Tepary bean (Phaseolus acutifolius A. Gray), indigenous to the arid climates of northern Mexico and the Southwest United States, diverged from common bean (Phaseolus vulgaris L.), approximately 2 million years ago and exhibits a wide range of resistance to biotic stressors. The tepary genome is highly syntenic to the common bean genome providing a foundation for discovery and breeding of agronomic traits between these two crop species. Although a limited number of adaptive traits from tepary bean have been introgressed into common bean, hybridization barriers between these two species required the development of bridging lines to alleviate this barrier. Thus, to fully utilize the extant tepary bean germplasm as both a crop and as a donor of adaptive traits, we developed a diversity panel of 422 cultivated, weedy, and wild tepary bean accessions which were then genotyped and phenotyped to enable population genetic analyses and genome-wide association studies for their response to a range of biotic stressors. Population structure analyses of the panel revealed eight subpopulations and the differentiation of botanical varieties within P. acutifolius. Genome-wide association studies revealed loci and candidate genes underlying biotic stress resistance including quantitative trait loci for resistance to weevils, common bacterial blight, Fusarium wilt, and bean common mosaic necrosis virus that can be harnessed not only for tepary bean but also common bean improvement.

Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars.

Consumer food choices are often focused on protein intake, but the chosen sources are frequently either animal-based protein that has high fat content or plant-based protein that is low in other nutrients. In either case, these protein sources often lack dietary fiber, which is a nutrient of concern in the 2020–2025 Dietary Guide for Americans. Pulse crops, such as dry edible beans (Phaseolus vulgaris L.), are a rich source of dietary protein and contain approximately equal amounts of dietary fiber per 100 kcal edible portion; yet the consumer's attention has not been directed to this important fact. If product labeling were used to draw attention to the similar ratio of dietary protein to dietary fiber in dry bean and other pulses, measures of carbohydrate quality could also be highlighted. Dietary fiber is categorized into three fractions, namely, soluble (SDF), insoluble (IDF), and oligosaccharides (OLIGO), yet nutrient composition databases, as well as food labels, usually report only crude fiber. The objectives of this research were to measure the content of SDF, IDF, and OLIGO in a large genetically diverse panel of bean cultivars and improved germplasm (n = 275) and determine the impact of growing environment on the content of DF. Dietary fiber was evaluated using the American Association of Analytical Chemist 2011.25 method on bean seed grown at two locations. Dry bean cultivars differed for all DF components (P ≤ 0.05). Insoluble dietary fiber constituted the highest portion of total DF (54.0%), followed by SDF (29.1%) and OLIGO (16.8%). Mean total DF and all components did not differ among genotypes grown in two field environments. These results indicate that value could be added to dry bean by cultivar-specific food labeling for protein and components of dietary fiber.

Genetic vulnerability refers to (sometimes catastrophic) actual or potential losses in the production of a crop (in quantity and/or quality), attributable to spatial or temporal reduction in the crop's biodiversity. Conversely, genetic resilience refers to the natural and anthropic capabilities of this biodiversity to mitigate these reductions in crop production. Here, an assessment is provided of genetic vulnerability and resilience of Phaseolus beans, which provide an abundant and sustainable source of protein and micronutrients for populations around the world. We provide an overview of the economic, nutritional, and cultural role of Phaseolus beans and phylogenetic and diversity analyses of the genus, its five domesticated species, and seven domestications, which provide key foundational information for this appraisal. We then assess the uniformity of the crop in the United States and the main drivers of genetic erosion in the centers of origin of the genus in the Americas. Next, the current and emerging breeding constraints are discussed for biotic and abiotic stresses, morphological and phenological traits, and dietary and cooking needs. To address these vulnerabilities, several resources have been developed and, which have been applied to increase the genetic resilience of Phaseolus beans. The resilience resources include genetic resources collections such as the global collection at the Centro Internacional de Agricultura Tropical (CIAT, Colombia), national collections in the United States, Brazil, the European Union, and elsewhere, which include wild and domesticated types across the genus but focus primarily on domesticated species. Resilience resources also include genome-wide reference DNA sequences for three of the five domesticated species, multiple diversity panels and recombinant inbred populations, and large sets of whole-genome diversity data based on single-nucleotide polymorphism (SNP) arrays, genotyping by sequencing, and whole-genome sequencing of germplasm sets. Numerous marker–trait associations and genes affecting agronomic traits have also been characterized in the genus. In turn, these resources have been successfully utilized to make Phaseolus beans more resistant against biotic and abiotic stresses (including those incurred by climate change) and to improve dietary and culinary quality through significant breeding efforts in the United States, at CIAT (mainly Latin America and Africa) and in national programs in Latin America and Eastern Africa. Future challenges remain, however, which include (1) a continued need for ex situ and in situ conservation of diversity, with agroecologically informed germplasm explorations and integration of farmers into conservation and breeding activities; (2) increased pre-breeding efforts involving gene bank curators and bean improvement scientists; (3) expansion of breeding of domesticated species other than common bean, where appropriate based on their potential adaptation to global climate change and consumer preferences; (4) an increased focus on culinary and dietary improvement; and (5) inclusion of microorganisms (both pathogenic and beneficial) in genetic conservation. We conclude that in the short term (~5 years), Phaseolus beans have limited genetic vulnerability. However, over the longer term, vulnerability due to several factors will increase, which can be addressed by a wide range of the resilience resources presented here.

Common bean (Phaseolus vulgaris L.) is an important staple food crop in households worldwide. Genotype and location influence phenotypic nutrient composition. However, there are limited data on the magnitude of this variation for common bean yield and nutritive value. The objective of this study was to determine the effect of location on yield and seed nutritional composition. Four globally important varieties (dark red kidney/‘Montcalm’, great northern /‘Taurus’, black /‘Eclipse’ and yellow Mayocoba/‘MY06326’) were planted for two years in four locations (Iowa, Colorado, Michigan, in the USA, and Masaka, Uganda). Yield and seed weight differed among locations and varieties. Yield in Colorado and Michigan was 42% and 56% higher than in Iowa and 76% and 81% greater than in Uganda, respectively. Eclipse had greater yield than Taurus (6%), MY06326 (16%), and Montcalm (35%). Concentration of P, K, Mg, S, and crude protein (CP) differed among varieties. Montcalm had 18%, 7%, and 4% greater P concentration and 13%, 9%, and 5% greater CP than Eclipse, MY06326 and Taurus, respectively. The location × variety interaction was significant only for seed Zn concentration. Despite differences in edaphic factors among locations, elemental concentrations other than Zn were comparatively stable among locations. Stability in seed elemental concentrations across locations and environments is important knowledge for better understanding human nutrition and malnutrition.

Snap beans are a significant source of micronutrients in the human diet. Among the micronutrients present in snap beans are phenolic compounds with known beneficial effects on human health, potentially via their metabolism by the gut-associated microbiome. The genetic pathways leading to the production of phenolics in snap bean pods remain uncertain. In this study, we quantified the level of total phenolic content (TPC) in the Bean Coordinated Agriculture Program (CAP) snap bean diversity panel of 149 accessions. The panel was characterized spectrophotometrically for phenolic content with a Folin-Ciocalteu colorimetric assay. Flower, seed and pod color were also quantified, as red, purple, yellow and brown colors are associated with anthocyanins and flavonols in common bean. Genotyping was performed through an Illumina Infinium Genechip BARCBEAN6K_3 single nucleotide polymorphism (SNP) array. Genome-Wide Association Studies (GWAS) analysis identified 11 quantitative trait nucleotides (QTN) associated with TPC. An SNP was identified for TPC on Pv07 located near the P gene, which is a major switch in the flavonoid biosynthetic pathway. Candidate genes were identified for seven of the 11 TPC QTN. Five regulatory genes were identified and represent novel sources of variation for exploitation in developing snap beans with higher phenolic levels for greater health benefits to the consumer.

Common bean ( L.) is the most consumed edible grain legume worldwide and contains a wide range of nutrients for human health including dietary fiber. Diets high in beans are associated with lower rates of chronic diseases such as obesity and type 2 diabetes, and the content of dietary fibers varies among different market classes of dry bean. In this study, we evaluated the dietary fiber content in a Middle American diversity panel (MDP) of common bean and evaluated the genetic architecture of the various dietary fiber components. The dietary fiber components included insoluble and soluble dietary fibers as well as the antinutritional raffinose family of oligosaccharides (RFOs; raffinose, stachyose, and verbascose). All variables measured differed among market classes and entries. Colored bean seeds had higher levels of insoluble dietary fibers with the black market class showing also the highest raffinose and stachyose content. Cultivars and lines released since 1997 had higher insoluble dietary fibers and RFO content in race Durango. Higher levels of RFOs were also observed in cultivars with type II growth habit that was a recent breeding target in Durango race germplasm. Candidate genes for dietary fiber traits, especially homologs to two main genes in the RFO biosynthesis pathway, were identified. The knowledge of diversity of dietary fibers in the MDP accompanied with the identification of candidate genes could effectively improve dietary fiber components in common bean.

Plant physiology and metabolism are important components of a plant response to microbial pathogens. Physiological resistance of common bean (Phaseolus vulgaris L.) to the fungal pathogen Sclerotinia sclerotiorum has been established, but the mechanisms of resistance are largely unknown. Here, the physiological and metabolic responses of bean varieties that differ in physiological resistance to S. sclerotiorum are investigated. Upon infection, the resistant bean variety A195 had a unique physiological response that included reduced photosynthesis and maintaining a higher leaf surface pH during infection. Leaf metabolomics was performed on healthy tissue adjacent to the necrotic lesion at 16, 24, and 48 hr post inoculation, and 144 metabolites were detected that varied between A195 and Sacramento following infection. The metabolites that varied in leaves included amines/amino acids, organic acids, phytoalexins, and ureides. The metabolic pathways associated with resistance included amine metabolism, uriede-based nitrogen remobilization, antioxidant production, and bean-specific phytoalexin production. A second experiment was conducted in stems of 13 bean genotypes with varying resistance. Stem resistance was associated with phytoalexin production, but unlike leaf metabolism, lipid changes were associated with susceptibility. Taken together, the data supports a multifaceted, physiometabolic response of common bean to S. sclerotiorum that mediates resistance.

Tepary bean is a highly abiotic stress tolerant orphan crop for which there has been limited research on its nutritional value and cooking characteristics. These are key aspects when considering the potential for broader adoption of tepary bean. Therefore, the goal of this study was to evaluate a large set of seed composition and cooking traits related to human nutrition using both landraces and breeding lines of domesticated tepary bean from replicated field trials and to compare the traits in tepary with those in common bean. Tepary bean showed reduced fat and ash concentration and higher sucrose concentration as compared to common bean. Of the twelve amino acids evaluated, only proline in one of the two trials was statistically different between the two species. There were statistically significant differences between tepary and common bean for the concentration of some elements in this study; however, the elemental concentrations fell within the range of those found for common bean in previous studies. The majority of tepary bean lines showed consistently short cooking times and a high percentage of seeds showed measurable water uptake, while some showed a hardshell trait (low water uptake) and longer cooking times. Principal component analysis on a subset of traits showed a distinct group of common beans and two tepary bean groups that were divided on the basis of several agronomic, cooking, and elemental composition traits. Tepary bean, as with other pulses, is a highly nutritious crop with the range of composition and cooking characteristics similar to those of common bean. The variability for seed composition and cooking traits found within tepary bean can be exploited for its improvement.

Dry beans are typically consumed as a whole food, and cooking time is one of the most important processing quality attributes. A panel of eight dry bean entries with variability in cooking time was established, grown in three locations, and used to test the hypothesis that carbohydrate components are major underlying contributors to genetic variability in cooking time. The cooking times ranged from 17 to 160 min. In general, faster cooking bean genotypes had higher levels of soluble dietary fiber in both the raw and cooked samples. Resistant starch levels in the raw beans, although not correlated with cooking time, were of interest because of the large genotypic variability, and they ranged from 1.5 to 35%. One genotype in particular, a yellow bean from Africa, Cebo Cela, had low resistant starch levels in the raw seeds of 1.5–2.5%, whereas average resistant starch levels in the entire panel were 26–30%. Resistant starch levels (3.9–4.2%) in the cooked seed of Cebo Cela were comparable to the other genotypes (3.4–4.3%). Based on light microscopy, the cell walls did not remain intact in the raw milled seed used for the analyses, but they did remain intact in the cooked samples, suggesting the differences in resistant starch in the raw seed are related to starch structure.

Matrix-assisted desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) is a fast and effective tool for microbial species identification. However, current approaches are limited to species-level identification even when genetic differences are known. Here, we present a novel workflow that applies the statistical method of partial least squares discriminant analysis (PLS-DA) to MALDI-TOF-MS protein fingerprint data of Xanthomonas axonopodis, an important bacterial plant pathogen of fruit and vegetable crops. Mass spectra of 32 X. axonopodis strains were used to create a mass spectral library and PLS-DA was employed to model the closely related strains. A robust workflow was designed to optimize the PLS-DA model by assessing the model performance over a range of signal-to-noise ratios (s/n) and mass filter (MF) thresholds. The optimized parameters were observed to be s/n = 3 and MF = 0.7. The model correctly classified 83% of spectra withheld from the model as a test set. A new decision rule was developed, termed the rolled-up Maximum Decision Rule (ruMDR), and this method improved identification rates to 92%. These results demonstrate that MALDI-TOF-MS protein fingerprints of bacterial isolates can be utilized to enable identification at the strain level. Furthermore, the open-source framework of this workflow allows for broad implementation across various instrument platforms as well as integration with alternative modeling and classification algorithms.

Pinto bean (Phaseolus vulgaris L.) cultivars ‘Blackfoot’ (Reg. No. CV‐316, PI 680632), ‘Nez Perce’ (Reg. No. CV‐317, PI 680633), and ‘Twin Falls’ (Reg. No. CV‐318, PI 680634) were developed at the University of Idaho, Kimberly Research and Extension Center in collaboration with researchers in Colorado, Nebraska, and Washington. Blackfoot and Nez Perce are sister cultivars derived from the same bulk population, UIP35 (USPT‐CBB‐1/3/‘Othello’/‘UI 906’//‘Topaz’/‘Buster’). Twin Falls was selected from the bulk population UIP40 (USPT‐CBB‐1/3/CO12650/USPT‐ANT‐1//Othello/ABL15). The F8 of both population bulks and checks were yield tested in the Western Regional Bean Trial in 2014 and 2015 and in the Cooperative Dry Bean Nursery in 2015. The three cultivars were yield tested in Idaho in 2015. They were also yield tested across nine production environments in Colorado, Idaho, Nebraska, and Washington in 2016. Blackfoot, Nez Perce, and Twin Falls are the first indeterminate erect Type II growth habit pinto bean cultivars resistant to Bean common mosaic virus (an aphid‐vectored potyvirus) and bean rust developed at University of Idaho. Blackfoot has a compact Type IIA growth habit and produces little or no vine (i.e., elongated terminal axis with intertwined internodes that help the plant climb when provided support). In contrast, Nez Perce is tall and produces medium to long vines, with a Type IIB growth habit. Blackfoot has a mean maturity of 85 d and Nez Perce 95 d in southern Idaho. Twin Falls is a full‐season cultivar (≥100 d) and relatively tall, with very small or no vines for climbing. The three cultivars have relatively smaller seed (<35 g 100−1 seeds) than early‐maturity pinto ‘Othello’ (≥35 g 100−1 seeds) in the Pacific Northwest.

In developed countries which are at the epicenter of the obesity pandemic, pulse crop consumption is well below recommended levels. In a recent systematic review and meta-analysis of 21 randomized controlled clinical trials, pulse consumption was associated with improved weight control and reduced adiposity, although the underlying mechanisms were a matter of speculation. Common bean (Phaseolus vulgaris L.) is the most widely consumed pulse crop and was the focus of this investigation. Using outbred genetic models of dietary induced obesity resistance and of dietary induced obesity sensitivity in the rat, the impact of bean consumption was investigated on the efficiency with which consumed food was converted to body mass (food efficiency ratio), body fat accumulation, adipocyte morphometrics, and patterns of protein expression associated with lipid metabolism. Cooked whole bean as well as a commercially prepared cooked bean powders were evaluated. While bean consumption did not affect food efficiency ratio, bean reduced visceral adiposity and adipocyte size in both obesity sensitive and resistant rats. In liver, bean consumption increased carnitine palmitoyl transferase 1, which is the rate limiting step in long chain fatty acid oxidation and also resulted in lower levels of circulating triglycerides. Collectively, our results are consistent with the clinical finding that pulse consumption is anti-obesogenic and indicate that one mechanism by which cooked bean exerts its bioactivity is oxidation of long chain fatty acids.

Dry bean ( Phaseolus vulgaris L.) seeds are a major protein, carbohydrate, and mineral source in the human diet of peoples in multiple regions of the world. Seed mineral biofortification is an ongoing objective to improve this important food source. The objective of this research was to assess the seed mineral concentration of five macroelements and eight microelements in a large panel ( n = 277) of modern race Durango and race Mesoamerica genotypes to determine if variability existed that could be exploited for targeted seed biofortification. Varieties that derive from these races are found in many diets throughout the world. The panel was grown in replicated trials under typical production conditions in the major bean growing regions of the United States, and a subset of the panel was also grown in replicated trials at three locations under control and terminal drought conditions. Except for K, seed mineral concentrations were higher for race Mesoamerica genotypes. Significantly higher seed concentrations for the majority of the minerals were observed for white‐seeded genotypes and race Durango genotypes with the now preferred indeterminate, upright growth habit. Modern genotypes (since 1997) had equal or increased mineral concentrations compared with older genotypes. Drought affected mineral content differentially, having no effect on the microelement content but increased Co, Fe, and Ni concentrations. The correlation of Ca and Mn concentrations suggests that these elements may share seed deposition mechanisms. The high heritability for seed mineral concentration implies that breeding progress can be achieved by parental selection from this panel.

Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter- and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango-Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome-wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ∼30 candidate genes based on a priori and candidate gene search strategies centered on the 100-kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.

Dry beans (Phaseolus vulgaris L.) are a nutrient-dense food rich in protein and micronutrients. Despite their nutritional benefits, long cooking times limit the consumption of dry beans worldwide, especially in nations where fuelwood for cooking is often expensive or scarce. This study evaluated the nutritive value of 12 dry edible bean lines that vary for cooking time (20-89 min) from four market classes (yellow, cranberry, light red kidney, and red mottled) of economic importance in bean-consuming regions of Africa and the Americas. When compared to their slower cooking counterparts within each market class, fast-cooking dry beans retain more protein and minerals while maintaining similar starch and fiber densities when fully cooked. For example, some of the highest protein and mineral retention values were measured in the fast-cooking yellow bean cultivar Cebo Cela, which offered 20% more protein, 10% more iron, and 10% more zinc with each serving when compared with Canario, a slow-cooking yellow bean that requires twice the cooking time to become palatable. A Caco-2 cell culture model also revealed the bioavailability of iron is significantly higher in faster cooking entries (r = -0.537, P = 0.009) as compared to slower cooking entries in the same market class. These findings suggest that fast-cooking bean varieties have improved nutritive value through greater nutrient retention and improved iron bioavailability.

Chickpeas, common beans, dry peas, and lentils are pulse crops that have been a cornerstone of the human diet since the inception of agriculture. However, the displacement of pulses from the diet by low fiber protein alternatives has resulted in a pervasive deficiency referred to as the dietary fiber gap. Using an analytical method American Association of Analytical Chemists (AOAC) 2011.25 that conforms to the Codex Alimentarius Commission consensus definition for dietary fiber, the fiber content of these pulse crops was evaluated in seed types used for commercial production. These pulse crops have 2 to 3 times more fiber per 100 g edible portion than other dietary staples. Moreover, there is marked variation in fiber content among cultivars of the same crop. We conclude that pulse crop consumption should be emphasized in efforts to close the dietary fiber gap. The substantial differences in fiber content among currently available cultivars within a crop can be used to further improve gains in fiber intake without the need to change dietary habits. This provides a rationale for cultivar-based food labeling.