also susceptible to SCN, with the potential for up to 50% seed yield losses before plants show symptoms (Poromarto et al., 2010). SCN is becoming an important production issue in North Dakota and Minnesota, the largest producing region in the country. Studies have shown that different market classes of dry bean exhibit varying levels of susceptibility to SCN, with kidney and snap bean tending to be more susceptible than pinto and black bean (Poromarto and Nelson, 2009). Importantly, it was also observed that SCN inoculum from dry bean plants could successfully infect and reproduce on soybean plants, increasing the risk of contamination between soybean and dry bean fields. Any movement of the soil, such as with machinery, irrigation, tillage, or human interference, will also facilitate SCN spread within and across fields (Arjoune et al., 2022).  Pathogen variability also contributes to epidemics as multiple populations of SCN have been identified and characterized in North Dakota, with HG type 0 being the most common, followed by HG types 7 and 2.5.7 (Chowdhury et al., 2021). The presence of these additional HG types poses a new challenge, as cultivars resistant to one HG type may not be resistant to others. Some genomic regions associated with SCN tolerance have also been identified (Jain et al., 2016 and 2019). Recent breeding efforts led to the release of the first dry bean cultivar with tolerance to SCN (Osorno et al., 2020a).

Southern root-knot nematode (RKN): Meloidogyne incognita, is an increasing threat to lima bean production in sandy soils on the Delmarva Peninsula and in certain California production regions. Meloidogyne javanica also damages lima bean in California. Chemical and cultural controls for these two root-knot nematode species are limited and field surveys in Delaware have identified local populations that are 60 times over the high damage threshold. None of the green baby lima varieties currently used for production in the Mid-Atlantic region are resistant to RKN. Some white seeded cultivars used in California production are resistant to one or both RKN species. A program to breed new green baby lima varieties with RKN resistance was initiated at the University of Delaware in 2013 (Traverso et al., 2024), and RKN resistance is also a goal of the UC Davis lima breeding program. Screening of diverse lima accessions from the USDA National Plant Germplasm System and recombinant inbred line populations for resistance to both species is underway by nematologists at UC Riverside as part of a collaborative lima project across states (including the UC Davis, Delaware, and Clemson breeding programs, USDA NPGS, and the National Center for Genome Resources).

Insects (CA, FL, ND, PR):

Asian bean flower thrip, Megalurothrips usitatus (Bagnall) (Thysanoptera: Thripidae), is an invasive insect pest originating from the Asian tropics that became established in south Florida in 2020 (Soto-Adames 2020). Since 2020, M. usitatus has become established in the Caribbean, Central America, and Mexico. Megalurothrips usitatus damages foliage, flowers, and pods of Phaseolus vulgaris and other legumes through feeding and egg laying (Chang, 1987; 1988). As a major pest of common bean, M. usitatus poses a significant threat to food security in Central America and the Caribbean. In the U.S., M. usitatus is still confined to south Florida, where it has significantly impacted the state’s snap bean industry. Crop consultants and bean growers in south Florida have communicated that M. usitatus infestations require them to apply insecticides earlier and more frequently to snap bean than was necessary prior to its establishment. There is a need to i) describe the importance of alternate hosts, ii) identify temporal and spatial factors influencing M. usitatus abundance and risk, and iii) examine insecticide efficacy and resistance profiles for M. usitatus.

 

Bruchids: Common bean in the tropics and subtropics is subject to severe damage from post-harvest insect pests, including the common bean weevil/bruchid (Acanthoscelides obtectus [Say]) and the Mexican bean weevil/bruchid (Zabrotes subfasciatus [Boheman]) (Myers et al., 2021). Genetic resistance was initially found in wild common bean genotypes (Singh and Schwartz, 2010). Additional sources of resistance within P. vulgaris have been scarce and mostly anecdotal with few exceptions (Li et al., 2022; Maro et al., 2017, 2022, Porch and Beaver 2022). Effective resistance to both species of bruchids was identified in wild tepary bean (P. acutifolius Gray) accession G40199 (Myers et al., 2001). Recent screening of Tepary Diversity Panel (TDP) has allowed the identification of additional accessions of wild tepary bean (Porch et al., 2023) with levels of resistance either better or similar to G40199 (Myers et al., 2001). Interspecific hybridization between G40199 and common bean resulted in the development of an introgression line AO-1012-29-3-3A resistant to A. obtectus (Kusolwa et al., 2016).  This resistance combined with other sources has led to bruchid resistance in commercial market classes of importance in Africa and Latin America such as Mesoamerican black and red beans (Beaver et al., 2024b) and Andean yellow, cranberry (sugar types), red-mottled, and purple-speckled (Kablanketi types) beans (Myers et al., 2021). MAS for resistance is a major focus because screening for resistance using seed weevil infestations is laborious and difficult. Bruchid resistant bean cultivars have not been widely deployed, therefore questions remain concerning the durability of resistance when exposed to different biotypes of common bean and Mexican bean weevils (Beaver et al. 2024b).

Lygus:  Damage to lima bean leaves, pods, and seeds by the lygus bug (Lygus hesperus) continues to reduce yield and seed quality in dry (i.e., harvested from mature pods) lima beans. Cyanogenic glucosides are biosynthesized in limas (unlike in common bean, though also appearing in sorghum and cassava among other food crops) and were found in limas to be protective against a generalist herbivore and seed storage pests (Cuny et al. 2019, Shlichta et al. 2018, Lai et al. 2020). In the past few years, lygus tolerance has been evaluated and mapped in the UC92/UC Haskell recombinant inbred line population and in a lima diversity panel under sprayed and unsprayed conditions, and cyanogenic glucoside levels were evaluated in multiple tissues using Feigl-Anger paper (Dohle et al. 2017, Zullo et al. 2021, and Gibson et al. 2022). Those results are being written up for publication and are being made available to inform breeding.

 

Abiotic Stresses (CA, DE, MI, NE, ND, PR, SC, WA, WY):

Drought and high temperature stress are the primary environmental production constraints of common bean and the major components of climate change. Based on current models, 20-50% of the worldwide production area may be unsuitable for common bean by 2050 (Rippke et al., 2016). Extreme weather events have become more frequent which can result in flash droughts (Christian et al., 2023) or flooding (Stott, 2016).

 

Drought tolerance: Drought represents a threat to about 70% of common bean production areas, while improvements in heat tolerance and drought tolerance could increase areas suitable for common bean production by 54% and 31%, respectively (Beebe et al., 2011). Western U.S. production is currently being affected by an extended period of drought, or Megadrought (Williams et al., 2022; 2020). The combination of heat and drought stress in the U.S. Midwest has been blamed for recent broad yield reductions in crops (Hatfield et al., 2018), while changes in the environment can affect the composition, severity, and regularity of pests and diseases (Fisher et al., 2012; Deutsch et al., 2018).

 

Early genetic studies found that seed yield was the most reliable phenotypic measure of drought tolerance (Ramirez-Vallejo and Kelly, 1998; White et al., 1994). Recent studies investigated the genetics of drought response in terms of yield in diverse environments (Diaz et al., 2020; Hoyos‐Villegas et al., 2017; Valdisser et al., 2020) and identified QTL for mechanistic traits such as photosynthetic response (Dramadri et al., 2021). Izquierdo et al. (2023) also conducted a meta-analysis of yield, yield components, and phenology under well-watered and drought conditions; they cross-examined QTL mapping and GWAS results and identified orthologous regions shared with two other legume species. These genetic studies have provided useful insights into the genetic complexity of drought and shown site-specific QTLs for drought. Exotic germplasm evaluation and introgression of drought tolerance using novel methods, such as bulk breeding, are being achieved in the Andean gene pool (Sadohara et al., 2024) and through use of interspecifics in the Middle American gene pool (Souter et al., 2017). Wild common bean with an elevated ability to grow despite water-limited conditions (Berny-Mier y Teran et al., 2018), using photosynthate remobilization (Berny-Mier y Teran et al., 2019), and decreased pod dehiscence (Parker et al., 2019a) are examples of promising traits. The development of a collaborative drought nursery (DBDN) and the use of the shuttle breeding approach between NE and PR (Urrea et al., 2022b) has helped to identify broad drought adaptation and integrate new sources of tolerance into breeding programs. As a result of these breeding efforts, common bean (Miklas et al., 2023) and tepary bean (Porch et al., 2024a) cultivars with drought tolerance have been released in the U.S.

Tepary bean is a major focus as a source of abiotic stress tolerance. Several tepary bean accessions adapted to drought, heat, and well-irrigated conditions across multiple climate zones were identified (Barrera et al., 2024). Tepary bean showed the statistically strongest adaptation to terminal drought, followed by lima and common bean (Barrera et al., 2024) as determined by the reduction in grain yield under terminal drought compared to well-irrigated conditions in two California locations with arid summer conditions. Several bridging lines that contain three species, P. vulgaris, P. acutifolius, and P. parvifolius, developed by CIAT, have been able to introduce complex traits from the tepary bean into the common bean without embryo rescue (Barrera et al., 2022). Developing these bridging lines opens the possibility of improving both common and tepary species.

 

Heat tolerance: It is predicted that by 2050, common bean production area worldwide will be reduced by 50% from current production due to global warming (Ramirez-Cabral et al., 2016). High average maximum daytime (> 30°C) and minimum nighttime (> 20°C) temperatures can significantly affect common bean yields (Rainey and Griffiths, 2005a). Common bean reproductive development is particularly sensitive to high temperature stress, resulting in increased floral abscission, damage to male reproductive development resulting in pollen sterility, and a reduction in pod set, seed set, and yield (Rainey and Griffiths, 2002, 2005b; Porch and Jahn, 2001). Post-anthesis embryo and seed abortion can result in reduced seed numbers per pod and reduced seed size and quality (Soltani et al., 2019). Excessive temperature stress can decrease photosynthesis and increase leaf senescence (Traub et al. 2018; Siebert and Ewert, 2014) and affect source-sink relationships (Soltani et al., 2019). Leaf cooling and interactions with vapor pressure deficit (VPD) can affect vegetative response to heat in beans (Deva et al., 2020) and needs further investigation. Early flowering, pollen viability, and seed fill are key reproductive traits recently associated with heat tolerance in the field environment (Vargas et al., 2021). Collaborative work from this group has resulted in the identification of improved sources of heat tolerance for breeding (Oladzad et al., 2019b; Rosas et al., 2023), the elucidation of the genetics of heat tolerance (Oladzad et al., 2019b; Vargas et al., 2021), introgression of tepary bean traits (Rosas et al., 2023), and the generation of improved dry bean (Beaver et al., 2018; Porch et al., 2010; 2012; Rosas et al., 2020), snap bean (Wasonga et al., 2010; 2012), and tepary bean (Porch et al., 2023; 2024) cultivars and germplasm. Due to the concurrence of high temperature stress with other abiotic and biotic stresses, such as common bacterial blight, ashy stem blight, root rot and drought, breeding work has focused on combining multiple stress tolerance in several major market classes and on the elucidation of mechanisms related to heat tolerance. GWAS (Oladzad et al., 2019b; Vargas et al., 2021) and QTL studies are showing key genomic regions for the development of markers to facilitate MAS in environments where high temperature stress is not yet prevalent or consistent.

 

Flooding tolerance: Legumes, especially common bean, are classified as extremely sensitive to waterlogging, especially at early development stages (Soltani et al., 2017, 2018). In addition, soil salinization is an increasing problem that negatively impacts agricultural lands. Producers in North Dakota (ND) have identified excess moisture and soil salinity as major problems to crop production throughout the state. Similarly, biological nitrogen fixation (BNF) is reduced by the presence of waterlogged and saline soil conditions (Rhodes, 2024). Despite common bean being highly susceptible to waterlogging, few studies have been reported. Soltani et al. (2017, 2018) screened both the Middle-American Diversity Panel and the Andean Diversity Panel under waterlogging stress. In the Middle-American Diversity Panel, they mapped a total of 32 and 28 genomic regions associated with seven traits in non-flooded and flooded conditions, respectively, which were largely unique for each condition (except in the case of hypocotyl length). Races Durango and Jalisco were reported as the most tolerant at the seedling stage. In the Andean Diversity Panel, they detected a total of 45 associations (four in both conditions, 19 only in non-flooded conditions, and 22 only in flooded conditions) for eight traits. However, the number of tolerant genotypes found across market classes was very low. Therefore, testing wild accessions and closely related species of common bean under waterlogging condition in the greenhouse is important to identify additional sources of tolerance and to understand the morpho/physiological mechanisms that common bean can use to cope with this abiotic stress (Velazquez, 2024). Continued research and development of lines with increased waterlogging and salinity tolerance is warranted.

 

National/Regional Nurseries (CA, CO, MD, MI, ND, NE, NY, OR, PR, WA):

This multi-state project coordinates five nurseries grown every year: the Bean Rust Nursery (BRN) grown in Beltsville, MD, the national Cooperative Dry Bean Nursery (CDBN) grown at eight locations across the country and one in Canada, the Midwest Regional Performance Nursery (MRPN) grown in three states, the Bean White Mold Nursery (BWMN) grown at seven locations, and the Dry Bean Drought Nursery (DBDN) grown in five states. The Succulent Bean Heat Stress Nursery (HSN) will be added to the W-5150 to evaluate heat stress tolerance in breeding lines and commercial cultivars of snap and lima beans in South Carolina and Delaware. These nurseries have facilitated the evaluation of genotypes across multiple environments and consequently, the release of several cultivars and germplasm lines that have been used in more than one production area.

Private bean breeding programs are invited to submit genotypes to the CDBN and HSN, which allows mutual benefits, communication, and collaboration between the public breeding programs and the private sector. In addition, these nurseries provide long-term databases with genetic and agronomic information that can be used as a tool to estimate genetic gains and for modeling effects of climate and photoperiod on performance.

Health, Nutrition, and End-Use (CA, NE, ND, NY, MI, SC, WA)

 

Phaseolus dry beans are a rich source of many important shortfall nutrients in the U.S., including dietary fiber, folate, calcium, magnesium, and iron (Papanikolaou et al., 2024; USDA and Health and Human Services, 2020). While snap beans have less protein and total carbohydrates than dry beans, they possess certain vitamins and carotenoids that dry beans lack or have only in trace amounts. These include vitamin C, β-carotene, lutein and zeaxanthin, α-tocopherol, and phylloquinone (Myers et al., 2019).  Dry beans are an abundant source of health promoting bioactive compounds, such as polyphenols, alpha-amylase inhibitors, and resistant starch (Preuss, 2009; Wiesinger et al., 2022).  Consumption of 150 g (~1 ½ servings) of cooked pulses per day is associated with positive health outcomes related to blood lipid profile, blood pressure, inflammation markers, and body composition (Ferreira et al., 2021). Pulse consumption is associated with increased satiety and weight loss (Clark and Duncan, 2017; Kim et al., 2016).

As a low glycemic food, beans help in the management of blood sugar after a meal, especially for individuals with type 1 or type 2 diabetes (Jenkins et al., 2012). Bean consumption may also lower factors associated with cardiovascular disease including LDL cholesterol and blood pressure (Bazzano et al., 2011). Adding beans to a diet may reduce a person’s risk for and the incidence of some cancers, such as colon cancer. Polyphenolic compounds as well as the non-digestible carbohydrates, including soluble and insoluble fiber, resistant starch and oligosaccharides have all been shown to be important factors in the anti-cancer properties of beans (Bobe et al., 2008; Haydé et al., 2012).

 

Dry beans are traditionally consumed as a whole grain and require long cooking times in boiling water to become palatable, thereby limiting utilization globally. Large genetic diversity for cooking time has been characterized (Cichy et al., 2015b). Phenotypic selection for fast cooking beans has thus far proven to be a successful breeding strategy, and cooking times as fast as 15 minutes have been achieved under ideal conditions. Several physical and chemical characteristics that vary among different bean genotypes and market classes can influence the physico-chemical properties of the final cooked products (Baidhe et al., 2024; Choe et al., 2022). Other avenues to improve the convenience of dry beans for consumers include use as canned products and as an ingredient. Cans are the major form in which American consumers access beans. The value of canned bean products was $2.5 billion in 2020, and canned beans represent 82% of all bean dollars (personal communication, Nielsen Consumer LLC, 2021).  Based on the importance of canned beans, canning quality, defined as how beans hold together during thermal processing, is an important consideration for variety improvement in bean breeding programs.  A standardized small-scale canning processing and evaluation protocol is used to assess genetic variability for canning quality in multiple U.S. bean breeding programs (Wang et al., 2022).  Given the new interest in plant-based protein, dry bean flours have the potential to increase convenience and use of beans among U.S. consumers. Pulse milling is a relatively new industry without clear specifications for particle sizes, target protein and fiber levels, and moisture contents in place (Thakur et al., 2019). Standardized bean flour specifications are needed to promote the greater use of pulse flours as ingredients in products. There is an opportunity to improve beans through plant breeding to make them more amenable to use as a flour. Popping beans (aka nuña beans) also offer the potential to expand bean consumption as a convenient, nutritious snack food (Rezaey et al., 2024).

Flavor is a major reason consumers choose a food. In the case of dry beans, flavor is an especially important consideration for flours. Beans may contribute strong off-aromas and off-flavors described as beany, vegetative, musty, green, and bitter to flours (Roland et al., 2017). Developing bean cultivars with mild flavor and aroma offers the potential to expand market opportunities for bean products. Market class and genotype have been shown to contribute to variability in aroma and flavor, and a trained sensory panel found total flavor and beany to be the most highly heritable flavor attributes (Bassett et al., 2021). Lima beans may present a partially distinct set of sensory challenges, as limas have been noted to taste starchy or chalky; identification and optimization of off-flavors and preferred flavors by various consumer segments is of interest, and sensory/culinary evaluations are ramping up.

Significant advances have been made over the past few years in knowledge of factors and genes that promote and inhibit the nutritional quality of iron (Fe) in beans.  Flavonoids present in the seed coat are the primary factors that influence the bioavailability (absorbability) of Fe from beans (Hart et al., 2015, 2017, 2020). Many of these compounds are inhibitors of Fe absorption, however, some have been shown to be promoters of Fe bioavailability (Hart et al., 2017; Wiesinger et al., 2018, 2019a,b). Moreover, recent studies have demonstrated that significant opportunities and potentials exist to identify and develop varieties across multiple market classes that provide high levels of bioavailable Fe (Wiesinger et al., 2021; Glahn et al., 2024). Given that dry beans are an integral component of food systems worldwide, these nutritional advances have the potential to alleviate Fe deficiency worldwide and domestically for individuals at risk of anemia.

Genomics (CA, MI, ND, PR, WA)

Genomics: Extensive SNP data sets for the Middle American (MDP) and Andean Diversity Panels (ADP) (Cichy et al., 2015a; Moghaddam et al., 2016; Schröder et al., 2016) were used to discover genetic loci associated with agronomic traits (maturity, growth habit, lodging) under non-stress, heat and drought stress environments (Oladzad et al., 2019b). These panels were also evaluated under flooding conditions, and genes associated with growth parameters were discovered (Soltani et al., 2017, 2018). Other traits including seed mineral content (McClean et al., 2017) and dietary fiber (Moghaddam et al., 2017) in the MDP, and the genetics of phenolic content in a Snap Bean Diversity Panel were investigated (Myers et al., 2019). The cloning of the P gene which conditions seed color was a major discovery (McClean et al., 2018). These panels were utilized to discover resistances to Rhizoctonia root rot (Oladzad et al., 2019a) and HBB (Tock et al., 2017) diseases. Dense SNP data sets were used to fine map QTL (Mamidi et al., 2016) for white mold resistance. Recent research revealed that the soybean cyst nematode Is now present in the ND bean production region, and the first efforts to identify germplasm and genes that provide resistance has been completed (Jain et al., 2019). Finally, the first disease resistance gene was successfully cloned in common bean (Lorang et al., 2018).

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

Specific research procedures currently in the project can be found in previous W-3150 and W-4150 proposals. The following are new components, based on feedback from scientists and other stakeholders:

1.Increase productivity and stress tolerance for sustainability of bean cropping systems

1a. Productivity and sustainability (CA, DE, ND, NE, PR, WA)

Architecture (pod height, pod distribution, stem diameter, lodging): Research will continue for key architectural traits, including growth habit (determinate or indeterminate) and type (I to IV), plant height, stem strength and thickness, branching pattern, leaf size and orientation, and pod distribution, among others. These traits interact with environmental factors to determine light interception, resource allocation, and overall plant performance. Field trials will be conducted in ND, CA, DE and important components of plant architecture will be measured. Both phenotypic and genotypic data will be used to develop a prediction model that would allow for selection of genotypes with optimal architecture traits while maintaining productivity. Understanding plant architecture (and the main and interaction effects of genotype and environment on plant architecture, for which multi-state testing can be valuable) is crucial for breeding programs aiming to develop cultivars with improved yield potential, disease resistance, and adaptability to diverse growing conditions.

Symbiotic Nitrogen Fixation (SNF) and Tolerance to Low Fertility: Nitrogen is a frequent yield constraint, especially for beans produced on the weathered soils of Puerto Rico. In the temperate northern regions, nitrogen fertilizer increases production costs and can result in environmental contamination if not used properly. The QTLs related to SNF reported by Oladzad et al., 2020 still need to be tested and validated across additional environments. Bean breeding lines in Puerto Rico will be screened for performance on low fertility soils with an emphasis on the identification of lines having enhanced symbiotic nitrogen fixation. Bradyrhizobium is better adapted to low soil fertility and has greater survivability in diverse environmental conditions. Therefore, interspecific (Pv x Pa) lines will be screened for promiscuous nodulation with Rhizobium and Bradyrhizobium. An optimal isolate/strain must have two main characteristics: high competitiveness and high fixation efficiency. Then, an optimal association with specific bean genotypes (or market classes or gene pools) is needed to obtain the most efficient host x symbiont combinations. A new testing pipeline to identify optimal combinations of bean genotypes (host) with Rhizobia strains/isolates (symbiont) is under development at NDSU and could be used by other teams of the multistate project (e.g., those working on lima beans). Selection for low fertility tolerance and broad resistance to root rot will continue through using multiple-stress “purgatory” plots in common bean breeding programs at USDA-ARS Washington State and USDA-ARS Puerto Rico.

Organic production: On-farm organic variety trials will be conducted in Michigan with emphasis on black and pinto bean market classes.  Trait evaluation will include early season vigor, disease resistance, dry down at maturity and canning quality.  Breeders across the U.S. will be asked to submit entries for evaluation.

Weed control: To date, there are no herbicide-resistant cultivars of dry beans due to the difficulty of applying genetic transformation in dry beans. The sensitivity of dry beans to Dicamba drift is well documented. Several studies have shown the presence of natural resistance/tolerance to Dicamba in soybean. Therefore, an effort is underway at NDSU to screen dry bean cultivars and germplasm for natural tolerance to Dicamba under greenhouse conditions. Selected genotypes will be subsequently tested under field conditions for validation purposes.

Yield potential: Increasing dry bean productivity is one of the most important efforts of almost any breeding program. In the specific case of dry beans, slow but steady increments in seed yield have been documented (Vandemark et al., 2014). Nevertheless, these small increases have resulted in the doubling of seed yields per acre during the last ~100 years. Now with the availability of new genotypic and phenotypic tools, efforts will be focused on the development of genomic prediction models and pipelines to continue increasing seed yields and overall productivity. A current effort at NDSU focuses on the development of trait-based chip with ~4,000 SNP markers. The hope is to share this valuable resource with all the bean community once the chip is validated. Another focused effort is on High Throughput Phenotyping (HTP). Efforts are currently focused on facilitating the measurement of important agronomic traits and seed yield components such as emergence, plant height, foliar diseases, days to maturity, and yield components such as number of pods per plant (or total number of pods per plot), to make accurate predictions of seed yield using machine learning algorithms and pipelines.

Characterization/Utilization of Exotic Germplasm and Crop Wild Relatives:

The use of exotic germplasm as a source of genetic diversity is of key importance to broaden the genetic base of dry, snap, and lima beans. The study of the genetic and molecular basis of traits that distinguish wild and domesticated beans, and the evaluation of candidate genes based on the recent genome sequence and synteny with other Phaseolus species will speed the introgression and pyramiding of favorable alleles and QTL, especially from wild beans and from closely related species, thereby increasing genetic diversity (Porch et al., 2013; Rao et al., 2013; Viteri et al., 2014a,b). From recent studies, specific genes of interest for introgression into common bean from tepary bean include unique rust immunity (Porch et al., 2022; Barrera et al., 2022), Asian bean flower thrip resistance (Porch et al., 2024b), and resistance to Bean common mosaic necrosis virus (Bornowski et al., 2023).

Continued collection of new populations through leveraged USDA-ARS Plant Exploration Grants will ensure that gaps in the Phaseolus collection are filled and populations from unique environments with unique tolerances to salt, heat, drought, soil conditions, etc. are captured. Recent wild tepary bean collections in New Mexico in 2023 and 2024 resulted in the collection of novel populations of P. acutifolius, P. anguistisimus, P. filiformis, P. grayanus, P. maculatus P. montanus, and P. parvulus from locations with little previous representation in the NPGS or other global collections. The collection team included breeders and researchers based in New Mexico, Puerto Rico, Washington, and the International Center for Tropical Agriculture Genetic Resource Unit in Colombia.  Collected seed will be conserved, regenerated, and distributed through the GRIN-global website from the NPGS Pullman, WA location. In addition to seed the collection trips resulted in new herbaria specimens (with copies at New Mexico State University Herbaria (NMC-NMCR)), soil, and rhizosphere samples with potential for conserving coevolved nitrogen fixing microbes from soils associated with these wild desert beans. These new soil microbes conserved in Beltsville, MD as part of the National Rhizobium Germplasm Resource Collection, may have direct application to cultivated commercial tepary especially under hot dry growing conditions. Continued collection and characterization of unique populations in New Mexico and Texas will be completed in the coming years and unique traits identified will then be incorporated into pre-breeding efforts including opportunistic crosses to create F₁-hybrids between wild and cultivated germplasm during regenerations by NPGS, as well as at other breeding programs. 

Many Phaseolus wild relatives and exotic germplasm that are not part of U.S. breeding programs are photoperiod sensitive requiring long nights to promote flowering and seed set. To produce seeds from these or synchronize flowering for crosses, short days, and long nights. This photoperiod requirement can make it challenging for breeding programs to incorporate exotic genetics with potential novel alleles of interest into their breeding lines. Prebreeding whereby exotic germplasm is crossed to backbones of temperate adapted cultivars is a way breeders can access broader genetics for creating improved bean varieties. Some effort is being made by the NPGS to create F1-hybrids and F2-populations to help make diverse genetics more available to more breeders.

1b. Biotic Stresses (AZ, CA, FL, DE, ND, NE, PR, SC, WA)

Viral diseases

Potyvirus: BCMV isolates and other bean-infecting potyviruses will continue to be collected from infected bean fields and characterized using sequence analysis for molecular phylogenetic groups (Feng et al., 2019) and host differential response. BCMV isolates recovered from infected tepary bean seed will be compared with common bean isolates to determine if host-adaptation of naturally seed-transmitted isolates (potentially, without aphid transmission) evolve uniquely in this host. Research will continue to investigate the role of six different bc-u alleles in conditioning resistance to BCMV and BCMNV and to develop markers for mutations within the Vps4 candidate gene which distinguishes them. Transcriptomic and metabolomic analyses will be used to examine tepary bean host tolerance to BCMV seed-transmitted tepary bean isolates. Genetic mapping of the virus-tolerance genes in tepary bean will be conducted, in part, to facilitate introgression into common bean. New recommendations for ideal BCMV/BCMNV strains to use for deployment of effective and sustainable resistance gene combinations will be provided. BCMV/BCMNV strains for all the pathogroups will continue to be increased and maintained in infected seed for long term storage.

Geminivirus: Breeding for resistance to BCTV and BGYMV will continue to rely on marker-assisted selection for the Bct and bgm-1 genes and occasional field nurseries with uniform natural infection pressure. Existing and improved markers for BGY4.1, BGY7.1, and BGY8.1 QTL (Soler-Garzón et al., 2021c) will continue to be validated for enhancing BGYMV resistance in breeding populations. 

Successful bean cultivars in Puerto Rico need resistance to multiple biotic constraints. Genes for resistance to Bean golden yellow mosaic virus (BGYMV) and Bean common mosaic necrosis virus (BCMNV) are routinely screened in UPR and ARS breeding lines using marker-assisted selection and under field BGYMV pressure in Honduras. Breeding lines having different market classes of seed are under development in Puerto Rico that combine multiple virus resistance (MVR) with other biotic constraints. A red mottled bean breeding line has been developed with MVR and resistance to common bacterial blight at the UPR. In addition, white bean breeding lines have been selected to combine MVR with Ur-11 and Ur-5 rust resistance genes. Pinto breeding lines are under development that combine multiple virus and leafhopper and/or multiple virus and common blight resistance.

 

Bacterial diseases

Common bacterial blight: The differential reaction between resistance genes/QTL and Xap strains collected across the U.S. and worldwide will continue to be studied, and a differential set of host cultivars will continue to be developed. Diverse strains will be employed in greenhouse inoculation tests to identify and combine sources of CBB resistance. Better markers for MAS of new and existing QTL (SAP6, SU91, Xa7.1) will be generated using segregating populations including diversity panels and breeding populations (Simons et al., 2021).

CBB reactions will be evaluated in the greenhouse using differential Xap strains. Development of cultivars with CBB resistance, using a combination of phenotyping and MAS, will continue to be employed by most U.S. breeding programs.

Halo blight: The race identity of Psp isolates causing epidemics will be determined primarily by inoculation of host differentials. Novel isolates will be tested using repetitive element PCR to assess whether they have distinct DNA fingerprints from the differential races. Breeding for HB resistance will focus primarily on deployment of the HB4.2 and HB5.1 QTL (Tock et al., 2017). High LD across the genomic regions with HB4.2 and HB5.1 has made it difficult to design tightly linked markers and narrow the QTL intervals. Fine mapping these QTL that are effective against Race 6 will continue by using haplotyping strategies across diversity panels and other segregating populations.  Overlapping QTL conditioning resistance to both bacterial brown spot and HBB will be monitored in additional segregating inbred populations. Andean germplasm lines that combine the four independent HBB resistance loci, Pse-2, Pse-3, HB4.2 and HB5.1, will be released.

Fungal diseases

Anthracnose: A panel of wild common bean accessions will be screened with a series of virulent races of anthracnose to identify new and novel sources of resistance. A recombinant inbred line population has been developed to characterize resistance gene(s) on the proximal end of chromosome Pv02 and linkage with I gene. The Co-4² gene is currently present in elite navy, black, great northern, pinto and otebo bean classes and is being moved into red and pink classes. The emergence of a new race 2 in Michigan necessitates the introgression of additional resistance into all new kidney and yellow bean varieties prior to release. Race structure will be monitored to ensure that the most effective resistance genes are being deployed in breeding programs.

A lima bean anthracnose resistance screening protocol will be developed that is suitable for breeding program-scale phenotyping. This protocol will be used to evaluate a diverse panel of genotyped GRIN lima bean accessions to identify potential sources of resistance to Colletotrichum truncatum via association mapping. The 2024 NPGS Horticultural Germplasm Evaluation Grant is being leveraged to support this ongoing research. Resistant parents will be incorporated into breeding efforts for the Southeast U.S., where the disease is endemic and often affects marketable yield.

Root rots: For Fusarium species, disease surveys will be conducted and root samples collected from grower fields across selected production regions. Pathogen isolation and identification will be conducted based on virulence and molecular sequencing in some cases. Breeding lines will be screened in the greenhouse for Fusarium root rot and/or in the field using root rot nurseries with diverse root rot complexes. For Rhizoctonia species, an inoculated pot test will test both virulence on differential bean lines and resistance of breeding lines (Peña et al., 2013). Selection for broad resistance to root rot and low fertility is being facilitated by using multiple-stress “purgatory” plots in common bean breeding programs at Oregon State University (Huster et al., 2021), USDA-ARS Washington State (Miklas et al., 2023), and USDA-ARS Puerto Rico (Porch et al., 2014). A field breeding nursery focused on kidney beans and with high pressure of root rots is grown every year in Minnesota, where root rots scores as well as seed yield are measured.

Rust: Combinations of effective Andean (Ur-4, Ur-9) and Mesoamerican genes (Ur-3, Ur-5, Ur-11) will continue to be deployed in cultivars in all U.S. market classes using traditional phenotyping against endemic and differential races and MAS with existing and new markers. Interactions between rust resistance genes segregating in the above breeding populations will continue to be examined for efficacy of resistance to specific races of the bean rust pathogen. Inheritance and mapping studies of the new Andean sources (PI 260418, G19833) of genes with broad rust resistance will be conducted. Continued fine mapping and candidate gene analyses will contribute more tightly linked markers for MAS of the major rust resistance genes, including Ur-5, Ur-6, Ur-7, and Ur-11 from the PI 190078 source.  Fine mapping of some rust resistance genes presented in the Differential Cultivars will be conducted, including Ur-4 in Early Gallatin, Ur-6 in Golden Gate Wax, Ur-13 in Redlands Pioneer and Ur-7 in Great Northern 1140. A document describing bean rust research techniques will be prepared for publication in the Annual Report of the Bean Improvement Cooperative (BIC) and posted on the web site of the BIC.

White mold: Haplotyping with SNPs and indels combined with recombination events in segregating early generation backcross, and diversity panel populations will be used to generate improved markers for MAS of narrowed QTL intervals for major QTL including WM2.2, WM3.1, WM5.4, and WM7.4. Although recent efforts have focused on developing resistant germplasm using the straw test, obtaining improved germplasm with field resistance identified in white mold screening nurseries is a current focus. Advanced breeding lines with levels of resistance incorporated into preferred seed types with high agronomic performance will continue to be tested in the BWMN. Pathogen haplotypes and their relationship to MCGs and aggressiveness relationships (Miorini et al., 2018) will continue to be studied. Characterization of pathogen genotypes will be facilitated by development of a reference panel of allele sizes known to be present within the population, to enable synthesis and comparison of genotype data generated by different lab groups. Fungicide resistance (Amaradasa and Everhart, 2016) is of increasing concern worldwide so fungicide sensitivity screening of S. sclerotiorum isolates from BWMN and producer fields is already underway for selected isolates maintained by W-5150 researchers (Kamvar et al., 2017; Lopez et al., 2019).

Pythium pod rot in snap beans (Oomycete): Screening methods for response to Pythium pod rot in field trials will be optimized from the only previously published field trial for this disease (Damicone et al., 2012). Isolates of P. aphanidermatum and P. ultimum were collected from natural outbreaks in research plots in South Carolina and characterized to the species-level with molecular markers (Uzuhashi et al., 2010; Robideau et al., 2011). The SnAP accessions (N=378) will be screened in replicated field trials in South Carolina in early (P. ultimum) and late (P. aphanidermatum) spring to allow the optimal temperatures for each Pythium spp. Disease incidence ratings of the accessions will be used for genome wide association studies with pre-existing SNPs from GBS to identify genomic regions associated with Pythium pod rot resistance in snap beans.

Nematodes: ND Falcon pinto (Osorno et al. 2020a) is the first report of a SCN tolerant dry bean cultivar. This cultivar was rated as moderately tolerant to SCN HG type 0, which is the most common in North Dakota. In addition, preliminary results have shown some level of tolerance to other HG types (Kaur, 2024). However, it is susceptible to the less frequent but more aggressive HG Types (7 and 2.5.7), which highlights the importance of screening with multiple HG types. Fortunately, recent screening of the core collection has allowed the identification of new potential sources of SCN resistance/tolerance. Additional work is underway to screen breeding lines and germplasm for reaction to other HG types. In addition, numerous crosses have been developed using ND Falcon as a parent to better understand the genetics of resistance and to incorporate and maintain resistance in the pinto bean market class.

Recent screens of diverse lima bean germplasm for RKN resistance in Delaware and California have identified potential sources of resistance in the Andean and Mesoamerican gene pools and field and greenhouse screening methods have been incorporated into the Delaware breeding program (Traverso et al., 2024) to utilize these new resistance sources in the breeding program. RIL populations derived from RKN resistant x susceptible crosses have been developed in DE and CA and are being used to better understand the genetics of resistance and develop markers to use for indirect selection.

Insects

Lygus: A subset of the USDA NPGS lima collection is being evaluated for cyanogenic glucoside levels in seed (with protocol refinement currently underway across states) to verify levels are below the threshold for safe consumption of lima beans by humans, as has been the case in mature seeds of cultivated limas thus far (e.g., Gibson et al. 2022). We plan to submit the refined protocol for consideration to be posted on the BIC Research Methods webpage. Sensors were also used in Gibson et al. (2022) to detect insect presence/abundance, and findings suggested lygus were not necessarily most active during standard human business hours, which could limit the accuracy of vacuum- or sweep net-based trapping methods. Early detection of lygus damage on plants via field-based sensing is an area that will be explored in this next five-year period while also conducting ground-based (and/or low-altitude UAV-based) sensing for other priority traits and will benefit from continued ground truth scoring of lygus damage in a subset of plots (and on harvested seed). Breeding trials are also typically conducting only one spray as a check for tolerance. Finally, we aim to continue discussing insect (and/or plant damage) control strategies with other crop communities such as strawberry and alfalfa that are affected by lygus, particularly from a sustainable cropping systems (and rotation) perspective.

Bruchids: The common bean weevil (Acanthoscelides obtectus) is an endemic pest of beans in Puerto Rico that requires the seed of beans to be fumigated after harvest. The bean breeding programs in Puerto Rico, in collaboration with bean research programs in Central America, have developed and released Mesoamerican bean germplasm lines that combine multiple virus and common bean weevil resistance. These sources of resistance have been used as parents to develop breeding lines that should lead to the release in Puerto Rico of weevil resistant cultivars. Additional sources of resistance to field infestation by the weevil will be studied. Seed storage methods that do not require fumigation will be evaluated. SNP markers S04_46273822 and S07_5221126 associated with the APA lectin and phaseolin loci on Pv04 and Pv07, respectively, have been developed for MAS of bruchid resistance (Kamfwa et al., 2018; Kami et al., 2006). However, the use of these markers requires validation by phenotype screening with insects. Genetic populations segregating for G40199 and other resistance sources from tepary (TDP) and P. vulgaris sources will be used to validate existing and new markers for improved MAS, for breeding and to further study inheritance of resistance derived from diverse sources.

Asian bean flower thrip: Flowers of leguminous weeds, hedgerows, and trees adjacent to farms in major production regions of Puerto Rico and south Florida will be sampled for the presence of M. usitatus and predators. Data will be collected on the total number of adult and larval thrips and predators per flower by plant species, location, and date. In addition, at least nine Megalurothrips usitatus populations will be collected from managed legume fields in distinct growing regions in Puerto Rico and south Florida and reared on potted bean plants in cages in screen houses at the Juana Diaz Experiment Station in Puerto Rico and at the UF IFAS Gulf Coast Research and Education Center near Tampa, Florida. The F₂-F₃ generations will be screened for susceptibility to the top labeled rate of key insecticides. Bean seedlings are treated in the top labeled rate of the insecticide, allowed to air dry, and then confined in a Petri dish with ten adult M. usitatus of the population being tested (Ivey et al. 2023). After 72 hours, the number of surviving and dead thrips is recorded. Information of percentage survival is generated and analyzed by population and treatment. Common bean and tepary bean breeding populations have been developed in PR for screening using preliminary sources of resistance (EMP 319, common bean) and several tepary bean accessions. These populations will be advanced and screened in the field to identify novel sources of resistance to the pest.

Leafhoppers: Bean plantings in Puerto Rico are persistently challenged by endemic populations of leafhopper (Empoasca spp.). Consequently, bean cultivars released in Puerto Rico often have superior levels of resistance to this pest. UPR bean breeding lines will continue to be screened indirectly in the field for resistance to leafhoppers and should lead to the release of a black bean line that combines multiple virus resistance and bruchid resistance in Puerto Rico. QTL for leafhopper resistance (Brisco et al., 2014) will be tested for KASPR marker development.

1c. Abiotic Stresses and mechanisms (CA, NE, PR, WA, WY)

Drought tolerance: The Dry Bean Drought Nursery (DBDN) will continue to be used to identify and incorporate new sources of drought tolerance. Novel traits for drought tolerance from the Durango Diversity Panel, the Andean Diversity Panel, Andean PIC Panel, and the Tepary Diversity Panel, as well as in bi-parental populations, will be incorporated into breeding efforts.

Recent GWAS or QTL analysis for drought stress (e.g. in Andean beans: Sadohara et al., 2024a) will be used to identify molecular markers and candidate genes for potential use in breeding. Rapid evaluation techniques in ongoing collaborative projects (e.g. GEMINI project; Pan-Genomic Selection), including the use of drones and robots, will be evaluated for incorporating traits and methods into breeding programs and for dissection of plant response to abiotic stress.

Novel traits previously identified, such as canopy temperature, reflectance indices, canopy height, deep rooting, and improved seed fill under drought will continue to be employed.

Shuttle breeding between NE and PR will use KASP markers to rapidly pyramid biotic traits with drought, heat, and broad adaptation improvement, in the pinto and great northern market classes.

 

Barrera et al. (2024) recently tested common, tepary, and lima bean under well-watered and terminal drought conditions in California and found tepary was most drought-adapted but with substantial variation exhibited even within tepary, suggesting the continued importance of multi-environment trialing within and across regions to characterize the effects of adaptive loci and to effectively deploy them in breeding.

 

Heat tolerance: Collaborative breeding for high ambient temperature tolerance in the dry, snap, and lima bean market classes will continue under hot summer field conditions (33C/23°C) in Puerto Rico, and under high daytime temperatures in NE and WA (and two environments in CA that experience high day and/or nighttime temperatures). Thus, both high day and high night temperature conditions will be effectively tested in these environments. A Phaseolus interspecific population (Barrera et al. 2022) has been evaluated in CA under high-temperature stress and control conditions, and genetic mapping of agronomic (both groundtruth- and sensing-derived), nutritional quality, and cooking time traits is underway. Results from evaluation of a subset of these interspecific lines (with common checks also included in each growout) are being examined across NE (well-watered vs. drought), WA (well-watered vs. terminal drought), PR (high-temperature stress), and CA (well-watered with incidental high-temperature stress at flowering). Greenhouse evaluation will also be conducted at several sites, where high ambient temperatures can be achieved. RIL populations and diversity panels (Oladzad et al., 2019b) will be phenotyped and evaluated using QTL and GWAS analyses.

The bush-type accessions within the SnAP (~250 accessions) have been assessed for pod count under heat stress in two years of summer field trials in Charleston, SC. The highest producers (N=36) were evaluated for yield in two additional years of summer field trials. Crosses have been made from the highest yielding SnAP accessions to initiate a breeding program for heat-tolerant snap beans for production in the Southeastern US. Selections will be made from populations (F₂ – summer 2025) screened in summer fields and advanced generations throughout the W-5150 timeline. Heat-tolerant lines from the program will be evaluated in multi-state trials through the HSN.

In the Northeast, pole beans are an attractive rotation crop for high tunnel growers. They provide a break in the typical tomato-cucurbit rotation that avoids the need to apply nitrogen and the associated salt build up in the soil. Diversified vegetable growers can hand harvest a vertical crop more ergonomically than a bush crop, and the indeterminate growth habit provides a flexible harvest window when coupled with cultivars selected for use as both snap and fresh shelling (similar to edamame). While high tunnels extend the season and reduce disease by shedding rain, they can be quite warm in the summer, resulting in temperatures in excess of 50°C. Cultivars developed as part of the previous multistate project that thrive in these conditions will be augmented by the addition of new traits and progeny will continue to be selected in these environments in the high tunnels of a participating grower.

Collaborative breeding for high ambient temperature tolerance in the dry and snap bean market classes under moderate daytime and high night-time summer field conditions in PR, SC, and DE, and high daytime temperatures in CA, NE, and WA will result in germplasm with both high day and high night temperature tolerance. Beans in Puerto Rico are often harvested at the green-shelled stage of development and there is a local market for freshly harvested beans throughout the year. UPR bean breeding lines will continue to be screened for heat tolerance at Isabela, Puerto Rico, during the summer months (May to August) when nighttime lows generally exceed 22° C.

 

Phenotypic selection of advanced lines will incorporate key traits identified to date, including phenology, yield components, and seed fill, and reproductive traits such as flower abscission, pollen shed, and pollen viability. Additional phenotypic traits will be implemented as they are developed facilitating rapid evaluation. For example, traits identified in recent studies such as source-sink relationships, canopy temperature, leaf cooling and interactions with vapor pressure deficit (VPD), and photosystem tolerance will also be investigated in contrasting environment types. RIL populations (e.g., Redhawk x Sacramento) and diversity panels will be phenotyped for heat response using conventional and high-throughput techniques and evaluated using QTL and GWAS analyses.

 

Flooding tolerance: A greenhouse screening protocol developed at NDSU is now used on a routine basis to rapidly screen hundreds of genotypes for waterlogging tolerance at early stages. The NDSU dry bean breeding program will be requesting additional genotypes from other breeding programs to be screened with the goal of identifying genomic regions associated with waterlogging tolerance (via GWAs). New tolerant genotypes will be identified that could be used both for genetic studies as well as new crosses.  A field validation using selected genotypes will allow the confirmation of the results observed in the greenhouse (Soltani et al., 2017, 2018; Rhodes, 2024). Efforts will also continue to understand the negative combined effects of flooding and salinity and how this also impacts SNF and overall productivity. New crosses using tolerant genotypes from closely-related species such as P. acutifolius and P. coccineus and P. vulgaris var. aborigenous (Velazquez, 2024) will be generated and evaluated.

2. Enhance collaborative regional trials and winter nurseries (CA, ND, NE, NY, MI, PR, SC, WA, WY)

National Cooperative Dry Bean Nursery (CDBN): has been planted for the last 74 years and has been coordinated since 2015 by the University of Nebraska. This trial is usually grown in 7 locations across the US and one in Canada. For the renewal, data to be recorded will include stand counts, days to flower, days to harvest maturity, growth habit, lodging, yield, and weight of 100 Seeds. Results have been published on the https://cropwatch.unl.edu/Varietytest-DryBeans/2019%20CDBN%20Final.pdf web page. Past, present and future trial data will be curated on the BIC website to enhance continuity and shareability of the CDBN trial data. New checks will include Pink Panther (LRK), Kona (black), and Monterrey (pinto) and will replace CELRK, Eclipse, La Paz, and Othello, which are no longer grown on a larger scale in the U.S.

Dry Bean Drought Nursery (DBDN): coordinated by the University of Nebraska since 2014 assesses drought tolerance of dry bean based on yield under drought and non-drought stress treatments across multiple states: NE, MI, PR, and WA. A tepary bean and SR20-11-6 will replace Marquis and Merlot in the updated list of reference checks used for this nursery. The report is compiled and shared with the participant's states.

 

Midwest Regional Performance Nursery (MRPN): These regional trials have been conducted since the early 2000s and coordinated by North Dakota State University. This nursery enables testing of lines for which disease-free seed is not available yet, which is a requirement for including a line within the CDBN. It also provides a way to evaluate adaptation of new genetics to the Midwest production areas, which are drastically different from the Western production region. Each year, approximately 25-30 pinto and great northern breeding lines along with checks, and a few pink and small red beans in recent years, are grown across three states (MI, NE, ND). Several lines tested in these cooperative trials, DBDN, CDBN, and MRPN, have eventually been released as cultivars.

 

Puerto Rico Winter nurseries: The UPR will continue the long-term collaboration with mainland U.S. bean breeding programs by conducting winter nurseries at Isabela, Puerto Rico. Breeding lines at early generation stages are advanced one generation, allowing US programs to do two selection cycles per year instead of one. Breeders usually visit winter nurseries to evaluate agronomic and seed traits and to screen for resistances to bean diseases endemic in Puerto Rico. Evaluating the performance of bean breeding lines in this tropical environment may aid in the selection of bean genotypes having broader adaptation.

Succulent Bean Heat Stress Nursery: SC and DE breeding programs for succulent (snap and lima) beans at the University of Delaware and Clemson University (Charleston and Florence, SC) will coordinate a new nursery as part of the W-5150 to trial heat tolerant breeding lines (as they become available) and accept entries from private breeding programs. Field trial design and evaluation metrics will follow well-established protocols established through years of variety trials at the University of Delaware (https://www.udel.edu/academics/colleges/canr/cooperative-extension/sustainable-production/variety-trials/).

Bean White Mold Nursery (BWMN): A nursery organized through the National Sclerotinia Initiative will be a leveraged activity coordinated by participants in each project.

 

Other related collaborative efforts

 

Rust Evaluation: The USDA-ARS Beltsville Bean Disease/Genetics Laboratory associated with Soybean Genomics and Improvement Laboratory (SGIL) routinely identifies new U. appendiculatus isolates (races) by phenotyping them across a set of differential cultivars. Hundreds of races of the bean rust pathogen Uromyces appendiculatus have been identified and reported in many bean production areas of the world. More than ninety of these races have been identified and maintained in storage in SGIL. This is the unique resource for studying the pathogenesis of common bean rust and the virulence diversity of U. appendiculatus in the U.S. and worldwide. One of the main services that the bean pathology team in SGIL provides to the scientific and industry communities of common bean in the US is the annual evaluation of advanced breeding lines for resistance to U. appendiculatus. This activity is conducted in the fields and greenhouses of USDA-ARS Beltsville, MD, by inoculating hundreds of breeding lines with a number of different races of U. appendiculatus. This and other additional collaborative activities will contribute to the delivery of bean lines containing some of the major Ur resistant genes and/or harboring resistance to bean rust.

 

Donor parent nursery: A nursery with lines harboring genes of broad interest for diseases/insects/abiotic stress. Public bean breeding programs need access to parental lines that broaden the genetic base of cultivars released in the U.S. These programs also need access to specific genes for resistance to diseases and pests. Ideally these sources of resistance genes should come from recently released cultivars or in adapted breeding lines that combine the specific resistance with additional resistances to biotic and abiotic stresses. A donor gene nursery will be assembled to include adapted Mesoamerican breeding lines and cultivars that can serve as sources of biotic and abiotic stress resistance. The donor nursery will also include the differential lines for rust, anthracnose, angular leaf spot and BCMNV. The differentials are also useful for monitoring virulence patterns of bean pathogens and for the identification of the most effective combination of resistance genes for target environments.

 

3. Develop databases and -omic tools to improve breeding efficiency (AZ, CA, ND, NY, MI, PR, SC, WA, WY)

3a. DNA Sequencing (low and high density) and markers

Sequence variability is a key to understanding phenotypic diversity.  Modern genetics relies on discovering variants for two phenotypic states such as resistance or tolerance to pathogen infection or to an abiotic stress such as heat, drought, or waterlogging. Those variants can be classified as single nucleotide polymorphism (SNPs) or structural variants (SVs) such as duplications/insertions of protein coding or non-coding sequences. Those variants are best captured by developing multiple reference scale genome assemblies that capture the large-scale diversity in a species, and subsequently mapping sequence reads of many genotypes to an appropriate reference assembly.

 

Bean Genome Sequencing: 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. This includes updating the earlier assemblies of UI111, 5-593, and G19833 that are currently in use by bean geneticists.  Based on short read resequencing data, SNP diversity data has been captured for ~700 genotypes representing wild, landrace, and improved genotypes from all races of common bean.

 

Structural variant (SV) diversity data will be captured by de novo assembly of long reads of 130 additional genotypes. This will capture additional structural diversity not discovered in the eight reference genome assemblies. Full reference genome annotations for each reference grade assembly will be built with RNA-seq and full-length cDNA read data. This data will aid gene modeling with a focus on capturing a large collection of alternatively spliced genes. To understand the biotic resistome, all nucleotide-binding leucine repeat genes, the major class of disease resistance genes will be captured across the full range of common bean diversity. All sequencing data will be coalesced into a single graph pangenome that incorporates the genic and non-genic diversity in common bean. This tool will aid the efforts of researchers to discover SNP or SV variants that are associated with their phenotype of interest.

 

A set of 555 recombinant inbred lines and the eight-parents of a black bean MAGIC population have been whole genome sequenced at MSU and McGill U., and this data will be available for the community to collaborate and utilize. The purpose of this effort is to detect, characterize, and partially validate the impact of the accumulation of deleterious mutations in common bean. The prediction of deleterious mutations in this project has involved development of machine learning models and implementation of practical haplotype graphs; both approaches will prove useful as the community moves into development of high-density genotyping arrays and more SNP genotyping data is collected, which will require more efficient SNP calling pipelines, databasing, modeling and representation of datasets.

 

Tepary bean sequencing: Genome assemblies, using Oxford Nanopore Technologies genomic long read sequencing data, will be completed for tepary bean accessions with traits of interest: G40022 (RIL parent), G40168 (terminal raceme), G40177E1 (large seed, BNF capacity), G40178 (BCMNV resistance), and G40199 (bruchid resistance) (Wang et al., 2024). A Practical Haplotype Graph, using PHG version 2, will be developed to impute tepary haplotypes from genotypes with reduced representation (Bradbury et al, 2022) that is compatible with breeding API (BrAPI) databases. To explore important agronomic traits from tepary bean, in a common bean genetic background, 175 interspecific lines will be sequenced using whole genome shotgun sequencing and tepary introgressions will be mapped in a collaboration between ARS, UGA, and MSU.

 

Genotyping and Markers

Mid-density genotyping: The BARCBean12K chip will continue to be used for germplasm genotypic characterization in common bean, and is being used for the pan-genomic selection (pan-GS) project to be described in Section 3e. Discussions among multi-state researchers will continue as genotyping solutions for use in Phaseolus beans are developed and deployed in collaborative projects.

 

Lima genotyping: An ongoing collaborative project in lima bean is testing a low-coverage, short-read sequencing-based platform and cross-comparing it with other platforms such as reduced representation sequencing (in which restriction enzyme ApeKI has returned a low number of SNPs in limas and will be compared with CviAII). There will be continued discussion and profiling of heterogeneity/heterozygosity in USDA NPGS stocks for Phaseolus beans, focused especially on landraces and wild accessions. Markers are also being developed for key adaptation/domestication loci in lima bean, with leveraging of synteny/homology with common bean and other legumes.

 

Bean Markers: Commercial common bean market classes are distinguished by seed color and pattern. Eleven genes (P, T, Z, C^st, C^pi, J, Bip, G, B, V, and Rk) controlling these traits have been mapped to chromosomal positions, and candidate genes or linked markers were defined for all of the genes. Intermarket class cross, while desirable to mobilize useful genes between market classes, are not used often because of the difficulty of maintaining market class integrity in progeny. Based on genes necessary to define a market class, MAS schemes will be developed that will enable the mobilization of important production traits between market classes while maintaining market class seed coat color and pattern integrity in the progeny.

 

As SNP markers are developed with applications for MAS they will be added to the BIC webpage and converted to KASP markers when appropriate. Approximately 100 KASP assays have been developed at MSU for the purpose of true hybrid detection in common bean. At present, only the Andean gene pool set of markers have been validated. Additionally, ~30 KASP markers developed by the bean community are currently publicly available through the Intertek (Sweden) platform.

Tepary markers: Building on the study of the genetic structure of tepary bean based on 290 accessions from the tepary diversity panel (Bornowski et al., 2023), GWAS on additional traits of agronomic interest will be completed, including response to powdery mildew, cercospora leaf spot, BNF, and seed and root traits. KASP markers will be developed for these key biotic traits, for MAS and interspecific breeding efforts and made available to the bean community through the BIC webpage and the Intertek KASP platform.

 

Synteny across Phaseolus: The synteny and homology across the Phaseolus species is a powerful tool for quickly identifying key agricultural traits across species. The Practical Haplotype Graph (PHG), a pangenome pipeline that allows for efficient haplotype imputation in lines with limited sequence information, will be implemented and used for breeding through the Breeding API (BrAPI) web service. Another approach leveraging synteny and homology between species will be the use of mutations, now identified in the lima bean homologs, that represent key gene models regulating five of the six core domestication traits of common bean. Results from these studies will be published and uploaded to databases such as those on the BIC website and the Legume Information System.

Quantitative Genetics Analyses: Multi-state participants will continue to discuss methods and platforms for quantitative genetics analyses, e.g. for genetic mapping in multi-parental populations and for fitting of major genes as fixed effects in genomic selection (described briefly below).

Pathogen sequencing

White mold: The Michigan State University Dry Bean Breeding and Genetics program is in the process of sequencing approximately 300 Sclerotinia sclerotiorum genomes. This effort is in part to assemble sufficient information to catalogue variants contained within this collection. With this information, collaborators can then deploy large scale efforts to dissect genetic sources of resistance and improve horizontal resistance towards white mold in common bean.

Rust: For U. appendiculatus and the anthracnose pathogen C. lindemuthianum, the two most notable characteristics are their extremely strong host specificity and virulence diversity. To generate genomic resources for pathogen population studies, we will develop two phased genomes of an Andean and a Mesoamerican isolate for each of these two pathogens. High quality reference genomes will serve as an excellent resource for future genomics, transcriptomics, and functional studies of bean rust and anthracnose. A number of race-typed global isolates will be re-sequenced by using Illumina sequencing technology to study the pathogen population diversity and structural variants at the DNA level.

RNA-seq and full-length cDNA data was collected from each of the eight reference genotypes from multiple tissues. That data has been collated for each genotype, and empirical expression data is now available for each gene model.  That data has been quite valuable when researchers searched for candidate genes based on genetic studies that narrow genetic effect to a narrow interval.

 

3b. Proteomics and metabolomics: As proteomics and/or metabolomics become feasible in funded projects, multi-state researchers will continue to discuss analytical platforms and standards relevant to Phaseolus beans for maximized comparability across projects and programs. Examination of protein fractions has been underway and will continue in these next five years.

3c. Genomic Prediction/Selection: An ongoing effort is being made to develop consortium-level genomic selection models. The U.S. and global bean community is presently involved in assembling an approximate 1500 elite line SNP genotyping dataset (all being genotyped with the BARCBEAN_12k SNP array). This data set will explore the feasibility of developing a robust, durable and highly accurate genomic selection model that multiple breeding programs can implement at once. The premise of this project is underpinned by the idea that robust models in genomic selection tend to decay in accuracy due to under sampling. Thus, by pulling resources from multiple breeding programs, deficiencies and advantages can be complemented across programs that work in common market classes.  The following steps from the pan GS project will be the development of an online website that breeders can then access and upload data to ensure continued relevance and utilization of the genomic selection model.

We will continue to cross-compare software platforms, custom scripts, and specific methodological implementations; e.g., for integration of large-effect genes in prediction (PanQTL for viewing of large-effect genes, QTLome).

3d. Phenomics—drones, robots, spectral, AI, computer vision: Drones have been deployed over the same set of common bean/tepary bean interspecific lines in multiple states, one of which had well-watered and terminal drought treatments. Performance of that germplasm is being compared within and across groundtruth and UAV data streams. Low-altitude UAV flights are picking up individual plant features and could show promise if ground-based rovers are not an option (e.g., for various logistical/operational reasons, or in environments where plants grow into furrows). Ground-based rovers are being tested in multiple states for use in Phaseolus beans.

Both structural (e.g., growth habit) and functional (e.g., canopy temperature) traits, and both new and replacement traits, are being tested via drone. Drone imaging is also being utilized to enhance the accuracy and quality of yield trial data by improving experiment-wide plant stand counts. Drone imagery can be used directly with the implementation of GIS tools and without the need of developing Training model datasets that require maintenance costs. Drone data extraction protocols have been developed and published by this project team (e.g., https://youtu.be/obRng3LLkRs?si=UH4iiJslVtvXXh89), and these will continue to be developed.

 

High-throughput methods for quantifying hundred-seed weight, such as SmartGrain/Marvin, the OneKK Android application (based on OpenCV), machine learning methods, and parameterized 3D-printed seed trays, will be evaluated for suitability in Phaseolus bean breeding programs. These methods capture measurements such as seed weight, length/width, and circularity. Protocols for validated methods will be shared among the Phaseolus bean community.

 

3e. Databases: Considerable activity has taken place in sequencing of Phaseolus spp., through the development of whole-genome reference sequences (Schmutz et al., 2014; Vlasova et al., 2016; Rendón-Anaya et al., 2017), whole-genome sequencing (WGS) (Lobaton et al., 2018; Garcia et al. 2021; Wisser et al. 2021; Lozano-Arce et al. 2023; Parker et al. 2024), and genotyping-by-sequencing (GBS) (e.g., Ariani et al., 2018; Bhakta et al., 2015; Katuurama et al., 2018). These sequences provide considerable additional sequence information from which new markers can be developed. The PhaseolusGenes database was established as a resource for the bean research and breeding community in 2008. It subsequently has been used as a resource for dozens of studies ranging from disease resistance to genomics (reviewed in Canales Holzeis et al. 2024). The database has now been transferred to LegumeInfo and is searchable at https://mines.legumeinfo.org/phaseolusmine/begin.do. Further genomics advances, discussed throughout this proposal, will also be added to LegumeInfo.

Ontologies: A crop ontology is a structured set of terms and definitions specifically curated for a particular crop. Crop ontologies provide a shared vocabulary that enables consistent data collection, sharing, and analysis across research groups, facilitating interoperability between datasets. The Crop Ontology project (https://cropontology.org/; Shrestha et al., 2012) provides a platform for the development and sharing of crop ontologies that describe phenotypes and phenotyping methods. This tool already houses a common bean ontology (CO_335) that contains traits related to abiotic and biotic stress, agronomic, biochemical, morphological, phenological, physiological, postharvest, and quality traits, but no such ontology is yet available for lima bean. We have begun to draft a lima bean crop ontology for inclusion in the Crop Ontology collection. Over the next five years, this ontology will be finalized and posted publicly via the Crop Ontology website for use by all lima bean researchers and breeders.

 

We have established a Breedbase instance for lima beans that allows for the tracking of accessions, seedlots, crosses, and phenotyping trials (Morales et al. 2022). While this database is already available for community use, it is currently empty. Over the next five years, we will work together to populate this database with our agreed upon lima bean crop ontology, GRIN accessions and other shared germplasm resources, and coordinated lima bean phenotyping trials across the W-5150 project.

 

4. Enhance nutrition, processing and quality traits, and develop products to increase consumption of beans (CA, MI, NY, SC, WA)

 

Multistate genotype x environment trials will be conducted to assess the nutritional and processing qualities of dry beans. One trial will be conducted with 30 Great Northern bean genotypes grown in multiple years in MI, NE, ND, and WA along with check varieties from the major U.S. market classes.  Beans will be evaluated for protein content, flour milling quality, cooking time, canning quality, mineral content, and iron bioavailability. The data will be used to understand the genetic variability and to breed beans with improved end-use qualities. Other multistate sample sets are also under analysis in both common/tepary bean and lima bean.

 

The methods to be used include:

Total seed protein: Non-destructive NIR models will be developed to predict total seed protein on dry beans with the purpose of breeding high protein beans for use as an ingredient. Whole seeds (100 g samples) will be scanned via NIR (near-infrared reflectance) (Foss DS2500) analyses to predict bean protein content, and other multi-state participants are using a smaller sample mass of ground beans. Total protein will be determined by measuring total nitrogen via the Dumas combustion method at A&L Great Lakes Laboratories (Fort Wayne, Indiana) in accordance with AOAC method 968.06, and the crude protein will be estimated by multiplying the dry weight total nitrogen concentration by a factor of 6.25 (Horwitz, 2010). Prediction models (pre-built calibrations available from the instrument manufacturer and/or custom calibrations based on newly collected wet-chemistry reference data) will be compared across labs, e.g., across common bean and lima bean programs having the same make and model of NIRS instrument.

Flour milling quality: Whole seed samples of 100 g will be milled via a benchtop hammer mill (PX-MFC 90 D; Kinematica) passed through a sieve of 0.5 mm. Flour particle size distribution will be determined by laser diffraction with a Microtrac S3500 Particle Size Analyzer (Microtrac, Pennsylvania).

Cooking time: will be determined using a Mattson pin drop cooker (Wang et al., 2010). The cooker utilizes 25 stainless steel 70 g piercing tip rods, each placed in contact with the middle surface of a presoaked bean and the entire device placed in a beaker of boiling distilled water. Cooking time is recorded as the time required for 80% of the 2 mm diameter piercing tip rods to pass completely through each bean under a low-steady boil.

Canning quality: will be measured using a small-scale canning protocol (Wang et al., 2022) with a 100 to 110 g seed sample per can based on dry matter. Approximately one month after the beans are canned, visual appeal is evaluated by 10-20 trained panelists on a hedonic scale of 1 to 5, 1 being least desirable and 5 being most desirable.

Minerals: will be measured using ICP-AES (inductively coupled plasma-atomic emission spectroscopy) technology or (in other projects) ICP-mass spectrometry with potential testing of X-ray reflectance spectroscopy as a high-throughput assay to be routinely calibrated against ICP-MS.

In vitro iron bioavailability: is measured by exposing in vitro digested cooked bean powder to an immortalized Caco-2 cell culture assay (Glahn et al., 1998). The degree of iron uptake is determined by the level of ferritin production after 24 hours of exposure to digested bean medium.

Sensory and culinary evaluation of dry and succulent lima beans is taking place in a collaboration between the CA, DE, and SC lima breeding teams and in coordination with the IA consumer team. A set of descriptors is being developed for lima bean, and descriptive analysis (with a trained panel), central-location consumer testing, and focus groups are being conducted. A team of professional chefs will also be assessing the same samples for a smaller set of culinary attributes.

We will also continue to discuss, across multi-state participants, methodologies for traits that are expensive to measure such as dietary fiber and levels of individual metabolites that may be underlying sensory attributes.

Measurement of Progress and Results

Outputs

• Develop/release germplasm/cultivars with multiple disease resistance and/or resilience to climatic conditions.
• Develop/release at least one cultivar within each market class of common bean grown in the U.S.
• Deploy novel disease resistance into new market classes, such as pink, pinto, and snap beans, using traditional and marker-assisted selection approaches.
• Introgress traits of economic importance from exotic tropical bean germplasm into beans adapted to temperate environments.
• Germplasm with improved cooking time, canning quality and flavor attributes will be developed. Survey data will identify key constraints to greater bean usage by U.S. consumers.
• Continued co-development and cross-testing of pre-breeding resources in lima bean.
• Summarize results from the multistate trials and share with participants and the common bean community.
• Acceleration of the development of improved bean breeding lines by planting in Puerto Rico (and potentially also the Coachella Valley of California, particularly for limas) an additional generation each year in cooperative winter nurseries.
• Identify molecular markers for bacterial wilt that can be used in common bean breeding programs.
• Develop molecular markers close to genes of economic importance.
• Determine the genetics of Pythium pod rot resistance and identify molecular markers that can be used in snap bean breeding programs.
• Elucidation of epistatic interactions between rust resistance genes.
• Identification of heat tolerance genes associated with germination and reproductive development.
• Continued improvement and addition of whole-genome sequences related to the 7 Phaseolus domestications.
• Information to inform breeding for resistance to Lygus, including marker-trait associations and biochemical and sensor-based information.
• Determine the genetics of lima bean Anthracnose resistance and identify molecular markers that can be used in lima bean breeding programs.
• Genetic/genomic findings regularly integrated into the Legume Information System.
• Evaluate methods for high-throughput methods for hundred seed weight and share recommendations with the bean breeding community
• Novel information on nutrition, canning quality and color retention, traits affecting the marketability, nutritional quality and health benefits of eating dry beans and snap beans will be generated.
• Development of a sensory wheel for use in lima bean breeding and outreach.
• Building and cross-comparison of near-infrared spectroscopy calibrations suitable for use in Phaseolus beans.
• Develop and disseminate a community-wide lima bean crop ontology.
• Populate a community-wide lima bean breeding database.
• Update the Bean Improvement Cooperative web page and research section.
• Train several postdoctoral scientists, graduate students and undergraduate students through their involvement in all project-related activities

Outcomes or Projected Impacts

• Improved high yielding bean cultivars resistant to multiple abiotic and biotic stresses (especially multiple diseases) will positively impact regional and national production. Areas planted to new cultivars may increase by more than 10%, leading to substantial production increases in the participating states.
• Adoption of multiple-disease (and -insect) resistant cultivars may reduce pesticide use by 25% or more, resulting in savings to producers and contribute to a cleaner environment.
• Adoption of abiotic stress tolerant cultivars that will require less irrigation, less N, and less P fertilizer while maintaining profitable yield and quality.
• The genes responsible for key agronomic, disease, nutrient and health-related traits will be discovered with novel diversity panels, genomic tools, and innovative analytical methods.
• The development and implementation of novel molecular markers for agriculturally important traits will accelerate the process of cultivar development.
• Improved sensory/culinary properties of common beans and lima beans could help support new uses of beans and encourage increased consumption.
• Increased usage of breeding databases and trait ontologies, among other community resources, will continue to facilitate information exchange.

Milestones

(2025):Release of Andean germplasm with climate resilience including tolerance to drought and high ambient temperatures.

(2025):Release of a Great Northern bean with multiple disease resistance.

(2025):Draft lima bean crop ontology circulated to project members for input. Revised lima bean crop ontology submitted to Crop Ontology and loaded into lima bean Breedbase instance.

(2025):Release of a Cranberry bean cultivar with multiple disease resistance.

(2025):GWAS of pod production under heat stress in the SnAP accessions.

(2025):Multi-environment results available from Coachella winter nursery testing for lima bean.

(2025):Continued multi-environment trialing of interspecific common bean/tepary bean lines.

(2025):Results from multi-state lima project disseminated.

(2025):Research coordination on project objectives at the biennial BIC/NAPIA meeting and annual W-5150 meeting (typically held concurrently).

(2026):Release of drought tolerant shuttle breeding pinto and Great Northern line with broad adaptation.

(2026):The DBDN will generate data to release at least three new bean lines with improved drought/heat tolerance.

(2026):Release of a yellow bean cultivar.

(2026):Pinto bean cultivars with improved abiotic and biotic stress resistance.

(2026):Results from multi-state lima project disseminated.

(2026):Research coordination on project objectives at the W-5150 annual meeting.

(2026):Screening and genetic analysis of the USDA GRIN lima bean collection for resistance to lima bean Anthracnose completed.

(2027):Screening and genetic analysis of the SnAP accessions for Pythium pod rot resistance will be completed.

(2027):Release of a heat tolerant shuttle breeding pinto bean with broad adaptation.

(2027):Pangenome assemblies across 100’s of sequenced genotypes across seven races and gene pools.

(2027):Research coordination on project objectives at the biennial BIC/NAPIA meeting and annual W-5150 meeting (typically held concurrently).

(2027):Functional KASP markers for selection of disease resistance in tepary bean.

(2028):Introgression of unique biotic resistance (rust and BCMNV) from tepary bean to common bean.

(2028):Research coordination on project objectives at the W-5150 annual meeting.

(2028):Functional KASP markers for selection of Pythium pod rot resistance in snap bean.

(2029):Research coordination on project objectives at the biennial BIC/NAPIA meeting and annual W-5150 meeting (typically held concurrently) and planning for project renewal/continuation.

(2029):Coordinated trials of new snap bean cultivars as through the Succulent Bean Heat Stress Nursery.

(2029):Release of heat and drought tolerant pinto bean.

(2030):Release of snap bean cultivars with improved abiotic and biotic stress resistance.

(2030):Research coordination on project objectives at the W-5150 annual meeting.

(2030):Submission of proposal for project renewal/continuation.

Projected Participation

View Appendix E: Participation

Outreach Plan

Research results from each sub-project will be promptly published in refereed journals and non-refereed extension bulletins, industry magazines, flyers, etc. They will also be posted on the websites of the participating institutions and programs including the Bean Improvement Cooperative (BIC) website (http://www.bic.uprm.edu/) and specialized sites such as the Legume Information System (LIS; https://www.legumeinfo.org/), BeanCAP (https://arsftfbean.uprm.edu/beancap/) among others. The project will facilitate the development and distribution of novel Phaseolus bean diversity panels, genomic, and phenomic tools to increase the use of these cutting-edge methods to accelerate Phaseolus bean research and crop improvement.

Common bean breeding lines and cultivars will be extensively tested statewide, regionally (e.g. Midwest Regional Performance Nursery, Dry Bean Drought Nursey, Succulent Bean Heat Stress Nursery), and nationally (e.g. Cooperative Dry Bean Nursery), including on-farm strip-plantings of the most promising or outstanding genotypes in different cropping systems. These lines can be used in crosses by any member of the W-5150 project. Breeder, Foundation, Registered, and Certified seed of the new cultivars will be produced and distributed to bean growers and the seed industry. Field days and tours will be held each year at or near crop maturity to enable breeders, growers, and other industry people to see how the breeding lines perform under different growing conditions. In addition, the most important findings will be shared with all interested parties through workshops, news media, and electronic mail. The released cultivars and germplasm lines will be registered with the Crop Science Society of America, BIC, or American Society of Horticultural Sciences, and the seed will be deposited with the National Center for Genetic Resources Preservation.

Many W-5150 Co-PIs collaborate with extension specialists and extension agents which facilitates disseminating W-5150 research achievements (e.g. release of improved bean cultivars) through winter meetings, summer field days, and co-authoring extension publications.

Organization/Governance

The Technical Committee officers include a Chairperson, Vice-Chairperson, and Secretary who are elected by the W-5150 representatives each year at the annual meeting. The representatives (participating researchers) are designated by the directors of each participating institution. Unless he/she/they declines to serve, the Vice-Chairperson will succeed the Chairperson. The Secretary is elected annually, and the previous Secretary will succeed the Vice-Chairperson, unless he/she/they declines to serve. An election will be held if any officer declines to serve in his/her/their office. In addition, the Western Association of Agricultural Experiment Station Directors selects an Administrative Advisor who has no voting rights. The Technical Committee meets annually, unless otherwise planned, at a date and location determined by majority vote of the W-5150 representatives. Minutes will be recorded by the Secretary, and an annual progress report will be prepared by the Vice-Chair and submitted through proper channels. Current officers are: Chair, Timothy Porch - USDA-ARS; Vice-Chair Christine Diepenbrock - University of California, Davis; and Secretary, Sandra Branham - Clemson University. Though the W-5150 is a Western Regional Research Project, it has always had substantial participation by institutions in bean producing states in other regions of the U.S. as well as USDA-ARS researchers.

Stakeholders and the general public are encouraged to attend the annual meetings. Accountability and transparency are maintained through annual reports by representatives from each participating state. Decisions are made collectively, with all participants having a voice in the decision-making. Research findings are shared in a timely manner through the minutes of the W-5150 annual meeting, the Bean Improvement Cooperative Journal, poster or oral presentations during biennial BIC meetings, web pages, industry magazines/newsletters, and/or scientific journals. In addition, annual field tours of the multistate national and regional trials (e.g. Midwest Regional Performance Nursey, Cooperative Dry Bean Nursery, Dry Bean Drought Nursey, National White Mold Monitor Nursery) allow project members to see how common beans developed by each state perform under different growing conditions and provide opportunities to share findings and develop new collaborations. Such collaborations enable project members to effectively and efficiently respond to emerging issues in the common and lima bean industries. The W-5150 Project is inclusive and encourages new participants to become involved. Objectives/sub-objectives are addressed by collaborative teams that take advantage of each participant’s areas of expertise. Leadership is shared with one or two team leaders coordinating activities for each objectives/sub-objective.

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