Statement of the Issues:

Phaseolus [mainly common bean (Phaseolus vulgaris L.), but other Phaseolus species as well] is an important crop in the United States (U.S.) with a one-billion-dollar farm-gate value, and is the most important pulse crop worldwide. Most common and lima beans (Phaseolus lunatus L.) are distributed as dry seeds, canned, or fresh as snap and lima beans. Demand is expected to remain strong or increase in the near future since consumer interest in plant-based diets for health is at an all-time high, and the expansion of population groups in the U.S. with culinary traditions of bean consumption is increasing. But, to compete with other commodities such as soybeans [Glycine max (L.) Merr.], and maize (Zea mays L.), dry bean seed yields need to continue to increase. More efficient use of inputs such as water and nitrogen, are needed to reduce production costs and to preserve scarce resources. Numerous abiotic and biotic stresses can threaten both dry and snap 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 (Vandemark et al., 2014).

Unlike soybeans, maize, wheat (Triticum aestivum L.), or rice (Oryza sativa L.), most common bean varieties provide greater nutrient density of protein, fiber, iron, folate, and other micronutrients required for optimal human nutrition (Leterme, 2002; Mitchell et al., 2009; Winham et al., 2008). The unique nutritional benefits of common beans were recognized in the 2015 Dietary Guidelines for Americans recommendations, which state that “beans may reduce your risk of heart disease and certain cancers” and “scientists recommend that adults consume three cups of beans per week to promote health and reduce the risk of chronic diseases” (De Salvo et al., 2016). In the U.S., dry beans are a minor part of the diet. From 1999 - 2002 about 8% of the population consumed beans, peas, or lentils on any given day (Mitchell et al., 2009). Per capita consumption of dry beans was 2.6 kg from 2010 to 2016 (Minor and Bond, 2017). The major classes consumed are pinto (1.2 kg per capita), followed by black, navy, and kidney beans (Minor and Bond, 2017). There is an opportunity to increase bean consumption by improving traits important to consumers such as convenience, nutrition and taste.

Several diseases can occur simultaneously and reduce dry and snap bean yield and quality within and across different production regions. Yield losses can range from 10 to 90%, depending on the incidence and severity of the diseases involved. For example, in the western United States, Beet curly top virus (BCTV), Bean common mosaic virus (BCMV), Fusarium root rot (caused by Fusarium solani f.sp. phaseoli) and Fusarium wilt (caused by Fusarium oxysporum f.sp. phaseoli), and white mold (caused by Sclerotinia sclerotiorum), can simultaneously infect susceptible cultivars. Fusarium wilt has re-emerged in fields in Colorado, Nebraska, and Wyoming. Similarly, in Michigan, Minnesota, North Dakota, and Wisconsin, anthracnose (caused by Colletotrichum lindemuthianum), bacterial brown spot [caused by Pseudomonas syringae pv. syringae (Psp)], common bacterial blight [caused by Xanthomonas axonopodis pv. phaseoli (Xcp) and X. axonopodis pv. phaseoli var. fuscans (Xcpf), Syn. with X. campestris], halo blight (caused by Pseudomonas syringae pv. phaseolicola), root rots (in most cases caused by a complex of fungal pathogens), rust (caused by Uromyces appendiculatus), and white mold can occur together and cause severe yield losses. Similarly, the root rot pathogens cause serious problems in snap beans and kidney beans across all production regions. In addition, snap beans are vulnerable to regional epidemics of viral diseases including CTV in the western states (e.g., California, Idaho and Washington), and to a virus complex in the Great Lakes states which includes Alfalfa mosaic virus (AMV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV), and Clover yellow vein virus (ClYVV), among others. Whitefly (Bemisia tabaci) transmitted Begomoviruses (family Geminiviridae) represent a threat to common bean production in Florida and Puerto Rico. Many of these pathogens are highly variable in their virulence and new races or strains can appear in different regions. One example is the new rust races reported in Michigan and North Dakota that overcame the widely deployed Ur-3 rust resistance gene (Markell et al., 2009; Wright et al., 2008). Many of these diseases are caused by seed-borne pathogens that are genetically variable, and cannot be economically controlled with chemicals (e.g., common bacterial blight). Moreover, the use of fungicides increases production costs and can result in environmental and human health hazards if improperly used.

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; Silbernagel and Hannan, 1992; Sonnante et al., 1994), because only a very small number of wild bean ancestors were domesticated (Gepts et al., 1986; Papa and Gepts, 2003; Kwak et al., 2009). 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 conversion of tropical germplasm is important in order to make traits available from photoperiod sensitive, non-adapted materials. Stringent requirements in terms of visual seed quality and canning quality for each market class slow genetic improvement (Singh, 1999; Kelly and Cichy, 2013).

The common bean reference genome sequence and the rapid development of associated genomic technologies has helped to accelerate the improvement of common bean (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 the development and deployment of markers for key disease and abiotic traits. The BARCBean6K_3 bead-chip with 5,398 SNPs developed through the BeanCAP project was broadly used by the W-3150 for the investigation of agriculturally important traits, and the SNP chip and genotyping-by-sequencing (GBS) is currently being implemented by W-4150 participants for Genome- wide Association Studies (GWAS) in conjunction with the numerous nurseries and multi-state trials coordinated by this research group. The new 12K common bean bead-chip containing newly selected 6K SNPs from Andean bean and the 6K SNPs in the pre-existing BARCBean6K_3 assay is available. The development of the PhaseolusGenes marker database has facilitated the design of several markers for marker assisted selection (MAS) (Miller et al., 2018). The integration of these SNP markers that allow for the development of dense genetic maps, their application to association and QTL mapping, and finally their use in MAS will allow for more precise identification of regions associated with the key traits of interest mentioned above. Given the extensive amount of information on resistance sources, many already mapped and tagged with molecular markers, 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 recent identification at the International Center for Tropical Agriculture (CIAT) of bridging genotypes (Barrera et al., 2018) that may facilitate interspecific crosses between tepary and common beans may help to broaden the genetic base and lead to the improvement of both crops.

Genomic resources have been developed, diversity panels have also been established that are advancing efforts to elucidate common bean genetics and are also serving as a novel source of widely characterized germplasm for breeding. These panels include a wild bean panel, a snap bean association mapping panel (SnAP), an Andean Diversity Panel (ADP), a BeanCAP Mesoamerican Diversity Panel (MDP), a Durango Diversity Panel (DDP), a Yellow Bean Collection (YBC), and a Tepary Diversity Panel (TDP). 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. The ADP is proving essential in the discovery of useful genes for the development of Andean bean varieties that are more productive, drought tolerant, and disease resistant than what is currently being grown in the U.S.

This interdisciplinary, multi-state, collaborative W-4150 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 resistance to major abiotic and biotic stresses. These cultivars will help reduce production costs and pesticide use, increase yield and competitiveness of

U.S. bean growers, and sustain production for domestic consumption and export. Researchers participating in each sub-project have complementary expertise and represent two or more institutions. The inclusive group of bean researchers jointly prepared the project renewal and is committed to collaborating with each other to achieve the overall objectives: 1. increasing common bean productivity and sustainability, including development of resistance/tolerance to biotic and abiotic stresses, characterization/utilization of exotic germplasm, and evaluation in multistate nurseries, 2. exploiting the nutritional value and health promoting qualities of common bean to enhance human health and well-being, and 3. development and application of genomic tools and bioinformatic databases.

Justification:

A multi-state collaborative research project for common bean is needed because many constraints 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 that can have broad impact. Communication during the formative stages of research allows for emerging information and shared experience to improve study design. New cultivars can be selected to have superior culinary 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 snap bean researchers to address the constraints that are shared. Ultimately, the whole bean industry (both seed and food) benefits from the knowledge and products developed by this project. Specific examples that identify the need and benefits for this multistate collaborative project are described in the following paragraphs.

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

Introgression and pyramiding of favorable alleles and QTL from 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 become increasingly important (Miklas et al., 2006) and requires collaborations among scientists across different states or countries (McClean et al., 2008; Gepts 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, to develop germplasm and cultivars with multiple-disease resistance and tolerance to abiotic stresses, and excellent culinary quality, researchers with limited expertise and facilities share responsibilities and exchange segregating populations and breeding lines to complement screening and selection in contrasting field environments, laboratories, and greenhouses regionally and nationally.

The use of winter nurseries in Puerto Rico 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 (e.g., Mayaguez, PR) 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.

Exotic germplasm is increasingly being used to broaden the genetic base and develop cultivars with higher yield potential, enhanced end-use and nutritional quality, and greater resistance to abiotic and biotic stresses. It is essential to evaluate advanced breeding lines and cultivars developed from the conversion process across production regions, in order 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-4150 project conducts annually several multi-location testing trials such as the Bean Rust Nursery (BRN), national Cooperative Dry Bean Nursery (CDBN), Midwest Regional Performance Nursery (MRPN), Bean White Mold Nursery (BWMN), and Dry Bean Drought Nursery (DBDN). These nurseries are essential for  identifying 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 form an integral part and foundation for strong collaborative efforts within the W-4150 project. For example, data from the CDBN was key for  estimating yield gains in dry beans for the four most important market classes in the U.S. since 1980 (Vandemark et al., 2014). In addition, plot tours to allow project members to view the performance of the lines under different growing conditions are conducted annually in Nebraska, North Dakota, Puerto Rico, 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. No single state or institution can conduct all the research necessary to develop improved bean cultivars for sustainable production, consumption, and export. This is especially true when most programs have inadequate resources and personnel to carry out a relevant and efficient breeding program for their own state. In addition, funding for dry bean research is significantly less than the resources available in other major crops in which scientific networks are larger and the volume of production and price allow higher investment in research. Unique expertise is available in a few states (e.g. nutritionists and pathologists), and there are several bean-producing states (e.g., Arizona, Florida, Minnesota, Montana, New Mexico, and Wyoming) that do not have public dry or snap bean breeding programs. Due to the collaborative nature of the W-3150 project, researchers in these states will also have access to new breeding lines and cultivars of all market classes. 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 snap bean. This comprehensive, multidisciplinary, and multi-state collaborative project is vital to maintain, monitor, and exchange pathogens, parental stocks and improved breeding lines and cultivars, to share research data among all related areas, and to allow a more efficient use of exotic germplasm (Vandemark et al., 2014).

The accomplishments for 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 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-4150 team includes both early career and experienced scientists, which provides a good balance between new cutting-edge technologies, but also the expertise and results gained through years of scientific work. Long-term collaboration among a multi-disciplinary group of scientists enables the multi-state W-4150 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-4150 group proposes to continue to enhance genetic resistance to biotic and abiotic stresses. Exotic bean germplasm needs to be characterized and utilized to broaden the genetic base of the crop. Improved nutritional and quality traits promise to enhance the health benefits and utilization of beans. Improved integrated pest management and agronomic/production practices should lead to more efficient and sustainable bean production systems.