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Background In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are crucial in plant development and immunity. These plasma membrane receptors belong to large gene/protein families that are not easily classified computationally. This detailed analysis of these plasma membrane proteins brings a new source of information to the legume genetic, physiology and breeding research communities. Results A computational approach to identify and classify RLK and RLP proteins is presented. The strategy was evaluated using experimentally-validated RLK and RLP proteins and was determined to have a sensitivity of over 0.85, a specificity of 1.00, and a Matthews correlation coefficient of 0.91. The computational approach can be used to develop a detailed catalog of plasma membrane receptors (by type and domains) in several legume/crop species. The exclusive domains identified in legumes for RLKs are WaaY, APH Pkinase_C, LRR_2, and EGF, and for RLP are L-lectin LPRY and PAN_4. The RLK-nonRD and RLCK subclasses are also discovered by the methodology. In both classes, less than 20% of the total RLK predicted for each species belong to this class. Among the 10-species evaluated ~ 40% of the proteins in the kinome are RLKs. The exclusive legume domain combinations identified are B-Lectin/PR5K domains in G. max , M. truncatula , V. angularis , and V. unguiculata and a three-domain combination B-lectin/S-locus/WAK in C. cajan , M. truncatula , P. vulgaris , V. angularis . and V. unguiculata . Conclusions The analysis suggests that about 2% of the proteins of each genome belong to the RLK family and less than 1% belong to RLP family. Domain diversity combinations are greater for RLKs compared with the RLP proteins and LRR domains, and the dual domain combination LRR/Malectin were the most frequent domain for both groups of plasma membrane receptors among legume and non-legume species. Legumes exclusively show Pkinase extracellular domains, and atypical domain combinations in RLK and RLP compared with the non-legumes evaluated. The computational logic approach is statistically well supported and can be used with the proteomes of other plant species.

The importance of legumes in sustainable cropping systems has been studied extensively. Among legumes, common beans (Phaseolus vulgaris L.) are a rich world resource of biodiversity with two centers of domestication (Andes and Central America) and over 10 major market classes cultivated globally. Common beans are recognized as a nutrient‐dense, healthy food source due to their high protein, dietary fiber, and minerals content and also being a rich source of resistant and slowly digestible starch, which elicits a lower glycemic response. Some bioactive compounds present in beans are reported to mitigate cardiovascular diseases, hypertension, hyper‐cholesterolemia, and cancer. Dry bean production systems provide unique advantages that support sustainability, including a low carbon footprint and short growth cycle, which facilitates crop diversification and cover crop integration. Symbiotic nitrogen fixation (SNF), a unique characteristic of legumes, promotes environmentally friendly production through modest fertilizer use. Advances to improve the upright plant architecture of beans during the last two decades have enhanced options for direct harvest thereby reducing the number of equipment passes required. Overall, the sustainability implications of diversifying crop rotation using beans result in reduced requirements for environmentally unfriendly inputs and buffering of crop productivity under variable weather conditions. This review article covers common beans' role in agricultural sustainability (biodiversity, SNF, rotational diversity, harvest management) and as a sustainable source of nutrition and food security. Further discussion includes measures to enhance dry beans sustainability through breeding and crop management practices by addressing biotic and abiotic stresses (diseases, drought, high temperature, waterlogging, conservation tillage).

Background Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses directly involve plasma membrane receptor proteins known as receptor-like kinases and receptor-like proteins. Evaluating the homology relations among RLK and RLP for seven legume species, and exploring their presence among synteny blocks allow an increased understanding of evolutionary relations, physical position, and chromosomal distribution in related species and their shared roles in stress responses. Results Typically, a high proportion of RLK and RLP legume proteins belong to orthologous clusters, which is confirmed in this study, where between 66 to 90% of the RLKs and RLPs per legume species were classified in orthologous clusters. One-third of the evaluated syntenic blocks had shared RLK/RLP genes among both legumes and non-legumes. Among the legumes, between 75 and 98% of the RLK/RLP were present in syntenic blocks. The distribution of chromosomal segments between Phaseolus vulgaris and Vigna unguiculata , two species that diverged ~ 8 mya, were highly similar. Among the RLK/RLP synteny clusters, seven experimentally validated resistance RLK/RLP genes were identified in syntenic blocks. The RLK resistant genes FLS2, BIR2, ERECTA, IOS1, and AtSERK1 from Arabidopsis and SLSERK1 from Solanum lycopersicum were present in different pairwise syntenic blocks among the legume species. Meanwhile, only the LYM1- RLP resistant gene from Arabidopsis shared a syntenic blocks with Glycine max . Conclusions The orthology analysis of the RLK and RLP suggests a dynamic evolution in the legume family, with between 66 to 85% of RLK and 83 to 88% of RLP belonging to orthologous clusters among the species evaluated. In fact, for the 10-species comparison, a lower number of singleton proteins were reported among RLP compared to RLK, suggesting that RLP positions are more physically conserved compared to RLK. The identification of RLK and RLP genes among the synteny blocks in legumes revealed multiple highly conserved syntenic blocks on multiple chromosomes. Additionally, the analysis suggests that P. vulgaris is an appropriate anchor species for comparative genomics among legumes.

Common bean (Phaseolus vulgaris L.) is an important high protein crop grown worldwide. North Dakota and Minnesota are the largest producers of common beans in the USA, but crop production is threatened by soybean cyst nematode (SCN; Heterodera glycines Ichinohe) because most current cultivars are susceptible. Greenhouse screening data using SCN HG type 0 from 317 plant introductions (PI's) from the USDA core collection was used to conduct a genome wide association study (GWAS). These lines were divided into two subpopulations based on principal component analysis (Middle American vs. Andean). Phenotypic results based on the female index showed that accessions could be classified as highly resistant (21% and 27%), moderately resistant (51% and 48%), moderately susceptible (27% and 22%) and highly susceptible (1% and 3%) for Middle American and Andean gene pools, respectively. Mixed models with two principal components (PCs) and kinship matrix for Middle American genotypes and Andean genotypes were used in the GWAS analysis using 3,985 and 4,811 single nucleotide polymorphic (SNP) markers, respectively which were evenly distributed across all 11 chromosomes. Significant peaks on Pv07, and Pv11 in Middle American and on Pv07, Pv08, Pv09 and Pv11 in Andean group were found to be associated with SCN resistance. Homologs of soybean rhg1, a locus which confers resistance to SCN in soybean, were identified on chromosomes Pv01 and Pv08 in the Middle American and Andean gene pools, respectively. These genomic regions may be the key to develop SCN-resistant common bean cultivars.

Background Physical seed dormancy is an important trait in legume domestication. Although seed dormancy is beneficial in wild ecosystems, it is generally considered to be an undesirable trait in crops due to reduction in yield and / or quality. The physiological mechanism and underlying genetic factor(s) of seed dormancy is largely unknown in several legume species. Here we employed an integrative approach to understand the mechanisms controlling physical seed dormancy in common bean ( Phaseolus vulgaris L.). Results Using an innovative CT scan imaging system, we were able to track water movements inside the seed coat. We found that water uptake initiates from the bean seed lens. Using a scanning electron microscopy (SEM) we further identified several micro-cracks on the lens surface of non-dormant bean genotypes. Bulked segregant analysis (BSA) was conducted on a bi-parental RIL (recombinant inbred line) population, segregating for seed dormancy. This analysis revealed that the seed water uptake is associated with a single major QTL on Pv03. The QTL region was fine-mapped to a 118 Kb interval possessing 11 genes. Coding sequence analysis of candidate genes revealed a 5-bp insertion in an ortholog of pectin acetylesterase 8 that causes a frame shift, loss-of-function mutation in non-dormant genotype. Gene expression analysis of the candidate genes in the seed coat of contrasting genotypes indicated 21-fold lower expression of pectin acetylesterase 8 in non-dormant genotype. An analysis of mutational polymorphism was conducted among wild and domesticated beans. Although all the wild beans possessed the functional allele of pectin acetylesterase 8 , the majority (77%) of domesticated beans had the non-functional allele suggesting that this variant was under strong selection pressure through domestication. Conclusions In this study, we identified the physiological mechanism of physical seed dormancy and have identified a candidate allele causing variation in this trait. Our findings suggest that a 5-bp insertion in an ortholog of pectin acetylesterase 8 is likely a major causative mutation underlying the loss of seed dormancy during domestication. Although the results of current study provide strong evidences for the role of pectin acetylesterase 8 in seed dormancy, further confirmations seem necessary by employing transgenic approaches.

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) reproduces on the roots of common bean (Phaseolus vulgaris L.) and can cause reductions in plant growth and seed yield. The molecular changes in common bean roots caused by SCN infection are unknown. Identification of genetic factors associated with SCN resistance could help in development of improved bean varieties with high SCN resistance. Gene expression profiling was conducted on common bean roots infected by SCN HG type 0 using next generation RNA sequencing technology. Two pinto bean genotypes, PI533561 and GTS-900, resistant and susceptible to SCN infection, respectively, were used as RNA sources eight days post inoculation. Total reads generated ranged between ~ 3.2 and 5.7 million per library and were mapped to the common bean reference genome. Approximately 70-90% of filtered RNA-seq reads uniquely mapped to the reference genome. In the inoculated roots of resistant genotype PI533561, a total of 353 genes were differentially expressed with 154 up-regulated genes and 199 down-regulated genes when compared to the transcriptome of non- inoculated roots. On the other hand, 990 genes were differentially expressed in SCN-inoculated roots of susceptible genotype GTS-900 with 406 up-regulated and 584 down-regulated genes when compared to non-inoculated roots. Genes encoding nucleotide-binding site leucine-rich repeat resistance (NLR) proteins, WRKY transcription factors, pathogenesis-related (PR) proteins and heat shock proteins involved in diverse biological processes were differentially expressed in both resistant and susceptible genotypes. Overall, suppression of the photosystem was observed in both the responses. Furthermore, RNA-seq results were validated through quantitative real time PCR. This is the first report describing genes/transcripts involved in SCN-common bean interaction and the results will have important implications for further characterization of SCN resistance genes in common bean.

Common bean (Phaseolus vulgaris 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.

This study investigated the thermophysical and cooking quality properties of both slow-darkening (SD) and regular-darkening (RD) pinto bean varieties, establishing genetic cooking variability in cooking traits and their interrelationships. The equilibrium moisture content (EMC) of the beans at 80, 90 and 100°C were determined. Thermal and physical properties were evaluated for both SD and RD pinto bean varieties at their respective EMC. Cooking quality properties, such as water absorption capacity and cooking time, were also assessed. Principal component and cluster analyses were used to establish interactive effects of the cooking-related traits to the cooking process. Bulk density and cooking time were significantly and negatively correlated (p < .05). The SD beans exhibited better cook characteristics compared to RD beans. Bulk density was the most influential trait during cluster formation. The findings highlight that physical and thermal properties play a critical role in the cooking process.

Kühn (teleomorph ) is an important root rot pathogen of common bean ( L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; = 273) and Middle American (MDP; = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP ( = 28) and ∼6% of the MDP ( = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.

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.