W-4150: Breeding Phaseolus Beans for Resilience, Sustainable Production, and Enhanced Nutritional Value

(Multistate Research Project)

Status: Active

W-4150: Breeding Phaseolus Beans for Resilience, Sustainable Production, and Enhanced Nutritional Value

Duration: 10/01/2020 to 09/30/2025

Administrative Advisor(s):


NIFA Reps:


Statement of Issues and Justification

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.

Related, Current and Previous Work

The following is a list of the most important accomplishments and current research activities of the W3150.

Biotic Stresses:

Potyvirus: Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are related potyviruses that infect common bean worldwide. For seed production regions of the western U.S. there is zero tolerance for BCMV/BCMNV because it is a seed-borne disease. The host-pathogen interaction for BCMV published by Drijfhout (1978) has held up well until recently. Recombination among virus strains (Larsen et al., 2005; Feng et al., 2015) has led to novel more virulent strains and a new pathogroup which threaten effectiveness of host resistance genes. Concurrently, new research on gene action (Feng et al., 2017; 2018) and the role for bc-u to protect the I gene (Miklas - unpublished), is uncovering flaws with current resistance gene deployment strategies. Continued examination of the host-pathogen interaction is needed to direct breeding for sustainable resistance to BCMV and BCMNV.

Common bacterial blight (CBB): The inheritance of resistance to Xanthomonas axonopodis pv. phaseoli (Xap), the causal agent of CBB, continues to reveal a few major genes/QTL with Mendelian inheritance namely BC420, SU91, SAP6, and Xa11.4 (reviewed by Singh and Miklas, 2015). Minor QTL conditioning resistance have been detected as well, but only Xa7.1 on Pv07 has been validated. The QTL interact in specific combinations to affect higher levels of resistance against pathogen strains with differential pathogenicity (Mutlu et al., 2008; Viteri et al., 2014a). The BC420 and SU91 QTL from tepary did not exhibit yield drag in small seeded white bean (Miklas et al., 2017), but recovering seed size when deploying SU91 in large seeded beans remains a challenge (Kelly et al., 2018a; Viteri et al, 2014b). Breeders continue to use MAS for major QTL in combination with pathogen testing to develop CBB resistant cultivars.

Halo bacterial blight (HBB): Race 6 of Pseudomonas syringae pv. phaseolicola (Psp) is the most prominent strain worldwide. The recently mapped R genes Pse-1, -2, and -6 (Miklas et al., 2014) are ineffective against Race 6. Duncan et al. (2014) identified an old pinto bean US14 with resistance to Race 6 conditioned by two independent recessive genes. This resistance traces back to Kentucky Wonder snap bean (Zaumeyer, 1947). A QTL HB4.2 for broad resistance to all races traces to PI 150414 (red landrace from El Salvador) (Tock et al., 2017). That same study identified a second QTL HB5.1 which provided specific resistance to Race 6. The HB5.1 QTL in the ADP and was correlated with yield response under severe disease pressure. Continued severe outbreaks of HBB in some major production areas (MN, ND, WI, WY), emphasizes the need to continue pathogen variability surveys and breeding efforts to deploy and enhance resistance to this disease.

Bacterial wilt (BW) (CA, NE, ND): 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).

Anthracnose (MI, ND): Anthracnose, caused by Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib., is a seed- transmitted fungal pathogen that is cosmopolitan in its distribution. It is a major disease with yield losses as high as 95% in susceptible bean cultivars (Melotto et al., 2000). To date, over 100 virulent races have been reported globally using the 12 differential cultivars and the binary naming system for race identification (Pastor-Corrales, 1991; Kelly and Vallejo, 2004; Ferreira et al., 2013). A summary of known resistance genes and their resistance spectrum was published by Ferreira et al. (2013). The rapid emergence of race 105/109 complex in Manitoba underscores the need to monitor virulence diversity in different production areas. In 2017, race 109 was detected in Northern MI and moved into the main production area by 2019. Given the spread of this and other races, breeders are especially interested in genes that confer broad resistance to multiple races. A new initiative to screen a wild bean collection to identify new and novel resistance genes is underway.

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; Kennan 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 (Oladzad et al., 2019b; Soltani et al., 2017; Wang et al., 2018).

Rust: Rust caused by Uromyces appendiculatus (Pers.) Unger, infects common bean worldwide. Many different pathogen races have been reported (Stavely and Pastor-Corrales, 1989; Pastor-Corrales, 2001; Araya et al., 2004; Jochua et al., 2008; Acevedo et al., 2013). A new set of differential cultivars and the binary system is used to identify races. Two new races appeared in MI (race 22-2) (Wright et al., 2008) and ND (race 20-3) (Markell et al., 2009) that overcame the widely deployed Ur-3 gene. A newer race 27-7 in ND overcameUr-4, Ur-5, Ur-9, and Ur-13 resistance genes (Monclova- Santana, 2019). The rapid rise of new races underscores the need for new resistance genes. The broad resistance found in landraces PI 310762 (Shin et al., 2014; Hurtado-Gonzales et al., 2016), G19833 (Chaucha Chuga), and PI 260418 is under investigation. 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 (Valentini et al., 2015; Hurtado and Pastor-Corrales, 2019; Hurtado-Gonzales et al., 2019). Dry bean cultivars with rust resistance have been released recently (Brick et al, 2015; Urrea et al., 2019; Beaver et al., 2019; Osorno et al., 2020).

White mold: Integrated management, including genetic resistance, is used to reduce losses from Sclerotinia sclerotiorum, the causal agent of white mold (WM). The multi-state bean white mold nursery (BWMN) is used to identify and verify resistance in advanced bean lines. Multiple field nurseries and greenhouse tests are used to assess field resistance and physiological resistance, respectively, of submitted entries. The BWMN assists in the development and release of white mold resistant germplasm, including most recently PRP 153 and VCP 13 pinto beans with resistance combined from multiple sources including P. coccineus (Singh et al., 2016). The recent red bean cultivar ‘Cayenne’ (Kelly et al., 2018b) exhibited effective field resistance in the BWMN. A meta-analysis of QTL for WM resistance identified nine major QTL (Vasconcellos et al., 2017). To develop MAS for WM resistance, breeders have focused on fine mapping the meta-QTL (Mamidi et al., 2016). 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).

Abiotic Stresses:

Drought tolerance (CA, MI, NE, PR, WA): Drought affects over 60% of production area worldwide (White and Singh, 1991), while the impact of drought on common bean is only expected to increase with climate change. Cultivars with drought tolerance have been released in the U.S. (Beebe et al., 2008; Urrea, 2009). Exotic germplasm evaluation and introgression (Souter et al., 2017) will continue to play an important role in the incorporation of new drought tolerance into U.S. germplasm, especially in the Andean gene pool, where higher levels of tolerance in kidney, cranberry, and snap bean market classes are needed. The development of a collaborative drought nursery (DBDN) and the use of the shuttle breeding approach between NE and PR (Porch et al., 2012) has played a key role in identifying broad drought adaptation and rapidly integrating new sources of tolerance into breeding programs. Inheritance studies of drought tolerance in common bean continue. Wild beans show a stronger ability to continue growth despite  water-limited conditions (Berny-Mier y Teran et al., 2018). Eight QTL for yield, three of which clustered with PHI QTL from the RIL population ICA Bunsi/SXB405 underscore the importance of photosynthate remobilization in productivity (Berny-Mier y Teran et al., 2019). A dirigent-like gene on chromosome Pv03, involved in lignin biosynthesis, was associated with decreased pod dehiscence (Parker et al., 2019a). Commercial classes showing limited pod dehiscence include Durango classes (great northern, pink, and pinto), while higher pod dehiscence was observed for the Andean cranberry and kidney, and the Mesoamerican navy and black bean classes (Parker et al., 2019b).

Heat tolerance (NE, PR, WA): High average maximum daytime (> 30°C) and minimum nighttime (> 20°C) temperatures can significantly affect common bean yields (Rainey and Griffiths, 2005). It is predicted that by 2050, common bean production area worldwide will be 50% of current production due to global warming (Ramirez-Cabral et al., 2016). Recent collaborative work within the W-4150 has resulted in an improved understanding of the heat stress response (Soltani et al., 2019; Traub et al., 2018), improved selection techniques focused on tolerance to high temperatures during reproductive development, the identification of improved sources of heat tolerance for breeding (Abbasabadi et al., 2019), the elucidation of the genetics of heat tolerance (Abbasabadi et al., 2019; Rainey and Griffiths, 2005; Román-Avilés and Beaver, 2003), and the generation of improved dry bean (Beaver et al., 2018; Porch et al., 2010; 2012) and snap bean (Wasonga et al., 2010; 2012) cultivars and germplasm. Due to the coincidence of high temperature stress with other abiotic and biotic stresses, such as CBB 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 (Abbasabadi et al., 2019) and QTL studies, are showing key genomic regions for development of markers to facilitate MAS in environments where high temperature stress is not yet prevalent or consistent.

National/Regional Nurseries (CA, CO, MD, MI, ND, NE, NY, OR, PR, WA): As mentioned previously, 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 nine locations across the country, the Midwest Regional Performance Nursery (MRPN) grown in four states, the Bean White Mold Nursery (BWMN) grown at seven locations, and the Dry Bean Drought Nursery (DBDN) grown in five states. 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, 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 and Nutrition (CA, CO, IA, NE, ND, MI)

Nutritional Value: Phaseolus beans are a rich source of many important short fall micronutrients for growing children and women in the U.S., including folate, calcium and iron (de Benoist, 2008; Health and Services, 2017; Rebello et al., 2014). Dry beans are also an abundant source of many health promoting bioactive compounds, such as fiber, polyphenols and oligosaccharides (Chen et al., 2016; Ganesan and Xu, 2017).

Health Benefits: There is evidence for health benefits associated with the frequent consumption of Phaseolus beans. Bean consumption is associated with an increase in 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 (Flight and Clifton, 2006; 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). There are conflicting reports from various studies regards to the type of pulses (i.e. beans vs. lentils), as well as the quantity of pulses that garners a major health-promoting outcome (Becerra-Tomás et al., 2017; Viguiliouk et al., 2017).

Processing Quality/Flavor. Dry beans often require long cooking times to become palatable, which limits broader utilization around the world. Compared to rice, beans require nearly 100 times more energy to cook (Brouwer et al., 1996). Cooking time also influences meal decisions of American households where convenience is very important. On average the American household spends only 20 minutes preparing each meal (Smith et al., 2013). In the U.S., while cooking dry seed is important, the canned product is the major form that beans reach consumers. An estimated 90% of navy beans, and 45% of pinto beans are sold as canned goods (Lucier and Glaser, 2010). Canning quality, defined as how beans withstand thermal processing, is an end use quality trait that influences the success of a new variety. Color retention is an integral component of canning quality in beans, especially for black beans. New research showed that Vis/NIR spectroscopy was able to predict canned bean color scores (Mendoza et al., 2017). Since there is a need to rapidly evaluate color of canned black beans in breeding programs to ensure acceptable color scores in new breeding lines, utilizing VIS/NIR to predict canned color scores on dry seed is an attractive option, and an appealing option to the dry bean industry. Flavor is a major reason consumer choose a food. For dry beans, very little research has been done to characterize genetic variability for flavor. Improving bean flavor profiles may help to increase utilization and expand opportunities for beans as ingredients. The optimal flavor profile for a whole boiled bean may be different than a bean that would be made into a powder and used as an ingredient in products.

Genomics

Epigenetics (DE, NE): Epigenetics deals with a change in molecular or morphological phenotype of an organism without alteration of the underlying nucleotide sequence. The area of epigenetics encompasses the understanding of histone modifications as well as DNA methylation. Both of these modifications are important because they have the ability to influence the phenotype even though the underlying genotype, and the genome sequence remains unchanged. This influence is based on the interaction of DNA modifiers such as chromatin modifying enzymes with the chromatin, which is the complex of DNA and protein. A chromatin immunoprecipitation (ChIP) protocol was developed in five common bean genotypes (G19833, Sierra, Olathe, BAT 93 and Jalo EEP558), and soybean. An area of focus in common bean abiotic stress includes drought, salinity, and flooding tolerance. Additionally, work in biotic stress includes understanding epigenomics in rust, white mold, and other diseases. Part of this work also involves the understanding of stress memory. The focus of this work with other bean breeding programs is to work on material that is of interest for developing a better understanding of integrated transcriptomics and epigenomics, i.e., a cause and action of turning on or turning off genes of interest.

Genomics (CA, MI, ND, PR, WA): Extensive SNP data sets for the Middle American (MDP) and Andean Diversity Panels (ADP) (Cichy et al., 2015; 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., 2019a). 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., 2019b) 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 sustainability
  2. Examine nutrition and quality factors which promote human health
  3. Develop and apply genomic tools

Methods

Specific research procedures currently in the project can be found in previous W-2150 and W-3150 proposals. The following are new components, based on feedback from scientists and other stakeholders:

Objective 1.) Increase productivity and sustainability:

Viral diseases:

BCMV and BCMNV isolates and other bean-infecting potyviruses will continue to be collected and characterized from infected bean fields, using sequence analysis for molecular phylogenetic groups (Feng et al., 2019) and host differential response. More tightly-linked SNP markers will facilitate MAS for the recessive bc-u, bc-1, and bc-2 genes. The role for bc-u in protecting the I gene in Andean and snap beans will be examined. Genetic populations will validate different evolution for bc-2 in Mesoamerican versus Durango races. New recommendations for ideal BCMV/BCMNV strains to use for deployment of effective and sustainable resistance will be provided. BCMV/BCMNV strains for all the pathogroups will be increased and maintained in infected seed for long term storage.

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 be developed. Diverse strains will be employed in greenhouse inoculation tests to identify and combine sources of CBB resistance. Better markers for MAS of SAP6 and Xa7.1 will be generated using the Durango Diversity Panel (DDP) which segregates for both QTL. The BAM nucleotide sequence files for the DDP from ND will assist in fine mapping the QTL. Phenotyping of the DDP will take place in the greenhouse using differential Xap strains. RIL populations with any VAX lines as a parent will be used to validate Xa11.4 QTL found in VAX -1 and -3. Cultivar development for improved resistance to CBB will continue for the major U.S. market classes.

Halo blight: The races represented by 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 interval. Fine mapping these QTL that are effective against Race 6 will continue in the ADP and in select MA accessions to obtain markers useful for MAS. The recessive resistance of the US14HBR6 pinto germplasm line will be studied in segregating populations to determine if the resistance genes are independent of HB4.2 and HB5.1. Andean germplasm lines that combine four independent loci: Pse-2, Pse-3, HB4.2 and HB5.1, conferring resistance to HB, will be developed.

Bacterial wilt: A RIL population developed by single seed descent (G18829/Raven) will be tested against seven BW isolates. The overall goal is to determine the genetics of BW resistance and to identify molecular markers that can be used in dry bean breeding programs. A linkage map will be constructed using SNP markers generated by Molecular Inversion Probes (MIPs) and QTL identified for host resistance. The genetics of the BW wilt isolates will be characterized by rep-PCR fingerprinting analysis using primers corresponding to the BOX and ERIC elements.

Fungal diseases:

Anthracnose: A panel of wild 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 is requiring that additional resistance be introgressed 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.

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 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).

Rust: Combinations of effective Andean (new gene in PI 260418, Ur-9, Ur-12, and Ur-4) and Mesoamerican (Ur-11, the new gene in PI 310762, Ur-5, and Ur-7) and new resistance coming from P. acutifolius will continue to be developed in cultivars in all US market classes. New Andean sources of genes with broad rust resistance will be identified. Interactions between rust resistance genes will be examined for efficacy of resistance to specific races of the bean rust pathogen. Phenotypic, genetic, and genomic tools will be used to map the position of new rust resistance genes in the genome of common bean (Hurtado- Gonzalez et al., 2017) and then incorporated in the Intertek SNP platform for MAS.

White mold: Association mapping, next generation sequencing, and RNA expression will be used for fine mapping resistance QTL and for candidate gene analysis. The meta-QTL WM2.2 and WM5.4 are next in the queue for fine-mapping. A MAGIC population to study white mold resistance within the Durango race has been developed (Escobar et al., 2019). Phenotyping and genotyping of the MAGIC population will lead to identification and validation of new and existing QTL for white mold resistance in the pinto bean background. Pinto bean RIL populations will be used to identify QTL from pinto USPT-WM-12 and pinto VCP-13 which represent the newest pinto bean resistance sources. Levels of resistance incorporated into preferred seed types with high agronomic performance will continue to be tested in a coordinated uniform 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-4150 researchers (Kamvar et al., 2017; Lopez et al., 2019).

Insects:

Bean lines in Puerto Rico will continue to be screened for resistance to leafhopper 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 (Briscoa et al., 2014) will be considered for KASPar marker development. The inheritance of resistance/tolerance to Lygus bug (mainly Lygus hesperus) will be analyzed in the recombinant inbred population UC92/yUC Haskell. This population will be genotyped with SNPs and phenotyped in the field in the presence or absence of insecticide treatment. Diverse lima bean lines (n ~ 100) will similarly be genotyped and phenotyped to conduct a genome-wide association study (GWAS). Concurrently, the potential role of naturally occurring biochemical compounds in lima bean in Lygus resistance will be investigated. Candidate genes for the metabolic synthesis of cyanogenic glucoside (CG) and polygalacturonase- inhibiting protein (PGIP) will be mapped in UC92/yUC Haskell population and the degree of coincidence of these candidate genes with QTL for yield and resistance/tolerance will examine potential biochemical basis for Lygus resistance and facilitate breeding for Lygus resistance.

Abiotic stresses:

Drought tolerance: Putative sources of drought tolerance will continue to be evaluated in the Dry Bean Drought Nursery (DBDN). The characterization of drought tolerance will be conducted on the Durango Diversity Panel, the Andean Diversity Panel, and the Tepary Diversity Panel using GWAS, as well as in bi-parental populations using QTL analysis. These panels and populations have been genotyped using GBS and/or the SNP chip, while GWAS or QTL analysis is underway. Genetically diverse Andean Phaseolus Improvement Cooperative (PIC) advanced breeding lines, are being tested in multiple states under drought stress and are being integrated into breeding programs. Some of the mechanistic studies conducted in past USAID projects will be implemented through rapid evaluation techniques, such as the use of drones, proximal sensing carts, and the MultispeQ photosynthesis device, and fed into the breeding objectives of this project when key traits are identified. Our goal is for rapid identification of promising drought tolerant germplasm, and the development of tools, such as molecular markers and key phenotypic traits, associated with drought tolerance to facilitate breeding efforts. Shuttle breeding will continue between NE and PR to achieve drought, heat, and broad adaptation improvement in the pinto and great northern market classes.

Heat tolerance: Collaborative breeding for high ambient temperature tolerance in the dry and snap 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. Thus, both high day and high night temperature conditions will be effectively tested in these environments. Greenhouse evaluation will also be conducted at several sites, where high ambient temperatures can be achieved. RIL populations and diversity panels (Abbasabadi et al., 2019) will be phenotyped and evaluated using QTL and GWAS analyses. Phenotypic selection of advanced lines will be based on yield components and on reproductive traits such as pollen shed, number and viability. Additional phenotypic traits facilitating rapid evaluation and associated with heat tolerance, will be implemented as they are developed.

Characterization/Utilization of exotic germplasm:

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. Further research into the drought tolerance of wild common bean has shown that two traits provided potential drought tolerance, including root depth plasticity under drought and the ability to continue growth and development under drought (Berny Mier Y Teran et al., 2018). A candidate gene could be transferred to other races as a factor for drought tolerance (Parker et al., 2019a). 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 species (e.g., Arabidopsis, soybean), 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., 2014b).

Objective 2.) Examine nutrition and quality factors which promote human health: Nutritional Value: Important nutrition traits of advanced breeding lines will be evaluated after cooking, including the measurements of minerals, vitamins and iron bioavailability. In addition, we plan to measure bioactive compounds unique to dry beans, such phytate, polyphenols and oligosaccharides (Wiesinger et al., 2019). Breeding programs often measure the nutritional quality of raw seed because it is the most cost effective and practical measurement (Blair et al., 2013), but genotypic variations in cooking time and nutrient loss during thermal processing is unaccounted for (Wiesinger et al., 2016). Minerals are measured using ICP-AES (inductively coupled plasma-atomic emission spectroscopy) technology, while vitamins and bioactive compounds are determined using LC-MS/MS (liquid chromatography-mass spectrometry) techniques. Iron bioavailability is determined with a Caco-2 bioassay and animal feeding studies. Breeding programs will benefit from high through-put analyses to help identify improved nutritional traits in advanced breeding lines.

Processing Quality/Flavor: Cooking time will be determined on advanced lines and seeds from regional nurseries using a Mattson pin drop cooker (Wang and Daun, 2005). Canning quality will be measured on advanced lines and seeds from regional nurseries using an updated small-scale canning protocol (Hosfield et al., 1984). The evaluation of canned samples will include visual ratings by 18-20 trained panelists, color evaluations via colorimeter, and texture via a standard shear- compression cell of a Texture Analyzer (Texture Technologies, MI) (Mendoza et al., 2017). Flavor will be evaluated on select germplasm by a sensory panel of four trained individuals who will be asked to rate flavor characteristics on a scale of 1 to 5.

The characteristics to be rated include cotyledon texture, seed coat chewiness, flavor intensity, aesthetics, bitter, sweet, starchy, earthy, and beany flavor. Fresh shelling and dry beans are an increasingly important outlet for bean growers that sell outside commodity markets where they can earn a premium for an identity preserved product. Breeding lines and parental material will be evaluated for nutritional traits after cooking from fresh shelling and dry bean stages. Fresh shelling beans that are harvested while still hydrated are predicted to retain more nutrients because they do not need to be soaked nor cooked as long. Dry beans are expected to retain less nutrition due to a longer cooking time and even less if they are soaked and the liquid discarded. This data will be used toward the creation of a designed path to new cultivars that uniquely target a cooking method, harvest date, distinctive cooked appearance, and nutrition interaction.

Health Effects: Gastrointestinal and satiety effects of common bean pastas in adults will be examined. Common bean usage as flour or an ingredient in processed foods has greatly increased. Most research has focused on the functional properties of bean flours, but not considered the effects of product form on the human gastrointestinal system. We will test six formulations of black and yellow bean pastas in an acute feeding trial for glycemic response (blood sugar), but also for changes in bloating, flatulence, and stool frequency. Alterations in subjective satiety measures will be evaluated as well. Our projected outcomes are that the bean pastas will produce increased flatulence, stool frequency, but less satiety in comparison to an equivalent amount of whole cooked beans.

Obesity and beans: Obesity has risen sharply around the world in the last 25 years (Thompson and Thompson, 2009). Obesity may predispose individuals to increased risk for type-2 diabetes, cardiovascular disease, and cancer. A mouse model will be used to test the effects of dry bean consumption on body weight regulation and on insulin resistance and chronic inflammation.

Consumer Surveys: Consumer taste preferences for dishes made with common vs. tepary beans will be examined. There is little research on the sensory properties of traditional foods made with tepary in comparison to their common bean analogues, e.g. refried beans, boiled beans. In anticipation of promoting bean crops in marginal lands, the acceptability and functional properties of tepary dishes will be explored.

Objective 3.) Develop and apply genomic tools:

DNA sequencing: The tepary genome will be completed and abiotic and biotic stress tolerance genes and mechanisms from P. acutifolius can then be applied to the common bean. Re-sequencing efforts and data will be shared through incorporation in genome databases.

GWAS analysis: Data will be collated from the trials and analyzed using GWAS techniques. The adjusted phenotypic data will be coupled with the imputed genotypic data, and GWAS analysis will be performed using statistical corrections that account for population structure and/or relatedness to inform the project on: 1) the regions of the common bean genome that affect the trait value; 2) the magnitude of the effect on phenotypic variance; and 3) candidate genes that may affect the trait.

Integrated Transcriptomics and Epigenomics: We are working on understanding drought tolerance and stress memory as related to integrated epigenomics and transcriptomics. Dry beans were exposed to drought stress at 35% field capacity, 50% field capacity and 100% field capacity (no drought). After 2 weeks of drought stress, leaf samples were collected and utilized for isolating DNA and RNA for studies with histone modifications and amplification with candidate drought response genes.

Updating the PhaseolusGenes database with sequence information: The PhaseolusGenes database (Miller et al., 2018) is a breeder-focused molecular marker database that has been used internationally to identify and develop new markers tagging agronomic traits (e.g., anthracnose, angular leafspot), cross-hybridization events and genetic identity, and genetic mapping of major genes and QTLs. It has also been used in studies of genetic diversity of common bean, other Phaseolus species, and non-Phaseolus species, as well as genomic studies. 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), 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. Thus, PhaseolusGenes can be updated by integrating this new sequence information. Additionally, newly developed genomic tools for lima and tepary beans should also be integrated into this database, both for development of new varieties of these two species and for use of tepary bean as a source of diversity for common bean. To update PhaseolusGenes, third-generation sequencing for each of the seven domesticated taxa in Phaseolus including two domestications each in common and lima beans, and one each in tepary, runner, and year beans (Phaseolus dumosus Macfady). These seven sequences will provide the backbone of the genome browser instance of PhaseolusGenes. Second, we will add WGS and GBS sequences to the PhaseolusGenes database. We will work with Dr. S. Cannon, USDA-ARS, to include the capability to compare and visualize sequences using GCViT (https://gcvit.phaseolus.legumeinfo.org; https://www.researchgate.net/project/GCViT-Whole-genome-visualization-of-SNP-data). Third, we will add new markers that were published since 2014, the last time PhaseolusGenes was updated. Fourth, we will work with Dr. Cannon and his team to incorporate PhaseolusGenes into LegumeInfo (https://legumeinfo.org).

Measurement of Progress and Results

Outputs

  • Develop/release germplasm/cultivars with multiple disease resistance and/or resilience to climatic conditions.
  • 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.
  • Summarize results from the multistate trials and share with participants and the common bean community.
  • Train several postdoctoral scientists, graduate students and undergraduate students through their involvement in all project-related activities
  • Develop/release at least one cultivar within each market class of common bean grown in the U.S.
  • Update the Bean Improvement Cooperative web page and research section.
  • Deploy BCMV/BCMNV resistance into new market classes, such as pink, pinto, and snap beans, using traditional and marker-assisted selection approaches.
  • Determine the genetics of bacterial wilt resistance and identify molecular markers that can be used in dry bean breeding programs.
  • Introgress traits of economic importance from exotic tropical bean germplasm into beans adapted to temperate environments.
  • Find molecular markers close to genes of economic importance.
  • Germplasm will be developed with improved cooking time, canning quality and flavor attributes. Survey data will identify key contraints to greater bean usage by U.S. consumers.
  • Inheritance of resistance to Lygus.
  • Markers associated with QTLs for resistance to Lygus. Information about biochemical basis of resistance to Lygus.
  • Updated PhaseolusGenes database.
  • Whole-genome sequences related to the 7 Phaseolus domestications.
  • Comparative analysis of all major white mold QTL.
  • Identification of heat tolerance genes associated with germination and reproductive development.
  • Race Durango reference genome sequence.
  • Race Guatemala reference genome sequence.
  • Elucidation of epistatic interactions between rust resistance genes.
  • Accelerate the development of improved bean breeding lines by planting in Puerto Rico an additional generation each year in cooperative winter nurseries.
  • Develop new, more tightly linked SNP markers to facilitate MAS for the loci of the recessive genes, bc-u, bc-1, and bc-2.

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 product Area planted to new cultivars may increase by more than 10%, leading to substantial production increases in the participating states.
  • Adoption of multiple-disease resistant cultivars may reduce fungicide use by 25% or more, resulting in savings to producers and contribute to a cleaner environment. Adoption of 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 analysis methods.
  • The development and implementation of novel molecular markers for agriculturally important traits will accelerate the process of cultivar development.
  • The human health effects studies will yield data on the capabilities of important bean market classes to protect against inflammation, a cellular stressor that has been linked to heart disease and other inflammatory based diseases. These data will benefit our stakeholders, as the information can be used to promote the consumption of dry beans and thus increase market demands.
  • Additionally, the health effects research has the potential to advance our understanding of potential differences between bean market classes and develop new dietary practices to help address major health concerns.

Milestones

(2020):Release of new upright great northern bean cultivar (NE1-17-10) with enhanced levels of common bacterial blight resistance.

(2020):Release of new slow darkening pinto bean cultivar (NE2-17-18).

(2020):Release of the great northern bean cultivar ND Pegasus.

(2020):Release of the pinto bean cultivar ND Falcon.

(2020):Release of Mesoamerican bean germplasm line(s) that combines disease resistance with greater tolerance to high temperatures and low N soils (derived from crosses between elite lines from the BASE 120 trial).

(2020):Release of a determinate red mottled cultivar that combines multiple virus resistance.

(2020):Release of tepary bean with leafhopper resistance, disease resistance, and improved culinary characteristics

(2021):Inheritance of bacterial wilt resistance will be elucidate.

(2021):Molecular markers for bacterial wilt resistance will be identified.

(2021):Release of a pink bean that combines multiple virus and CBB resistance with erect architecture appropriate for direct harvest.

(2021):Molecular markers tagging genes for resistance to the anthracnose and rust pathogens of common bean will be developed.

(2021):Release of Mesoamerican bean germplasm line(s) that has enhanced levels of resistance to web blight.

(2021):Release of drought tolerant shuttle breeding pinto line with broad adaptation.

(2021):Release of a viny baby lima ben cultivar with enhanced yield and Lygus resistance for arid environments.

(2022):Through 2019, the BWMN will generate data for release of at least five new bean lines with improved resistance to white mold in agronomically adapted backgrounds and with seed characteristics within commercially acceptable market classes.

(2022):The DBDN will generate data for release of at least three new bean lines with improved drought/heat tolerance.

(2022):Release of a white bean cultivar that combines multiple virus, common bacterial blight and angular leaf spot resistance.

(2022):Release of black and pinto bean germplasm lines that combines multiple virus resistance and Ur-11 rust resistance gene.

(2023):Release of Mesoamerican germplasm that combines multiple virus and bruchid resistance.

(2024):Release of a tropically-adapted snap bean cultivar with BGYMV and BCMV resistance.

(2024):Release of a tropically-adapted determinate lima bean cultivar.

(2024):Updated PhaseolusGenes database

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 Legume-ipm-PIPE system (http://legume.ipmpipe.org/cgi-bin/sbr/public.cgi) (Schwartz et al., 2009a). Results will also be distributed on related websites including, the Bean Improvement Cooperative (BIC) website (http://bic.css.msu.edu/) and specialized sites such as the Root Biology Resource (http://plantscience.psu.edu/research/labs/roots), the Bean Breeders Molecular Marker Toolbox (http://phaseolusgenes.bioinformatics.ucdavis.edu/), and the Feed the Future-ARS webpage and database (http://arsftfbean.uprm.edu/bean/), among others. The project will facilitate the development and distribution of novel common bean diversity panels, GBS tools, and SNP chips to increase the use of these cutting-edge tools to accelerate common bean research and crop improvement.

Breeding common bean lines and cultivars will be extensively tested statewide, regionally (e.g. Midwest Regional Performance Nursery, Dry Bean Drought Nursey), 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-4150 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-4150 Co-PIs collaborate with extension specialists and extension agents which facilitates disseminating W-4150 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-4150 representatives each year at the annual meeting. The representatives (participating researchers) are designated by the directors of each participating institution. Unless he/she 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 declines to serve. An election will be held if any officer declines to serve in his/her 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-4150 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, Karen Cichy, USDA-ARS, East Lansing, MI; Vice-Chair, Carlos Urrea, University of Nebraska; Secretary, Maria Munoz-Amatriain, Colorado State University. Though W-4150 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-4150 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. Mid-west 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 bean industry. The W-4150 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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