Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection.

The common bean (Phaseolus vulgaris L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for Fop race 1 and race 4 were matched with genotypic data from 4740 SNPs of BARCBean6K_3 Infinium Bea Chips. After ranking the 157-accession panel and revealing 21 Fusarium wilt-resistant accessions, the GWAS pinpointed 16 SNPs on chromosomes Pv04, Pv05, Pv07, Pv8, and Pv09 linked to Fop race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with Fop race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both Fop race 1 and race 4 resistances. Furthermore, within a 30 kb flanking region of these associated SNPs, a total of 17 candidate genes were identified. Some of these genes were annotated as classical disease resistance protein/enzymes, including NB-ARC domain proteins, Leucine-rich repeat protein kinase family proteins, zinc finger family proteins, P-loopcontaining nucleoside triphosphate hydrolase superfamily, etc. Genomic prediction (GP) accuracy for Fop race resistances ranged from 0.26 to 0.55. This study advanced common bean genetic enhancement through marker-assisted selection (MAS) and genomic selection (GS) strategies, paving the way for improved Fop resistance.

Common bean varieties demonstrate differential physiological and metabolic responses to the pathogenic fungus Sclerotinia sclerotiorum.

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.

Cross Pathogenicity and Vegetative Compatibility of Fusarium oxysporum Isolated from Sugar Beet.

Fusarium oxysporum f. sp. betae causes Fusarium yellows in sugar beet (Beta vulgaris). The F. oxysporum population from sugar beet can be highly variable in virulence and morphology and many isolates are nonpathogenic. Rapid and reliable methods to identify pathogenic isolates from nonpathogenic F. oxysporum generally are unavailable. Little is known about nonpathogenic isolates, including the role they may play in population diversity or virulence to sugar beet. Sugar beet is often grown in rotation with other crops, including dry edible bean (Phaseolus vulgaris) and onion (Allium cepa), with F. oxysporum able to cause disease on all three crops. Thirty-eight F. oxysporum isolates were collected from symptomatic sugar beet throughout the United States to investigate diversity of the F. oxysporum population and the influence of crop rotation on pathogenic variation. These isolates were characterized for pathogenicity to sugar beet, dry edible bean, and onion, as well as vegetative compatibility. Pathogenicity testing indicated that some F. oxysporum isolates from sugar beet may cause disease on onion and dry edible bean. Furthermore, vegetative compatibility testing supported previous reports that F. oxysporum f. sp. betae is polyphyletic and that pathogenic isolates cannot be differentiated from nonpathogenic F. oxysporum using vegetative compatibility.

Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance.

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.

Cell signaling pathways associated with a reduction in mammary cancer burden by dietary common bean (Phaseolus vulgaris L.).

Emerging evidence indicates that common bean (Phaseolus vulgaris L.) is associated with reduced cancer risk in human populations and rodent carcinogenesis models. This study sought to identify cancer-associated molecular targets that mediate the effects of bean on cancer burden in a chemically induced rat model for breast cancer. Initial experiments were conducted using a high dietary concentration of bean (60% wt/wt) where carcinoma burden in bean-fed rats was reduced 62.2% (P < 0.001) and histological and western blot analyses revealed that the dominant cellular process associated with reduced burden was induction of apoptosis. Further analysis of mammary carcinomas revealed changes in the phosphorylation states of mammalian target of rapamycin (mTOR) substrates (4E-binding protein 1 and p70S6 kinase) and mTOR regulators adenosine monophosphate-activated protein kinase and protein kinase B (Akt) (P < 0.001). Effects on mTOR signaling in carcinomas were also found at lower dietary concentrations of bean (7.5-30% wt/wt). Liquid chromatography-time of flight-mass spectrometry analysis of plasma provided evidence of altered lipid metabolism consistent with reduced mTOR network activity in the liver (P < 0.001). Plasma concentrations of insulin and insulin-like growth factor-1 were reduced by 36.3 and 38.9%, respectively, (P < 0.001), identifying a link to Akt regulation. Plasma C-reactive protein, a prognostic marker for long-term survival in breast cancer patients, was reduced by 23% (P < 0.001) in bean-fed rats. Identification of a role for the mTOR signaling network in the reduction of cancer burden by dietary bean is highly relevant given that this pathway is deregulated in the majority of human breast cancers.

Dietary dry bean effects on hepatic expression of stress and toxicity-related genes in rats.

Dry bean (Phaseolus vulgaris L.) consumption is associated with reduced risk for a number of chronic diseases. In westernised societies, dry bean consumption is particularly low (approximately 2-4 kg/capita per year) and little information is available about the safety of increasing dietary intake in humans to achieve levels that prevent and control chronic diseases. In anticipation of a human intervention study to address the safety and efficacy of increasing bean consumption, a dose-response study with dietary beans was conducted to establish whether increased bean consumption in rats exhibits changes indicative of hepatic stress or toxicity. Transcript levels from a panel of stress and toxicity-related genes were analysed in female Sprague-Dawley rats fed a dose range of dietary beans that bracketed amounts relevant to human consumption globally. Cooked red bean was incorporated into a purified diet formulation at 0, 7·5, 15, 30 or 60 % w/w for the assessment of adaptive patterns of gene expression using quantitative PCR array. Of the eighty-four genes evaluated, the expressions of Cyp3a11, Cyp7a1, Fmo1, Gstm1, Mif and Ugt1a6 were elevated, whereas the expression of Hspa8 was down-regulated. Liver gene expression was not modulated in a manner indicative of an adverse response. Only the expression of the cholesterol 7α hydoxylase and UDP-glucuronosyltransferase genes increased in a dose-dependent manner at nutritionally relevant dietary bean concentrations. These candidate genes may contribute to the health benefits attributed to increased bean consumption.

Dry Bean: A Protein-Rich Superfood With Carbohydrate Characteristics That Can Close the Dietary Fiber Gap.

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.

Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean (Phaseolus vulgaris) Core Collection.

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.

Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using 'omics' technologies.

BACKGROUND: Genetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fragment length polymorphisms, DNA sequence analysis, chloroplast DNA, and microsatellite markers. Yet, little is known about whether these traits, which distinguish among genetically distinct types of common bean, can be evaluated using omics technologies. RESULTS: Three 'omics' approaches: transcriptomics, proteomics, and metabolomics were used to qualitatively evaluate the diversity of common bean from two Centers of Domestication (COD). All three approaches were able to classify common bean according to their COD using unsupervised analyses; these findings are consistent with the hypothesis that differences exist in gene transcription, protein expression, and synthesis and metabolism of small molecules among common bean cultivars representative of different COD. Metabolomic analyses of multiple cultivars within two common bean gene pools revealed cultivar differences in small molecules that were of sufficient magnitude to allow identification of unique cultivar fingerprints. CONCLUSIONS: Given the high-throughput and low cost of each of these 'omics' platforms, significant opportunities exist for their use in the rapid identification of traits of agronomic and nutritional importance as well as to characterize genetic diversity.

Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content.

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.

Mechanisms associated with dose-dependent inhibition of rat mammary carcinogenesis by dry bean (Phaseolus vulgaris, L.).

The purpose of this study was to determine whether a dry bean (Phaseolus vulgaris, L.) containing diet exerts an inhibitory effect on mammary carcinogenesis in a well-characterized rodent model for breast cancer. Twenty-one-d-old female Sprague Dawley rats were given an intraperitoneal injection of 1-methyl-1-nitrosourea and 7 d after carcinogen injection were randomized to 1 of 5 groups fed a modification of the AIN-93G diet formulation containing 0, 7.5, 15, 30, or 60% (wt:wt) small red dry bean incorporated as cooked, freeze-dried, and milled powder. All experimental diets had the same macronutrient content based on proximate analysis. Compared with the control group, dry bean consumption resulted in dose-dependent reductions in mammary cancer incidence (P = 0.046), cancer multiplicity (P = 0.001), and tumor burden (P = 0.01). Dry bean consumption was associated with dose-dependent reductions in plasma concentrations of glucose, insulin, insulin-like growth factor-1, C-reactive protein, and interleukin-6 in food-deprived rats. Analysis of mammary adenocarcinomas indicated that a dominant mechanism accounting for reduced tumor burden was the induction of apoptosis. B cell lymphoma 2 and X-linked inhibitor of apoptosis protein levels decreased and BCL-2-associated X protein increased with increasing dry bean consumption, findings consistent with the induction of apoptosis via the mitochondrial pathway. These data demonstrate that a legume without noteworthy content of isoflavones inhibits the development of mammary carcinogenesis and are consistent with a recent report from the Nurses Health Study that bean or lentil intake is associated with a lower risk for breast cancer.

MALDI-TOF-MS with PLS Modeling Enables Strain Typing of the Bacterial Plant Pathogen Xanthomonas axonopodis.

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. Graphical abstract ᅟ.

Genetic Architecture of Dietary Fiber and Oligosaccharide Content in a Middle American Panel of Edible Dry Bean.

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.

Beneficial Effects of Common Bean on Adiposity and Lipid Metabolism.

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.

Perspective: Closing the Dietary Fiber Gap: An Ancient Solution for a 21st Century Problem.

An important gap exists between the daily amounts of fiber recommended in the human diet (28-42 g/d) and that which is actually consumed (median intake, 12-14 g/d). In fact, <5% of Americans meet the recommended intake for dietary fiber, and the magnitude of the gap is large, approximately a 50-70% shortfall. Because considerable evidence indicates that dietary fiber affects normal physiologic function and the onset of chronic diseases and their progression, the fiber gap represents an opportune target at which dietary interventions can be directed. This perspective considers whether a scientific basis exists for the current lack of emphasis on pulse crops, that is, grain legumes (common bean, chickpea, lentils, and garden pea) as a concentrated, inexpensive, and widely available source of dietary fiber. Attention is directed to this topic because the fiber gap has existed for decades with little improvement despite nutrition labeling, consumer education about the value of whole-grain cereal crop-based products, and the introduction of many fiber-enriched foods. The time is long overdue to identify additional approaches that have the potential to close the dietary fiber gap. To this end, the potential role of pulse crops in remediating this gap is examined.

Dietary Fiber Analysis of Four Pulses Using AOAC 2011.25: Implications for Human Health.

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.

Demonstrating a Nutritional Advantage to the Fast-Cooking Dry Bean (Phaseolus vulgaris L.).

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.

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean.

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.

Proteome Characterization of Leaves in Common Bean.

Dry edible bean (Phaseolus vulgaris L.) is a globally relevant food crop. The bean genome was recently sequenced and annotated allowing for proteomics investigations aimed at characterization of leaf phenotypes important to agriculture. The objective of this study was to utilize a shotgun proteomics approach to characterize the leaf proteome and to identify protein abundance differences between two bean lines with known variation in their physiological resistance to biotic stresses. Overall, 640 proteins were confidently identified. Among these are proteins known to be involved in a variety of molecular functions including oxidoreductase activity, binding peroxidase activity, and hydrolase activity. Twenty nine proteins were found to significantly vary in abundance (p-value < 0.05) between the two bean lines, including proteins associated with biotic stress. To our knowledge, this work represents the first large scale shotgun proteomic analysis of beans and our results lay the groundwork for future studies designed to investigate the molecular mechanisms involved in pathogen resistance.

A reference genome for common bean and genome-wide analysis of dual domestications.

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.