STATEMENT OF THE PROBLEM: The common bean (Phaseolus vulgaris L.) is an important crop in several regions of the United States (U.S.). Demand for dry and snap beans is expected to remain strong or increase as consumers search for healthy alternatives in their diet and there are greater numbers of citizens in the U.S. with a culinary tradition of consuming beans. In order to compete with other commodities such as soybeans and maize, dry bean seed yields need to continue to increase. More efficient use of inputs such as water and nitrogen is 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 drought, heat, soil mineral deficiencies, and short growing seasons reduce productivity and contribute to a yield-gap between on-farm and potential seed yield in many production areas (Vandemark et al., 2014).

Unlike soybeans, maize, wheat, or rice, the common bean varieties can provide greater nutrient density for 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 most recently by the 2005 and 2010 Dietary Guidelines for Americans. Dry beans are included in both the protein and vegetable categories of the policy document and the consumer-facing MyPlate web interface.

In addition to human health benefits, beans promote soil and environmental health through biological fixation of atmospheric nitrogen which allows beans to be produced with less N-fertilizer than other non-legume crops. The nitrogen fixation characteristic of common bean and other legumes promotes sustainable agriculture practices by reducing fertilizer use, the potential for water contamination through run-off, and crop expansion in low nitrogen soils.

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 diseases involved and the severity. For example, in the Western U.S., 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. Similarly, in Michigan, Minnesota, North Dakota, and Wisconsin, anthracnose (caused by Colletotrichum lindemuthianum), bacterial brown spot [caused by Pseudomonas syringae pv. syringae (Psp)], BCMV, 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 Beet mild curly top virus (BMCTV) 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. Many of these pathogens are highly variable in their virulence and new races or strains can appear in different regions. A recent example is the new rust races reported in Michigan and North Dakota (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 increase 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) 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 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 newly released common bean genome sequence and the rapid development of associated genomic technologies will help to accelerate the improvement of common bean (Schmutz et al., 2014). 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 BeadChip with 5398 SNPs developed through the BeanCAP project was broadly used by the W-2150 for the investigation of agriculturally important traits, and the SNP chip and genotyping-by-sequencing (GBS) is currently being implemented by W-2150 participants for Genome-wide Association Study (GWAS) in conjunction with the numerous nurseries and multi-state trials coordinated by this research group. Having access to the whole-genome sequence in the PhaseolusGenes genome database (http://phaseolusgenes.bioinformatics.ucdavis.edu/) will help in the fine mapping of many of these resistance sources. Given the formidable 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 area can affect outcomes in another.

At the same time that 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 300 wild bean panel, a 380 snap bean association mapping panel (SnAP), a 396 Andean Diversity Panel (ADP), a 300 BeanCAP Mesoamerican Diversity Panel (MDP), a 170 Durango Diversity Panel (DDP), and a 384 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 resilient than what is currently being grown in the U.S.

This interdisciplinary, multi-state, collaborative W-3150 project proposal 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 the 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. This research scheme has been very successful as evidenced by the “Excellence in Multistate Research Award” given to the W-1150 multistate project by the Western Association of Agricultural Experiment Station Directors (WAAESD) in March of 2009. The inclusive group of bean researchers jointly prepared the project renewal and is committed to collaborating with each other to achieve the overall objectives. For simplicity, these projects are grouped into the following priorities: biotic stresses, abiotic stresses, characterization/utilization of exotic germplasm, applied genomics, nurseries, nutritional and health related benefits in the human diet, and production/sustainability. Additional details of each sub-project listed in Appendix 1 can be provided upon request.

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 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, begomoviruses, curtoviruses, halo blight, rust, and other diseases caused by highly-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 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 unadapted 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). Most researchers often work within one or two tiers, and depend on other collaborators for the first step of gene introgression (Kelly et al., 1998). Furthermore, the role of genomics and marker-assisted selection as an additional tool for bean breeders is becoming increasingly important (Miklas et al., 2006a) 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 also 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, 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. Because exotic germplasm is increasingly being used to broaden the genetic base and develop cultivars with higher yield potential, enhanced 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-2150 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), Western Regional Bean Trial (WRBT) and the recently added Dry Bean Drought Nursery (DBDN). These nurseries are essential to identify high yielding broadly adapted cultivars and breeding lines with durable disease resistance, to estimate genetic progress over time, and to detect pathogen diversity in the shortest time possible. Therefore, these nurseries form an integral part and foundation for strong collaborative efforts within the W-2150 project and will continue to do so for the proposed W-3150. For example, data from the CDBN was key in estimating yield gains in dry beans for the four most important market classes in the U.S. since 1980 (Vandemark et al., 2014).

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. WAAESD Excellence Award). 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-3150 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-3150 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-3150 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.