W3150: Breeding Common Bean (Phaseolus vulgaris L.) for Resistance to Abiotic and Biotic Stresses, Sustainable Production, and Enhanced Nutritional

(Multistate Research Project)

Status: Active

W3150: Breeding Common Bean (Phaseolus vulgaris L.) for Resistance to Abiotic and Biotic Stresses, Sustainable Production, and Enhanced Nutritional

Duration: 10/01/2015 to 09/30/2020

Administrative Advisor(s):


NIFA Reps:


Statement of Issues and Justification

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.

Related, Current and Previous Work


The following is a list of the most important accomplishments and current research activities of the W-2150. Refer to Appendix 3 and preceding annual reports for more specific details on previous research activities and results.

Biotic Stresses:
Common bacterial blight and bacterial wilt. (CA, NE, ND, PR, WA). Cumulative work including QTL mapping and discovery on the inheritance of resistance to Xanthomonas axonopodis pv. phaseoli (Xap)/X. campestris pv. phaseoli (Xcp) and X. fuscans var. fuscans (Xff), the causal agent of common bacterial blight (CBB), has revealed the importance of a few major genes/QTL with Mendelian inheritance (Vandemark et al., 2008, Zapata et al., 2011). Discovered genes/QTL, namely BC420, SAP6 (syn. Xap-1; Zapata et al., 2011), SU91, and the newly identified QTL Xa11.4 present in the VAX lines (Viteri et al., 2014a) interact in specific combinations to affect higher levels of resistance against pathogen strains with differential pathogenicity. Recent studies (Viteri et al., 2014a) support the presence of a host-pathogen interaction (Mutlu et al., 2008a; Duncan et al., 2011) between resistance genes and pathogen strains.
Over the last decade, bacterial wilt, caused by Curtobacterium flaccumfaciens pv. flaccumfaciens has re-emerged in the Central High Plains (Nebraska, Colorado, and Wyoming) (Schwartz et al. 2010; Urrea and Harveson, 2014). This pathogen is considered an A2 quarantine pest in Europe and is subject to phytosanitary regulations in some countries (EPPO/CABI, 1997). Research during the last 5 years has focused on evaluations of commercial cultivars, germplasm, and selections from the USDA-GRIN and CIAT’s Core Collections against local isolates of the bacterial pathogen from Nebraska and Colorado. Results have been variable and may reflect differences in pathogenic isolates, environmental conditions, inoculation methodology, etc. For CIAT’s Core collection, 1685 accessions were susceptible (99.12%), and 15 accessions showed resistance (0.88%) to one great northern isolate and additional seven bacterial wilt isolates. Of those accessions, eight were wild beans, four P. coccineus, one P. acutifolius, and two cultivated (Urrea and Harveson, personal communication).

Halo blight/Bacterial Brown Spot. (CA, NE, ND, WA). Surveys of Pseudomonas syringae pv. phaseolicola (Psp), the causal agent of halo blight, continue to indicate that race 6 is the most prevalent across the U.S. and worldwide. The R genes Pse-1, Pse-2, and a new gene Pse-6 have been characterized, mapped, and tagged for marker-assisted selection (MAS) (Miklas et al., 2009, 2011, 2014), but the genes are not effective against race 6. Duncan et al. (2014a, 2014b) identified a selection US14HBR6 within pinto bean cultivar US-14 with resistance to race 6 conditioned by two independent recessive genes. Ghising et al. (2013) evaluated the US common bean core collection for reaction to halo blight and found five PI landraces with verified resistance to race 6 similar or superior to US14 HBR6 in some cases. Continued severe outbreaks of halo blight in some Midwestern production areas (e.g. Minnesota, North Dakota, Wisconsin, and Wyoming), emphasizes the need to continue pathogen variability surveys, and breeding efforts to deploy and enhance resistance to this disease.

Anthracnose. (MI, ND). Anthracnose, caused by the fungus Colletotrichum lindemuthianum (Sacc. & Magnus) -Briosi & Cavara, is a seed-transmitted pathogen of common bean and is cosmopolitan in its distribution. It is one of the most economically important diseases of common bean and can cause devastating 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 recently by Ferreira et al. (2013). The rapid emergence of race 105 in Manitoba underscores the need to monitor the virulence diversity in different production areas, particularly in geographically adjacent areas such as North Dakota and Minnesota. To date, race 105 has not been reported in these two states. However, given the impending appearance of this, and other races, breeders are especially interested in genes that confer broad resistance to multiple races, even though few races may dominate the population in a given region. This would allow for more durable resistance over time.

Root rots. (MI, NE, ND, OR, PR, WA). Root rot disease is caused by a complex of soil borne fungal pathogens, including Fusarium solani f.sp. phaseoli, Rhizoctonia solani, Pythium species, and Aphanomyces euteiches that attack roots and the crown of bean plants. In addition to direct damage caused by root rots, the tolerance of the plant to abiotic stress, such as drought, is compromised since a healthy root system is needed for tolerance to these constraints. Fusarium solani is considered to be the most common causal agent of root rot, and in Nebraska, North Dakota and Minnesota, is followed by Rhizoctonia solani in importance (Bradley and Luecke, 2004; Venette and Lamey, 1998; Steadman et al., unpublished). Recent findings have highlighted the ability of Fusarium species other than F. solani to cause root rot in dry beans (Bilgi et al., 2008, 2011; Gambhir et al., 2008). In addition, Aphanomyces euteiches f.sp. phaseoli is a poorly studied pathogen at the moment, but occurs frequently on sandy soils in the Upper Midwest. It can devastate some fields, and resistance is available in few dry bean genotypes, but is not commonly found in snap bean cultivars.

Rust. (CO, MD, MI, NE, ND, PR, WA). The common bean rust disease is caused by the basidiomycete fungal pathogen Uromyces appendiculatus (Pers.) Unger. Hundreds of different virulent strains (known as races) have been reported in the literature occurring worldwide (Stavely and Pastor-Corrales, 1989; Pastor-Corrales, 2001; Araya et al., 2004; Jochua et al., 2008; Acevedo et al., 2013). Two similar but not identical races had appeared in Michigan in 2007 (Wright et al., 2008) and North Dakota in 2008 (Markell et al., 2009). Although several established rust resistant cultivars were overcome by these new races, test results showed that several rust resistance genes are very effective in controlling the MI isolate characterized as race 22-2 and the ND isolate as race 20-3. These results demonstrably underscore the need for vigilance and are a reminder of the need to combine two, and preferably more effective rust resistance genes. A new Mesoamerican rust resistance gene discovered in PI 310762, a bean accession from Guatemala, is effective against all known races of the rust pathogen, including race 108 that overcomes Ur-11. The BARCBean6K_3 Beadchip was used with bulked segregant analysis to map the rust resistance allele in PI 310762 to Pv04 and develop linked SSR markers (Shin et al., 2014).

White mold. (ID, MI, ND, NY, NE, OR, WA, WI). Since no complete resistance to Sclerotinia sclerotiorum, the causal agent of white mold (WM), has been found in any host crop including common bean, integrated disease management is used to reduce yield and quality losses, improving the economic return for bean growers. The multi-state (CO, ID, MI, ND, NE, OR, WA, WI) bean white mold nursery (BWMN) has been and will continue to be used successfully to identify and verify resistance in advanced bean lines. The BWMN has been used to develop and release ten new white mold resistant germplasms in the last five years including pinto beans ‘Eldorado’ (Kelly et al., 2012) and USPT-WM-12 (Miklas et al., 2014). Comprehensive genetic maps of the QTL identified to date are serving as a blueprint for fine mapping and candidate gene analyses (Soule et al., 2011; Miklas et al., 2013). White mold resistance from secondary bean gene pools has been identified and transferred to common bean (Singh et al., 2009a; 2014a; 2014b), and will continue to be a focus in developing cultivars with partial resistance in the future (Schwartz and Singh, 2013).

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 in the U.S. Different QTL (Beebe, 2006; Blair et al., 2012; Schneider et al., 1997) or the same QTL (Mukeshimana et al., 2014a) were found to control yield response to drought in different drought stress environments. A seedling greenhouse assay for drought was developed that allows for the separation of root and shoot traits functional in drought tolerance (Mukeshimana et al., 2014b). Germplasms and cultivars with drought tolerance have been released (e.g. Kelly et al., 1999), while the combination of Mesoamerican and Durango races continues to be pursued for achieving higher levels of tolerance (Beebe et al., 2008; Urrea et al., 2009b). Exotic germplasm evaluation and conversion will 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, facilitated through the collaborative drought nursery and shuttle breeding (Porch et al., 2012).

Heat tolerance. (CA, NE, NY, PR). High average maximum daytime (> 30°C) and minimum nighttime (> 20°C) temperatures can significantly affect common bean yields (Singh, 1995). Considering rising temperatures due to global warming, heat tolerance needs to play an increasingly important role in common bean breeding programs. Collaborative work within the W-2150 has resulted in improved selection techniques focused on tolerance to high temperatures during reproductive development (Porch, 2006), the identification of improved sources of heat tolerance for breeding (Rainey and Griffiths, 2005a), the elucidation of the genetics of heat tolerance (Rainey and Griffiths, 2005b; Román-Avilés and Beaver, 2003; Shonnard and Gepts, 1994), and the generation of improved dry bean (Beaver et al., 2008; Porch et al., 2010; 2012) and snap bean (Wasonga et al., 2010; 2012) cultivars and germplasm.

Characterization/Utilization of exotic germplasm. (CA, MD, MI, NE, PR, WA). The use of exotic germplasm as a source of genetic diversity is of key importance to broaden the genetic base of both dry and snap beans. The traits that distinguish wild and domesticated beans have been described (Gepts and Debouck, 1991). The gene for the fin locus (Kwak et al., 2009; Repinski et al., 2012) and for slow darkening (Felicetti et al., 2014), have been identified which facilitates MAS and conversion. The study of the genetic and molecular basis of these traits, 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). Secondary and tertiary gene pools, including species such as P. coccineus and P. acutifolius, have already contributed resistance to diseases such as common bacterial blight, Bean golden yellow mosaic virus (BGYMV), and white mold. Although this is a long-term effort, a number of recent advances have resulted from collaborations within the W-2150, e.g. increased common bacterial blight resistance in Andean germplasm (Viteri et al., 2014b).

Applied Genomics
SNP Chip and SNP Calling Parameters. (CA, MD, MI, ND, NE, OR, PR, WA). Currently, the common bean research community has access to the BARCBean6K_3 BeadChip with 5398 SNPs whose development was funded by the Common Bean Coordinated Agricultural Project (BeanCAP). While this modest number of SNPs has limited utility for gene discovery, association panels, and monitoring of recombination, it is a highly adequate for bi-parental populations, which contain a limited number of recombination events (Brisco et al., 2014; Mukeshimana et al., 2014a; Davis et al., 2014; Viteri et al., 2014a). While the chip has proven useful for mapping in populations within the Middle American gene pool, it has only had limited utility in populations representing the Andean gene pool.

Genotyping-by-sequencing. (CA, ND, PR, WA). Genotyping-by-sequencing (GBS) is an alternative method to SNP genotyping. While the upfront costs are less per sample during library preparation and sequencing, the bioinformatics costs can be high, although solutions are being developed. The research proposed in the SNP Chip and SNP Calling Parameters section addresses the critical question regarding read mapping and SNP calling. That research will provide a bioinformatics framework for those who choose to adopt GBS for genotyping. ApeKI has recently been utilized to rapidly map a major dominant virus resistance allele to within approximately 1 Mb of the causative variant, and many additional SNPs within the interval were discovered for future fine mapping purposes (Hart and Griffiths, submitted). Other methodologies include using a two enzyme system which can capture additional sequence variability, and is also available for GBS.

PhaseolusGenes marker database. (CA, MI, ND). This database currently provides a high density of mapped sequences that can be used to design additional markers of known location on the whole-genome sequence (WGS) of common bean (Schmutz et al., 2014) and in some cases on the WGS of soybean (Schmutz et al., 2010). In addition, these same markers can also be located on genetic maps (Freyre et al., 1998; Galeano et al., 2011). Markers include microsatellites or SSRs, indels (Moghaddam et al., 2014), and a limited number of SNPs (Blair et al., 2013). Availability of this database has allowed the rapid identification of alternative markers when the original markers are monomorphic, lack consistent amplification, or map to more than one location in the genome (e.g., Gonçalves-Vidigal et al., 2011; T. Miller and P. Gepts, unpubl. data).

Epigenomics. (CA, MD). Epigenetics deals with a change in molecular or morphological phenotype of an organism without alteration of the nucleotide sequence. In plants, there is very limited work carried out on histone modifications, and none whatsoever in common bean. Ayyappan and Kalavacharla (unpublished) and Kalavacharla et al. (2014) developed a chromatin immunoprecipitation (ChIP) protocol in five common bean genotypes (G19833, Sierra, Olathe, BAT 93 and Jalo EEP558), and soybean. This has resulted in the development of reference histone-DNA interaction maps with identification of the binding of these histones to genic (transcription start site and gene body) or non-genic sites. This work has also been extended to understanding the common bean-bean rust interaction for both the resistant and susceptible interactions in response to specific races of the rust pathogen.

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, the Western Regional Bean Trial (WRBT) grown in four states, 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 among 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
Nutritional Value. (CA, CO, IA, IL, ND, NE, OR, TX). Increasing common bean consumption through greater utilization of beans is one way to take advantage of bean’s excellent nutritional profile. While the nutritional value of beans is clear, there is considerable variation in nutritional properties by genotype. Hayat et al. (2014) point out variations in carbohydrates, proteins, lipids, and ash content found by various researchers on bean. Drumm et al. (1990) found variability in the composition of the saccharides, protein and amino acids, phenolic acids, and saponins of four market classes of edible dry beans which contribute flavor. A broad range in protein, extractable and non-extractable phenolics, and phytate has also been found in nuña beans, and several adapted adapted germplasms have recently been tested and released (Pearson et al., 2012; Brick et al. 2013). Montoya et al. (2010) found more than 40 genetic variants of phaseolin, the main storage protein of beans. Brick et al. (2014) reported that total dietary fiber content among 282 cultivars ranged from 22.8 to 30.2 % based on a modified AOSA 2011.25 Total Dietary Fiber Assay (Kleintop et al., 2013). Genotype by environmental (GXE) interactions occurred for total dietary fiber but not for the oligosaccharides raffinose, stachyose, and verbascose.

Processing Quality/Flavor. (IL, MI, NE). The USDA Food and Nutrition Information Center strongly promotes the increased consumption of fruits and vegetables for better health due to increased soluble fiber, vitamins and minerals (USDA, 2012). While sweetness is generally not considered a quality attribute in snap beans, it has been reported that sensory panelists prefer cultivars considered sweeter in both dry beans and edamame (Mkanda et al., 2007; Wszelaki et al., 2005).
In the U.S., most dry beans are sold thermally processed in cans. The value of canned bean products has been increasing in the U.S. in recent years and in 2008, its $1.5 billion value was a 25% increase from 2007 (Lucier and Glaser, 2010). Canning quality has trumped seed yield in some instances, for example high yielding kidney bean varieties Isabella and Charlevoix were not grown by farmers because their canning quality did not meet industry standards (Kelly et al., 1998).
Color retention is an integral component of canning quality in beans and is probably most important in black beans, where anthocyanins are responsible for the black color. The ability to select for genotypes that do not leach their color is complicated by a correlation of color retention with slow water uptake. The ideal bean from a processor’s perspective is one with rapid and even seed expansion during soaking (Hosfield et al., 1984). Water uptake rate affects swelling capacity, which affects the number of cans of beans that can be produced from raw product, known as can yield (Hosfield, 1991).

Nutritional Databases. (CO, IL, NE, TX). There are many different market classes of dry edible beans (e.g. pinto, navy, black, great northern, kidney, etc.) and several different cultivars within each market class. Each has unique nutrient and phytochemical composition. Moreover, farming practices, regional production areas, and environmental conditions can affect the composition of the same type of beans. This information is important to determining the potential of beans to affect health parameters and reduce disease risk, and making this information widely available to the general public is an ongoing objective.

Health Effects. (CO, IA, IL, MO, NE, TX). Beyond their nutritive benefits, beans are rich in phytochemicals with health promoting activity (Thompson and Thompson, 2010). Adding beans to a diet may reduce a person’s risk for and the incidence of some cancers (i.e. mammary and colon) (Hangen and Bennink, 2002; Thompson et al., 2008). However, according to the 2010 Dietary Guidelines Advisory Committee (DGAC) Report, there is still insufficient evidence to make any health claims that bean intake influences body weight, cardiovascular health, or type 2 diabetes (USDA-NEL, 2010) or even the cellular stresses, such as chronic inflammation, that cause and perpetuate these illnesses. This lack of sufficient evidence about the health benefits of beans shows a real need for increased research in this area.

Sustainable and Profitable Agricultural Systems:
Integrated Pest and Disease Management (IPM). (MD, MI, ND, NE, OR, PR). The objective of pest and disease management for cultivated plants such as beans is to limit economic losses and to protect the value of the crop. Management measures are justified to the extent that their cost, in terms of money and effort, is less than losses caused by the problem. The most common management for bean diseases includes the use of disease-resistant cultivars, pathogen-free seed, and other cultural practices (e.g., crop rotation and crop residue management) that suppress the pathogen or restrict its ability to spread to or infect the plant, or through the treatment of soil, seed, or crop with chemical pesticides and biopesticides. The most effective and sustainable management of bean diseases is obtained when several disease management methods are integrated with each other and with the bean production practices.
Another management approach is through sustainable and profitable agricultural systems that improve and manage bean seed yield, conserve natural resources, and protect the environment and that facilitate interaction and information transfer (outreach) between W-3150 participants, the bean industry and other stakeholders (new and updated extension publications for state and regional uses, updating web-pages, smart phone apps, and grower and educational meetings).

Improved fixation, acquisition and utilization of nitrogen. (MI, ND, PA, PR, WA). Nitrogen fertilizer represents a significant crop production cost (Gutiérrez, 2012), while it is also a source of water contamination when fertilizer is applied using inappropriate rates or methods (Tilman et al., 2002), and soil acidification when ammonium is added to the soil as fertilizer. Improvements in the acquisition and utilization of nitrogen or enhanced biological nitrogen fixation, should increase the profitability and reduce the potential negative impact of bean production on the environment. Beans produced in the U.S. are often rotated with corn, potatoes, and sugar beets that use high rates of N fertilization. High levels of residual nitrogen in the soil may suppress nodulation and reduce biological nitrogen fixation. Little is known about the relationship of root architectural traits such as root hair density or number of basal roots with nodulation and the acquisition of soil nitrogen.
Organic bean production would especially benefit from the development of cultivars with increased biological nitrogen fixation and/or improved adaptation to low soil fertility (Singh et al., 2009b). This may require, however, the development of beans having morphological or phenological traits that are distinct from bean cultivars used for conventional bean production practices (Singh et al., 2011). The development of beans that could be planted earlier in the growing season to extend the period of vegetative growth might increase biological nitrogen fixation (BNF) and increase the ability of beans to compete with weeds. Other traits such as leafhopper resistance (Brisco et al., 2014) would contribute to organic bean production.

Objectives

  1. Improving bean yield potential by incorporating resistance/tolerance to major biotic and abiotic stresses, broadening the genetic base, implementing/integrating genomic resources and coordinating field trial nurseries.
  2. Analyze, document, and utilize genomic resources to enhance nutritional qualities and identify diversity within Phaseolus vulgaris to facilitate development of nutritious food products to promote human health and well-being.
  3. Implement sustainable and profitable agricultural systems that improve bean seed yield, conserve natural resources, and protect the environment.
  4. The overall strategy is based on collaborative research of constraints shared across production regions. This collaboration includes germplasm and pathogen exchange, sharing of protocols and techniques (e.g. DNA markers, virus isolates and infectious viral clones, field/greenhouse/lab. screening methodologies, etc.), regional nurseries and trials, and screening of genotypes for the traits of interest. As a result of this exchange of knowledge and material, breeding projects will be able to introgress and pyramid favorable alleles and QTL for enhanced seed yield potential, nutritional value, and resistance to multiple abiotic and biotic stresses using a multi-disciplinary and multi-institutional team approach. To accomplish these objectives, our research activities are divided into various sub-projects (see Appendix 1) in which researchers from two or more participating states and institutions conduct research on each major problem as a team. To identify and set priorities, all W-3150 participating researchers and stakeholders (such as growers and industry), will be periodically consulted about production problems and deficiencies in the available germplasm.

Methods

Objective 1: Improving Yield Potential Subobjective 1a. Resistance and pathogen variability for biotic stresses: Bacterial Diseases: Common bacterial blight and bacterial wilt. (CA, NE, ND, PR, WA). The differential reaction between resistance genes/QTL and Xap strains collected across the US (CO, ND, NE, UPR-Zapata, WI) and worldwide will continue to be studied. Diverse strains will be employed to identify sources of CBB resistance in pod tissue. Better markers for MAS of SAP-6 (Xap-1) will be generated. Numerous RIL populations, with a VAX line as a parent, will be used collectively to identify markers useful for MAS of the new Xa11.4 QTL. Development of cultivars with improved resistance to CBB using MAS and traditional breeding will continue for the major market classes. The complete genome sequences of strains of CBB will be determined using whole-genome sequencing via Illumina Hiseq and Pacific Biosciences sequencing focused on strains with maximum genetic and pathogenic variability (Mkandawire et al., 2004; Duncan et al., 2011), including globally predominant Xap strains, East African Xap strains, nonpathogenic xanthomonads and Xaf strains from a number of locations, and used to identify common virulence factors and strain specific virulence factors. For bacterial wilt, RILs in the process of development will be screened for reaction separately to yellow, purple, and orange bacterial wilt isolates. The RILs will be screened using the cotyledonary node inoculation method. In addition, there will be efforts to develop insight into the molecular basis of host-pathogen interaction and conduct QTL analysis of new bacterial wilt resistant sources to complement other genomic approaches within the W-3150 project. Halo blight/Brown Spot. (CA, NE, ND, WA). The races represented by Psp isolates sampled across regions will be determined primarily by inoculation of host differentials. Isolates will be assessed for phaseolotoxin production, for the presence of the phaseolotoxin gene with gene-based PCR primers and using repetitive element PCR to assess whether Psp races have distinct DNA fingerprints. Approximately 140 RILs from Rojo/CAL 143, 60 RILs from Canadian Wonder/PI150414, and RILS from other crosses involving five PI landraces with putative resistance to race 6 will be evaluated and markers for MAS will be developed. The two recessive resistance genes conditioning resistance to race 6 in the pinto breeding line US14HBR6 will be validated. Phenotypic data obtained from the screening of the USDA core collection will be used for GWAS to identify genomic regions associated with resistance to Psp. In response to the resurgence of brown spot disease in some Midwestern states, strains of the brown spot pathogen (Pss) will be characterized in a similar manner to that described above for Psp on the MDP and ADP in the greenhouse at NDSU. Fungal diseases: Anthracnose. (MI, ND). New resistance sources will be screened, characterized and mapped following suggested protocols for race characterization and allelism testing. Phenotypic data will be compiled on the reaction of the MDP and ADP panels to multiple and virulent races of anthracnose and the genetic location and associated markers determined. In addition, monitoring the pathogen will continue in order to detect changes in race structure to ensure that the most effective resistance genes are being deployed in breeding programs and that currently deployed genes are still effective. Research also is being conducted to improve molecular quantification of C. lindemuthianum as a tool for the seed industry and for evaluation of host/pathogen interaction. Root rots. (MI, NE, ND, OR, PR, WA). For Fusarium species, disease surveys will be conducted and root samples collected from grower fields across production regions (MI, MN, ND, NE, OR, PR, WA). Pathogen isolation and identification will be conducted using standard microbiological methods followed by molecular confirmation using PCR and sequencing. To minimize the resources needed, a multiplex PCR assay will be developed to identify Fusarium species in planta. Breeding lines will be screened in the greenhouse and field for Fusarium root rot and Fusarium wilt pathogen isolates from the Central High Plains and Michigan. PCR-based MAS methods for Fusarium wilt resistance genes/QTL exist (Singh and Schwartz, 2010) will be implemented. Promising breeding lines will be tested in adaptation and root rot nurseries and yield trials across the country. For Rhizoctonia species, an inoculated pot test will test both virulence on differential bean lines and resistance of breeding lines (Pena et al., 2013). Subgroups will be identified by morphology, mycelial compatibility (anastomosis groups), and use of informative primers (Singh and Schwartz, 2010). Pythium spp. have been encountered in the High Plains during wet early seasons and will be characterized and used to screen for resistance. Rust. (CO, MD, MI, NE, ND, PR, WA). 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) rust resistant genes will continue to be developed in cultivars in all US market classes, through collaboration between the ARS Bean Project in Beltsville, MD and W-3150 collaborators and private seed companies. Identification of new sources and genes for resistance through W-3150 collaboration will continue, as well as the development of markers for MAS. New Andean sources or genes with broad rust resistance from the ADP will be identified. Interaction between several rust resistance genes including Ur-4 and Ur-5, Ur-4 and Ur-11, Ur-3 and Ur-11, and Ur-4 and the gene in PI 260418 will be examined for efficacy of resistance to specific races of the bean rust pathogen. White mold. (MI, ND, NY, NE, OR, WA). Knowledge of genomic locations of QTL conditioning avoidance and partial physiological resistance to WM through fine mapping will allow pyramiding of small effect QTL and generate bean lines for release with higher levels of resistance. Association mapping, next generation sequencing, and RNA expression will be used for fine mapping and candidate gene analysis. Association mapping diversity panels and RIL populations will continue to be shared by the W-3150 research community for characterization of QTL for various traits including resistance to WM. A MAGIC population to study white mold resistance within the Mesoamerican gene pool is under development at NDSU. Metabolic profiling, will be deployed for identification of novel WM resistance mechanisms. Avoidance and physiological resistance from multiple and independent sources will be combined for increased WM resistance. Levels of resistance incorporated into preferred seed types with high agronomic performance will continue to be tested in a coordinated uniform BWMN. Characterization of isolates will involve collection of more grower field isolates in the Great Lakes, Red River Valley and High Plains bean production areas. Pathogen haplotypes and their relationship to MCGs and aggressiveness relationships as well as isolate comparison studies between grower fields and screening nurseries will be studied. In addition, another important characteristic of S. sclerotiorum isolates, fungicide sensitivity, will be determined for selected isolates maintained by W-3150 researchers (Otto-Hanson et al., 2011). Subobjective 1b. Abiotic stresses: Drought tolerance. (MI, NE, PR, WA). Putative sources of drought tolerance will be evaluated in a new annual trial, the Dry Bean Drought Nursery (DBDN), with drought trials planted in WA, NE, PR, CO and MI and shuttle breeding between NE and PR will continue. Segregating populations and diversity panels will be evaluated in drought stress (DS) and non-stress (NS) environments through a collaborative effort in several states, including the Durango Diversity Panel (DDP), the MA96 Mesoamerican panel, and the Andean Diversity Panel using AM, as well as in bi-parental populations using QTL analysis. Through collaboration with other funded projects, which also have a component of abiotic stress research, some of these trials will be conducted and the data and results shared. The goal will be the rapid identification of promising drought tolerant germplasm for breeding, and the development of tools, such as molecular markers and key phenotypic traits, associated with drought tolerance for selection of this critical trait. Heat tolerance. (CA, NE, NY, PR). Collaborative breeding for high ambient temperature tolerance in the dry bean and snap bean market classes will continue under hot summer field conditions (33C/24°C) in Puerto Rico. Thus, tolerance to both high day and high night temperature conditions will be effectively tested in this environment. Greenhouse evaluation will also be conducted at several sites, including NE, where high ambient temperatures can be achieved. Phenotypic selection based on yield components, reproductive traits such as pollen shed, and additional phenotypic traits facilitating rapid evaluation will be implemented. Improved heat tolerant germplasm will be developed in the snap bean and dry bean market classes using pedigree and recurrent selection. Advanced lines selected for drought tolerance through a shuttle breeding program between PR and NE will be tested for heat tolerance. The RCB 593 x INB 841 RIL population and diversity panels will be evaluated for the development of markers for MAS of heat tolerance. Subobjective 1c. Characterization/Utilization of Exotic Germplasm. (CA, MD, MI, NE, PR, WA). Evaluation of exotic common bean germplasm for root rot, common bacterial blight, rust, and angular leaf spot disease resistance; for Empoasca and bruchid insect resistance; for drought, heat, and low fertility stress tolerance; and for cooking time, nutrition traits, and efficient biological nitrogen fixation will continue. Selected exotic germplasm and sister species will continue to be used to introgress these specific traits into commercial market classes through long-term breeding efforts, for example use of interspecific P. vulgaris x P. acutifolius lines using methods previously developed for wide crosses (e.g. Beaver and Kelly, 1994) and cutting edge genotyping methods. The hypothesis will be tested that the environment of origin of wild germplasm is a preliminary indication of its potential to contribute useful genetic diversity, e.g. wild beans from the driest areas are likely sources of drought tolerance. Conservation of and preservation of wild species will involve the collection of the North American wild kidney bean or thicket bean (Phaseolus polystachios (L.) Britton, Sterns, & Poggenb.). Continued efforts in other domesticated Phaseolus species, such as lima bean (P. lunatus) or tepary bean (P. acutifolius), can provide alternative crops that, in turn, need to be improved, such as lima bean in California. Subobjective 1d. Genomics/Marker Assisted Selection: SNP Chip and SNP Calling Parameters. (CA, MD, MI, ND, NE, OR, PR, WA). Genome resequencing efforts will be initiated in both the Middle American and Andean gene pools. An adequate sequencing depth of 6x would be suitable for ~200 lines from each gene pool. This data will be augmented with 25x sequence coverage from a set of genotypes that are ancestral to modern varieties, and with SNP data from current GBS efforts including the wild bean, SnAP, DDP, MA96, and ADP panels. Appropriate mapping parameters (percent mismatches per read, number of gaps) will need to be calculated for each gene pool, as well as methods for SNP calls with VarScan. Once these parameters are established, the resequencing data can be mapped to discover SNPs throughout the genome. It is anticipated that ~5 million SNPs will be discovered from the 6x and 25x resequencing efforts. From the SNP discovery platform, individual SNPs can be selected that are 1) highly variable, and 2) have a high minor allele frequency. The community will determine the number of SNPs (>50,000) as well as the placement of the SNPs for the next generation chip Genotyping-by-sequencing. (CA, ND, PR, WA). Future work during this project will build on results from both the single-enzyme and two-enzyme reduced representation methods previously described. The advantage of using both methods is that imputation methods can be applied such that SNP calling data can be merged from sequencing multiple GBS libraries. The advantage of this approach is that the genotype data from multiple populations will provide deeper SNP coverage. This will allow the community to use the results from multiple labs to develop a much larger genotypic dataset that will be critical for association mapping approaches discussed in the next section. Association mapping. (CA, MI, ND, PR, WA). Data will be collated from the trials and analyzed using association mapping (AM) techniques. A critical question is environmental variability that will affect the trait value at each location. To account for this, all data will be adjusted using a Z transformation that places the multiple location data on an equivalent value and standard checks used across trials. The adjusted phenotypic data will be coupled with the imputed genotypic data, and an AM analysis will be performed using statistical corrections that account for population structure and/or relatedness. Those AM results will inform the project with regards to 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. PhaseolusGenes marker database. (CA, MI, ND). The PhaseolusGenes molecular marker database will be expanded given the increasing importance of DNA sequencing as both a way to generate new markers (SNPs, SSRs, and Indels) and to determine segregation and linkage (for example, by GBS). Sequences will be obtained from (re-)sequencing of multiple genotypes, such as germplasm collections for association mapping (e.g., Huang and Han, 2014; Morrison and Linder, 2014) or segregating populations for biparental linkage mapping (e.g., Gardner et al., 2014; Li et al., 2014). Alternatively, selected targeted regions of the genome will be sequenced because they contain genes of agronomic interest. A third application will be the use of the bean genome sequence as a reference for other Phaseolus genomes, like the lima and tepary bean, and for synteny efforts with other members of the clade (e.g. soybean and cowpea). Hence, we propose to develop a workflow/pipeline (e.g., Huang et al., 2014) to 1) filter, trim, assemble, and upload sequence data; 2) establish a list of polymorphisms according to chromosome and position on chromosomes in different genotypes; and 3) display sequence polymorphisms among different genotypes across the bean genome. Epigenomics. (CA, MD). We propose a common bean histone DNA interaction project that captures differential histone DNA interactions in key abiotic and biotic stresses (example bacterial blight, rust, anthracnose etc., or drought, heat, salinity etc.) with a limited number of histone modification marks known to be important to these stresses in plant and mammalian systems. This will lay the groundwork for future large scale projects in common bean and other legumes (similar to the mammalian NIH ENCODE and Epigenomics Roadmap projects) and will allow us to understand the effect of and inheritance of specific marks during the presence and absence of these stresses. Crampton and Kalavacharla (unpublished) are also comparing the standard sodium bisulfite treatment and next generation sequencing (Methyl-seq) with a modified immunoprecipation method called methylated DNA immunoprecipation (MeDIP-seq) to identify methylation patterns in the Mesoamerican bean genotype Sierra. Subobjective 1e. National/Regional Nurseries. (CA, CO, MD, MI, ND, NE, NY, OR, PR, WA). 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 Dry Bean Drought Nursery (DBDN) will continue to be conducted. In addition to these six nurseries, the winter nurseries in Puerto Rico allow W-3150 breeding programs to rapidly advance generations and multiply seed of breeding lines during the winter months. Collaborators will also be able to evaluate the performance of bean breeding lines in a low N nursery, and a new Winter Cooperative Dry Bean Nursery (WCDBN) to compare the performance of bean lines in Puerto Rico with their performance in the U.S. A multi-location analysis approach will be used to analyze the results from the CDBN and the WCDBN. Results from the analysis should help to determine how well the performance of bean breeding lines in Puerto Rico predicts the performance of bean lines in different bean production regions of the U.S. and the selection pressure that can be applied on bean lines in Puerto Rico. A similar approach will be used for other nurseries such as the MRPN and the WRBT in an attempt to estimate genetic gains across years and regions. Objective 2. Analyze, document, and utilize genomic resources to enhance nutritional qualities and identify diversity within Phaseolus to facilitate development of nutritious food products to promote human health and well-being Subobjective 2a. Nutritional Value. (CA, CO, IA, IL, ND, NE, OR, TX). Seed mineral concentrations will be evaluated using material grown in various regional trials, and as part of the Feed the Future Grain Legumes Project. Emphasis will be given to genotyped diversity panels (ADP, DDP, MDP, etc.), such that these data can be analyzed by association mapping to identify nutrient-related molecular markers. All data will be combined with previous year’s data from the Bean CAP and FtF Grain Legumes projects and will be made publically available. Additional whole-plant mineral investigations will be conducted to determine the spatial and temporal dynamics of mineral transport through bean plants, such that bottlenecks can be identified with respect to mineral flow to seeds. This information will enable the development of strategies to increase seed mineral concentrations. Subobjective 2b. Processing Quality/Flavor. (IL, MI, NE). Flavor is a very important consideration for consumers. Research is planned to gain knowledge regarding variation in sugar and flavor content among a sample of dry bean and green pod-type PI accessions from the USDA PGCC, Pullman, WA. From the USDA Phaseolus Core collection containing 423 accessions, a diverse sub-core of 94 Plant Introductions (PI) characterized as snap beans and 20 dry bean PI accessions will be evaluated using previously developed procedures (Vandenlangenberg et al., 2012a) with the stage of maturity of the tissue taken into account. In addition, the populations produced from crossing will be used for GBS to elucidate the genes responsible for the popping characteristic. Canning quality is also a trait that influences bean consumption. Canning quality will be measured on the CDBN from two locations annually according to the methods of Hosfield et al. (1984). Visual appeal will be evaluated by 18-20 trained panelists on a hedonic scale of 1 to 7 (Wright and Kelly, 2011). Following the visual rating, beans will be evaluated for color with a Hunter Lab Colorimeter Lab Scan XE (Reston, VA). Texture will also be measured with a standard shear-compression cell of a Kramer Shear Press. Seed nutritional composition will be measured in each of the canned bean samples. Specifically, minerals and protein will be quantified. Color retention is one aspect of canning quality that will be genetically dissected. Two QTL have been identified for color retention and canning quality appearance in the Shiny Crow x Black Magic population and one of the QTL for color retention on chromosome 5 overlaps with a QTL for anthocyanin content in the same population (Cichy et al., 2014). These QTL will be tested and validated. HPLC will be used for the analyses according to the method of Lin et al. (2008). Subobjective 2c. Nutritional Databases. (CO, IL, NE, TX). In collaboration with the USDA National Nutrient Databank Laboratory, results of nutrient composition analyses will be made available to the general public through several pipelines, including the National Database for Standard Reference, specialty databases including those that compile information on cultivar and growing region, and databases currently in development such as the flavonoids database. Compositional information will include, but not be limited to, proximates (total protein, moisture, ash, lipids, and carbohydrates), phenolic content (phenolic acids, flavonoids, anthocyanins, tannins), minerals, amino acids, prebiotics (stachyose and raffinose), dietary fiber, resistant starch, phytic acids, saponins, carotenoids, total lignin, starch, vitamins (A, B, and C), etc. This information will then be linked to regional production, environmental conditions, farming practices and processing operations described throughout this proposal, as it is expected that each will affect the composition profiles of beans. Further, data from nutrient analyses will be used to support and populate the USDA’s Database Modernization Project. Subobjective 2d. Health Effects. (CO, IA, IL, MO, NE, TX). The long term goal of this research is to establish dry beans as a food system able to prevent or remediate chronic inflammation and its associated disease risk factors. Our hypothesis is that beans will protect against chronic inflammation and/or its disease risks; however, certain bean classes will be more effective than others due to their diverse chemical composition. This hypothesis will be tested by completing the two studies. In Study 1, the effects of individual components present in dry beans and combinations thereof (particularly the phenols, flavonoids and their metabolites) on chronic inflammation will initially be studied using murine RAW 264.7 macrophages (Park et al., 2008; Zbasnik et al., 2009; Zhongshi et al., 2011). These screening experiments will thus provide information on the ability of the components present in beans 1) to induce a pro-inflammatory state, 2) to maintain or remediate to an inactive state, or 3) to evoke an anti-inflammatory state. The Study 2 will involve in vivo studies to determine the effects of select bean market classes, cultivars, and/or the potent extracts, determined from Study 1, on cholesterol levels and intestinal inflammation caused by a fatty diet. A hamster model will be used for this purpose as their lipid metabolic profiles are similar to humans. Briefly, hamsters will be fed an atherogenic diet supplemented with and without beans or bean extracts at different doses for 4 weeks according to Lee et al. (2014). After four weeks, the animals will be euthanized, and evaluated for liver / plasma cholesterol markers (Lee et al., 2014) and intestinal inflammation markers, as described in Studies 1 and 2. Lastly, the effects that beans have on the microbiome of these hamsters will be evaluated as described by Martinez et al. (2009). Objective 3. Implement sustainable and profitable agricultural systems that improve bean seed yield, conserve natural resources and protect the environment Sub-objective 3a. Integrated Pest and Disease Management (MD, MI, ND, NE, OR, PR). The development of integrated pest and disease management strategies is a multi-disciplinary task that requires good communication. The proceedings from the annual W-3150 meetings will be documented and distributed to participants and stakeholders via trade magazines, email and internet promotions. The project will develop strategies that are in tune with the needs and priorities of the bean industry and will share results from this project with colleagues involved with various research and extension projects (e.g., CAP, translational genomics, pathogen diagnostics, Root rot, Climate resilient beans, Legume innovation lab) funded in recent years by the USDA-NIFA, USAID and Specialty Crop Research Initiative (SCRI) regarding issues of relevance to the national bean industry. An annual report, including summaries and impact statements from each participant will be generated along with the minutes of the annual meeting and will be sent to committee members and archived on the BIC and NIMSS web sites. The annual report will also be sent to appropriate University Deans, Agricultural Experiment Station Directors, USDA-ARS administrators, key legislators, and other identified stakeholders. Sub-objective 3b. Improved fixation, acquisition and utilization of nitrogen (MI, ND, PA, PR, WA). Puerto Rico has ideal sites for screening the performance of beans in low N soils (Dorcinvil et al., 2010). The small red breeding line TARS SR05, which was selected in Puerto Rico for adaptation to edaphic stress (Smith et al., 2007), produced among the highest seed yield and had the highest rates of N accumulation and BNF in organic field trials conducted in Michigan (Heilig and Kelly, 2012). The UPR will plant the Cooperative Dry Bean Nursery (CDBN) at the Isabela Substation in a low N environment during the winter months and on the mainland of the U.S. to evaluate the adaptation of lines to the temperate climate. The cooperative nursery will not be fertilized. The trial will be inoculated with Rhizobium strains CIAT 899 and CIAT 632 to promote nodulation. In addition to seed yield and agronomic traits, a ‘shovelomic’ method (Trachsel et al., 2014) developed at Penn State University for common beans will be used to measure root traits and nodulation, and to identify root traits associated with adaptation to low N soils. The Middle American and Andean Diversity Panels will be used to evaluate the genetics of these traits using cutting edge SNP chip and GBS technologies and methods of association mapping. Ground peat inoculants have been largely used for seed inoculation, while the source of peat for inoculants is limiting and the inoculation of large numbers of genotypes for BNF can be challenging. Liquid inoculants are widely used for Bradyrhizobium in soybeans. Evaluation of Rhizobium liquid inoculants with different polymeric additives (Tittabutra et al., 2006), and different inoculant formulations (liquid and granular) will be compared with seed inoculation with peat based inoculants under greenhouse and field conditions. This study will contribute to the release of liquid inoculants for common beans.

Measurement of Progress and Results

Outputs

  • The extent and nature of genetic diversity of the pathogens causing economically important diseases in the U.S. will be obtained through phenotypic analysis and genome sequencing.
  • New germplasm, improved breeding lines, and cultivars of major market classes will be developed and released. The improved breeding lines and cultivars will possess high levels of resistance/tolerance to biotic and abiotic stresses.
  • Germplasm exchange, and tropical germplasm characterization and conversion will provide researchers with novel genes to broaden the genetic base of U.S. cultivars (e.g., new resistance genes to abiotic and biotic stresses).
  • Newly developed diversity panels, including the Mesoamerican Diversity Panel (MDP), the Andean Diversity Panel (ADP), the Durango Diversity Panel (DDP), the MA96 Mesoamerican drought panel, the Snap bean diversity panel (SnAP), and the Tepary bean Diversity Panel (TDP), will provide a broad framework for rapidly advancing the discovery of novel alleles for agriculturally important traits and for the development of markers for marker assisted selection.
  • Genome resequencing efforts will be initiated in both the Middle American and Andean common bean gene pools with about ~200 lines from each gene pool. This data will allow for the development of a SNP chip with at least 50,000 SNPs.
  • Association mapping analysis and QTL analysis will be conducted using cutting edge technologies, such as genotyping-by-sequencing (GBS) and the available SNP chips, to accelerate the genotyping efforts for the identification of key regions and markers for important traits. • New genes for resistance/tolerance and nutritional attributes will be discovered. Concurrently, KASPar, Indel and other breeder-friendly molecular markers for existing and new resistance alleles, abiotic stresses, and nutritional and processing quality traits will be generated from this project. • 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. • Germplasm will be developed with improved biological nitrogen fixation, combined with increased vegetative growth, low fertility tolerance, and leafhopper pest resistance that will benefit both conventional and organic common bean production. • W-3150 members will continue to share results from this project and learn from colleagues involved with various research and extension projects (e.g., CAP, translational genomics, pathogen diagnostics, root rot, climate resilient beans, legume innovation lab) funded in recent years by the USDA-NIFA, USAID and Specialty Crop Research Initiative (SCRI) regarding issues of relevance to the national bean industry.

Outcomes or Projected Impacts

  • Improved high yielding bean cultivars resistant to multiple abiotic and biotic stresses (especially multiple-diseases) will dominate the regional and national production. 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.
  • The genes responsible for key agronomic, disease, nutrient and health-related traits will be discovered through the use of novel diversity panels, genomic tools, and cutting edge analysis methods.
  • The development and implementation of novel molecular markers for agriculturally important traits will accelerate the process of cultivar development.
  • The 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. • Bean production systems that minimize certain inputs such as fertilizers, and that still obtain competitive yields, will allow for more sustainable production.

Milestones

(2014): Release of new upright great northern bean variety Powderhorn with enhanced levels of avoidance to white mold (Kelly et al., 2014).

(2014): Release of new pinto bean germplasm line USPT-WM-12 with partial resistance to white mold (Miklas et al., 2014).

(2015): New black bean cultivar Zenith released in 2015 possesses resistance to race 73 of anthracnose along with upright architecture, high yield potential and superior canning quality (Kelly et al., 2015)

(2015): Release of two new cultivars with Mexican seed types Flor de Mayo and Flor de Junio adapted to temperate growing conditions.

(2016): 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.

(2015):Association mapping will be used to identify novel QTL conditioning tolerance to high ambient temperature stress. (2016) Markers generated and validated for MAS of Xa11.4 QTL for resistance to CBB. (2016) Complete genome sequences of a diverse collection of CBB and annotate them. (2016-2017) Association mapping will identify novel QTL conditioning white mold avoidance and resistance in snap and dry bean diversity panels. (2017) Sources of pod resistance to CBB will be determined. New sources for halo blight resistance to race 6 will be verified and the resistance QTL identified and mapped. (2018) Variability among and fungicide sensitivity of at least 200 new pathogen isolates sampled from grower fields will be tested and added to 366 isolates to produce pathogen isolates widely dispersed to unique, with high to low aggressiveness and with ranges of fungicide sensitivity in various combinations for screening for WM resistance. (2018) Black, great northern, kidney, and pinto bean cultivars with combinations of rust, anthracnose and common bacterial blight resistance will be developed. (2019) Markers with utility for MAS of the QTL conditioning resistance to halo blight (race 6) and bacterial wilt will be developed. (2019) The genomic position of two to three robust QTL (WM2.2, WM7,1, WM7.3, WM8.3) for partial resistance to WM will be fine-mapped and tagged with markers applicable for marker-assisted breeding.

Projected Participation

View Appendix E: Participation

Outreach Plan

Research results from each sub-project will be promptly published in refereed and non-refereed journals, extension bulletins, flyers, etc., and posted on the web sites of individual institutions or programs, including the Legume-ipm-PIPE system (http://legume.ipmpipe.org/cgi-bin/sbr/public.cgi), which was coordinated by one of the previous project members (Schwartz et al., 2009a). Additional online resources include the Bean Improvement Cooperative website with information on the at http://bic.css.msu.edu/; and more specialized sites such as the root biology resource at http://plantscience.psu.edu/research/labs/roots; the Bean Breeders Molecular Marker Toolbox at http://phaseolusgenes.bioinformatics.ucdavis.edu/; and the Feed the Future-ARS webpage and database at http://arsftfbean.uprm.edu/bean/, among others. The development and distribution of novel common bean diversity panels, GBS tools, and SNP chips will also be facilitated in order to increase the use and application of these cutting-edge tools for the acceleration of common bean research and crop improvement.

Breeding lines and cultivars will be extensively tested statewide, regionally (e.g., the Midwest Regional Performance Nursery and Western Regional Bean Trials), and nationally (e.g., the Cooperative Dry Bean Nursery), including on-farm strip-plantings of the most promising or outstanding genotypes in different cropping systems. In addition, these lines can be used in crosses by any member of the W-3150 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 will be held each year at or near crop maturity. 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, Bean Improvement Cooperative, or American Society of Horticultural Sciences, and seed deposited with the National Center for Genetic Resources Preservation.

Many of the W-3150 Co-PIs collaborate with extension specialists and extension agents through participation in winter meetings and field days during the summer and as co-authors in extension publications that disseminates achievements of W-3150 research such as the release of improved bean cultivars.

Organization/Governance

Present officers of the W-2150 Regional Project are: Chair, Janice Rueda, ADM; Vice-Chair, Julie Pasche, North Dakota State University; Secretary, Khwaja Hossain, Mayville State University; Administrative Advisor, Donn Thill (assigned Dec. 2009), University of Idaho, Moscow, ID.

The directors of the various participating state institutions designate the W-3150 participating researchers, who elect the members or officers of the Technical Committee. The project is considered a Western Regional Research Project, but has always had substantial participation by states from other bean producing regions of the U.S. and USDA-ARS researchers. The Technical Committee officers are a Chairperson, Vice-Chairperson, and Secretary. 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. The officers will be elected from the officially designated representatives each year at the annual meetings. The Western Association of Agricultural Experiment Station Directors selects the Administrative Advisor who has no voting rights.

The Technical Committee will meet annually, unless otherwise planned, at a place and on a date designated by a majority vote of the committee. Minutes will be recorded and an annual progress report will be prepared by the Technical Committee and submitted through proper channels.

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