Common Bean Genotypes Research Articles

Genome‐wide association study of grain iron and zinc concentration in common bean (Phaseolus vulgaris)

AbstractCommon bean is one of the widely consumed food security crop in Africa, Asia and South America. It is a rich source of protein, minerals and micronutrients. High genotype by environment interaction is one of the main challenge in breeding for high grain micronutrient concentration. The objective of this study was to estimate SNP markers associated with grain Fe and Zn concentration using 289 common bean genotypes and 11,480 SNP markers. The study revealed that 43 quantitative trait loci (QTLs) were associated with grain Fe and Zn concentration. Five quantitative trait nucleotides (QTNs), that is, QTN Fe_1.1, QTN Fe_6.3, QTN Fe_6.5, QTN Fe_10.3 and QTN Fe_11.6 were detected both at Haramaya and Melkassa locations. Two of the markers, that is, QTN Fe_6.3 and QTN Fe_6.5, were located on chromosome 06 while QTN Fe_1.1, QTN Fe_10.3 and QTN Fe_ 11.6 were residing on chromosomes 01, 10 and 11, respectively. Among these, QTN Fe_11.6 had a large and positive consistent effect across locations. The five stable QTNs along with the potential candidate genes could be used for Fe biofortification through marker assisted selection.

Physiological and morphological responses of two beans common genotype to water stress at different phenological stages

Comprehension of the bean responses of beans common under to water deficit is an important tool in agricultural planning, like sowing time, and deficit irrigation management strategies. The study aimed to understand the morpho-physiological responses and yield attributes of two common bean genotypes submitted to water stress at different phenological stages. The study was carried out in a greenhouse, in randomized block scheme with five repetitions. To achieve the objectives deficit irrigation of 25% of crop evapotranspiration was practiced during vegetative (DI-V), flowering (DI-F), and pod filling (DI-PF) stages. A non-deficit irrigated (NDI) and deficit irrigated through vegetative to pod filling stages (DI-VP) treatments were added for comparison. The following morphophysiological responses and yield attributes were evaluated: net assimilation of CO2, stomatal conductance, and leaf transpiration, chlorophyll index, number of trifoliate leaves, chlorophyll index, leaf area, number of grains per plant, number of grains per pod, number of pods per plant, the mass of thousand grains, harvest index, and water use efficiency. The beans genotype under DI-V exhibited acclimation, observed by the relative increment with NDI of 195%, 759%, and 231% of net assimilation of CO2, stomatal conductance, and leaf transpiration, respectively. Plants under treatment DI-PF experienced dis-stress and plastic responses as leaf losses and exhaustion of gas exchanges. Treatment DI-V received 11% less water than NDI and exhibited equal yield, resulting in higher water use efficiency. Yield attributes correlations indicated that yield penalty might be related to pods abortion, which not occurred to plants under DI-V.

Physiological Responses of Common Bean Genotypes to Drought Stress

Drought compromises edible vegetable production worldwide, including common bean (Phaseolus vulgaris L.) an economically important crop that is highly dependent on optimum rainfall or abundant irrigation. In the present study, phenotypic data of 26 Bulgarian common bean mutant lines and cultivars subjected to drought stress has been summarized, and drought stress reaction was evaluated by chlorophyll fluorescence and proteomics approaches. Several basic photosynthetic parameters were examined during treatment to evaluate the drought stress response, and the mutant lines showed different responses. Subsequently, a relationship was found between productivity and photosynthetic performance with the expression of ribulose-1,5-bisphosphate carboxylase through comparative 2D-gel based electrophoresis; accumulation of the well-known stress-related proteins markers dehydrins and small heat shock proteins was established as well. These findings support the further selection of drought tolerant common bean lines for a sustainable agriculture.

TSWIFT: Tower Spectrometer on Wheels for Investigating Frequent Timeseries for high-throughput phenotyping of vegetation physiology

BackgroundRemote sensing instruments enable high-throughput phenotyping of plant traits and stress resilience across scale. Spatial (handheld devices, towers, drones, airborne, and satellites) and temporal (continuous or intermittent) tradeoffs can enable or constrain plant science applications. Here, we describe the technical details of TSWIFT (Tower Spectrometer on Wheels for Investigating Frequent Timeseries), a mobile tower-based hyperspectral remote sensing system for continuous monitoring of spectral reflectance across visible-near infrared regions with the capacity to resolve solar-induced fluorescence (SIF).ResultsWe demonstrate potential applications for monitoring short-term (diurnal) and long-term (seasonal) variation of vegetation for high-throughput phenotyping applications. We deployed TSWIFT in a field experiment of 300 common bean genotypes in two treatments: control (irrigated) and drought (terminal drought). We evaluated the normalized difference vegetation index (NDVI), photochemical reflectance index (PRI), and SIF, as well as the coefficient of variation (CV) across the visible-near infrared spectral range (400 to 900 nm). NDVI tracked structural variation early in the growing season, following initial plant growth and development. PRI and SIF were more dynamic, exhibiting variation diurnally and seasonally, enabling quantification of genotypic variation in physiological response to drought conditions. Beyond vegetation indices, CV of hyperspectral reflectance showed the most variability across genotypes, treatment, and time in the visible and red-edge spectral regions.ConclusionsTSWIFT enables continuous and automated monitoring of hyperspectral reflectance for assessing variation in plant structure and function at high spatial and temporal resolutions for high-throughput phenotyping. Mobile, tower-based systems like this can provide short- and long-term datasets to assess genotypic and/or management responses to the environment, and ultimately enable the spectral prediction of resource-use efficiency, stress resilience, productivity and yield.

A Note on an Outbreak of Cowpea Mild Mottle Virus (CPMMV) in Common Bean in the River Nile State, Sudan

An outbreak of a devastating virus disease occurred in common bean(Phaseolus vulgaris) in Berber area, the River Nile State, during the 2004/2005 croppingseason, with symptoms of stunting and yellowing. The disease incidence reached a levelof more than 85% in all visited fields. One hundred fifty symptomatic samples, collectedfrom different fields at Hudeiba, Berber and Shendi, were blotted on nitrocellulosemembranes and tested for the presence of different viruses, using the tissue blotimmunoassay (TBIA) technique. The results of the serological tests revealed that 95% ofthe samples were positive for cowpea mild mottle virus (CPMMV). Among the commonbean genotypes screened for resistance to CPMMV, only RO/2/1 and Giza 3 wereresistant to the disease.

Evaluation of Agronomic Traits and Genetic Diversity of Common Bean Genotypes under Irrigated and Rainfed Conditions

This study was conducted to determine agronomic performance of ten commercial common bean varieties (Karaman 2016, Adabeyazı, Akın, Göksun, Bulduk, Akman 98, Zirve, Göynük 98, Özmen and Topçu), and two advanced lines (KF-Arp and KF-Arj) under rainfed and irrigated conditions for two years in a split plot randomized block design with four replications. Özmen, Zirve and Adabeyazı cultivars had the highest grain yields (irrigated conditions; 4152, 4018 and 3691 kg ha–1, rainfed conditions; 1456, 1318 and 1322 kg ha–1, respectively) in terms of grain yield according to the average data of the two years under irrigated and rainfed conditions. Eight Inter Simple Sequence Repeat (ISSR) markers were used to reveal the genetic diversity of the genotypes. The ISSR markers used in the study produced 140 polymorphic alleles, while the allele number per primer was found as 17.5 and the average PIC value was 0.96. A dendrogram was created for common bean genotypes that consisted of two main groups, as Akın was the only cultivar in the first group, and the remaining eleven cultivars were grouped together in the second main group with 11% genetic similarity.

A novel fuzzy approach to identify the phenotypic adaptability of common bean lines

The genotype by environment interaction is the main factor that influences the response of evaluated genotypes in trials of value for cultivation and use. Adaptability and stability analyses are fundamental to understanding the performance of genotypes in a growing region. Some of these methodologies incorporate previous information for recommending an extra group of genotypes denominated as specific ideotypes under certain cultivation conditions. Based on this strategy, the centroid method and its modifications have been widely used due to the simplicity of classification of the evaluated genotypes. However, these methodologies present problems in identifying adaptability patterns of some genotypes. Artificial intelligence techniques, such as fuzzy C-means, can be an alternative to reduce these difficulties, since they use, in addition to distance information between genotypes, memberships (measures quantifying how much an observation belongs to a particular class) to increase discriminatory power. Therefore, our aim was to propose and evaluate the phenotypic adaptability method by fuzzy clustering to assist cultivar recommendations. The adaptation of the fuzzy C-Means method to classify the genotypes was implemented in BioFuzzy software. The grain yield data of black common bean genotypes were used to evaluate the potential of the method. The results obtained by this method were compared with those obtained by the centroid method. The phenotypic adaptability method by fuzzy clustering was effective in identifying the adaptability patterns of common bean genotypes. Moreover, the discriminatory power was higher than that observed with the centroid method.

A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris.

Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.

Metabolome profile variations in common bean (Phaseolus vulgaris L.) resistant and susceptible genotypes incited by rust (Uromyces appendiculatus).

The causal agent of rust, Uromyces appendiculatus is a major constraint for common bean (Phaseolus vulgaris) production. This pathogen causes substantial yield losses in many common bean production areas worldwide. U. appendiculatus is widely distributed and although there have been numerous breakthroughs in breeding for resistance, its ability to mutate and evolve still poses a major threat to common bean production. An understanding of plant phytochemical properties can aid in accelerating breeding for rust resistance. In this study, metabolome profiles of two common bean genotypes Teebus-RR-1 (resistant) and Golden Gate Wax (susceptible) were investigated for their response to U. appendiculatus races (1 and 3) at 14- and 21-days post-infection (dpi) using liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (LC-qTOF-MS). Non-targeted data analysis revealed 71 known metabolites that were putatively annotated, and a total of 33 were statistically significant. Key metabolites including flavonoids, terpenoids, alkaloids and lipids were found to be incited by rust infections in both genotypes. Resistant genotype as compared to the susceptible genotype differentially enriched metabolites including aconifine, D-sucrose, galangin, rutarin and others as a defence mechanism against the rust pathogen. The results suggest that timely response to pathogen attack by signalling the production of specific metabolites can be used as a strategy to understand plant defence. This is the first study to illustrate the utilization of metabolomics to understand the interaction of common bean with rust.

Genetic clustering, and diversity of African panel of released common bean genotypes and breeding lines

Genetic clustering, and diversity of African panel of released common bean genotypes and breeding lines

Stability of common bean (Phaseolus vulgaris L.) genotypes for root system architecture and seed yield in multi-environments

Stability of common bean (Phaseolus vulgaris L.) genotypes for root system architecture and seed yield in multi-environments

Phenotypic Variability for Root Traits in Andean Common Beans Grown with and without Aluminum Stress Conditions

Genetic variation in wild relatives, GenBank accessions, landraces, and cultivars can unlock key alleles for the traits of interest for breeding programs. Breeding programs often utilize different strategies to quantify the source of heritable variation for target traits. One neglected area of study is the root traits of diverse genotypes, and this is especially the case for aluminum toxicity effects on legumes such as the common bean, which is the most used pulse for direct human consumption. This study evaluated 267 genotypes of common bean that were part of the global Andean Diversity Panel (ADP), consisting mainly of genotypes assembled from public and private breeding programs in Africa and North America, as well as elite lines and land races from the USDA. The ADP was evaluated for root traits at the seedling stage in the Tennessee State University (TSU) greenhouse using a hydroponic system with a standard nutrient solution with and without aluminum (Al). The recorded data on the roots per trial were fit to a linear mixed model for the analysis of variance in order to test for the genotype differences. Adjusted means considered replication and blocks within replication as random effects and genotypes as fixed effects. These were then used for Pearson correlation tests and for principal component analysis (PCA), where the first two vectors accounted for 94.5% and 93% of the explained variation under the control and Al-treatment conditions, respectively. Genotypes were clustered based on the morphology of roots in response to Al-toxicity treatment using the Euclidean distance and Ward’s hierarchical agglomerative clustering method, identifying four distinctive groups significant at p < 0.01. The intra-cluster distance was lower than the inter-cluster distances, which indicated a heterogeneous and homogeneous nature between and within clusters, respectively. The results suggest that crossing between accessions from two of the clusters would result in the maximum genetic segregation. One cluster was found to have a higher Al-toxicity tolerance than the others.

Microsatellite Analysis of Common Bean (Phaseolus vulgaris L.) Genotypes in Tanzania for Diversity in Seed Iron and Zinc Micronutrients

Microsatellite Analysis of Common Bean (Phaseolus vulgaris L.) Genotypes in Tanzania for Diversity in Seed Iron and Zinc Micronutrients

English

Characterization and conservation of germplasm is a critical step toward the genetic improvement of the crop. This study assessed variation in 257 common bean genotypes which included 207 accessions obtained the National Gene Bank of Kenya, 33 accessions from Kenya Agricultural and Livestock Research Organization (KALRO), 13 landraces collected from farmers’ fields and four commercial varieties for various agronomic traits. The experiments were laid out in a randomized complete block design with three replicates at Jomo Kenyatta University of Agriculture and Technology (Kenya) for four seasons between 2019 and 2020. Significant differences (P≤0.05) existed among the common bean accessions for all traits studied. Seed yield ranged from 220.6 to 4641.9 kg/ha (KNB0106) among the accessions with a mean of 1267.0 kg/ha. Significant (P ≤0.05) positive correlation was recorded for days to flowering and days to maturity (0.73), while 100-seed weight had a significantly negative correlation with the number of pods per plant (-0.66) and the number of seeds per pod (-0.65). High (>20%) broad-sense heritability was recorded for 100-seed weight (89.0%), days to flowering (76.8%), and grain yield (60.5%). Nineteen accessions that combined early maturity and high-yielding traits were identified. On average, higher seed yields were recorded for large-seeded and climbing genotypes compared to small-seeded and bush types. Common bean accessions characterized can be exploited in breeding programs. Key words: Common bean, agronomic traits, Phaseolus vulgaris, variability, broad sense heritability.

Genetic Variability and Association of Yield and Yield-Related Traits under Moisture Stress in Common Bean Genotypes (Phaseolus vulgaris L.) at Melkassa and Miesso, Ethiopia

Twenty-five common bean genotypes were evaluated to assess the genetic variability, trait association, and determine the direct and indirect effects of traits on seed yield. The genotypes were grown in a lattice design at the research farm of the Melkassa Agricultural Research Center, Melkassa and Miesso, in the 2018 cropping season. Analysis of variance revealed that significant differences were observed among the genotypes at individual locations. The phenotypic coefficient of variation values were moderate for number of nodes, seeds per pod, plant height, and hundred seed weight at Melkassa. Moderate genotypic coefficient of variation values were obtained for pods per plant and seeds per pod. At Miesso, moderate phenotypic coefficients of variation values were recorded for number of nodes, hundred seed weight, and plant height. High heritability estimates were obtained for seed yield and hundred seed weight at Melkassa and for seed yield at Miesso, indicating that selection could be fairly easy and improvement is possible using these traits in a common bean breeding program. High genetic advances were obtained for seed yield and pods per plant at Melkassa, while moderate genetic advances as a percent of the mean were attained for plant height, hundred seed weight, and seeds per pod. Similarly, at Miesso, high and moderate genetic advances as percent of mean values were obtained for seed yield and hundred seed weight, respectively. Seed yield showed positive and significant phenotypic association with days to flowering, internode length, and pods per plant at Melkassa and had positive and significant phenotypic association with seeds per pod and hundred seed weight at Miesso. Hence, selection of those genotypes based on the traits with high genotypic coefficient of variability, heritability, genetic advance, and positive correlation coefficient and direct effect on seed yield can be recommended for further yield improvement at the respective location and at the national level in general.

Genome‐wide association study of variation in cooking time among common bean (Phaseolus vulgaris L.) accessions using Diversity Arrays Technology markers

AbstractStored grains of common bean (Phaseolus vulgaris L.) develop the hard‐to‐cook trait (HTC), which is manifested in a prolonged cooking time, thereby imposing time and energy constraints. The objective of this study was to determine variation in cooking time among common bean genotypes and to identify single nucleotide polymorphism (SNP) markers associated with cooking time.Seeds of 222 common bean accessions sourced from Kenyan institutions were multiplied in the Jomo Kenyatta University of Agriculture and Technology (JKUAT) field in 2019. The freshly harvested seeds and those stored at 35°C and 50% red haricot (RH) for 4 months for accelerated aging were soaked in distilled water for 16 h and evaluated for cooking time using the finger‐pressing method. The accessions were also genotyped to determine variation in SNP markers using Diversity Arrays Technology Sequencing (DArTseq). Genome‐wide association study (GWAS) analysis was conducted to identify SNPs significantly associated with cooking time.The study revealed significant differences (p ≤ 0.05) within and between fresh and aged bean accessions. Fresh seeds had a lower cooking time with a mean of 40.8 min and ranged from 28.1 to 72.2 min, whereas aged seeds had a higher average cooking time of 54.1 min and ranged from 32.1 to 96.3 min. GWAS identified a region in Chromosome 10 to be significantly (p ≤ 0.05) associated with the cooking time of aged seeds. Consequently, two potential candidate genes Phvul.010G038000 and Phvul.010G038100 were revealed. The characterized common bean accessions and the identified SNP markers can be utilized in breeding programs to improve the cooking quality of the common bean.

Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean (Phaseolus vulgaris L.) in Response to Terminal Drought Stress

We conducted a genome-wide transcriptomic analysis of three drought tolerant and sensitive genotypes of common bean to examine their transcriptional responses to terminal drought stress. We then conducted pairwise comparisons between the root and leaf transcriptomes from the resulting tissue based on combined transcriptomic data from the tolerant and sensitive genotypes. Our transcriptomic data revealed that 491 (6.4%) DEGs (differentially expressed genes) were upregulated in tolerant genotypes, whereas they were downregulated in sensitive genotypes; likewise, 396 (5.1%) DEGs upregulated in sensitive genotypes were downregulated in tolerant genotypes. Several transcription factors, heat shock proteins, and chaperones were identified in the study. Several DEGs in drought DB (data Base) overlapped between genotypes. The GO (gene ontology) terms for biological processes showed upregulation of DEGs in tolerant genotypes for sulfate and drug transmembrane transport when compared to sensitive genotypes. A GO term for cellular components enriched with upregulated DEGs for the apoplast in tolerant genotypes. These results substantiated the temporal pattern of root growth (elongation and initiation of root growth), and ABA-mediated drought response in tolerant genotypes. KEGG (kyoto encyclopedia of genes and genomes) analysis revealed an upregulation of MAPK (mitogen activated protein kinase) signaling pathways and plant hormone signaling pathways in tolerant genotypes. As a result of this study, it will be possible to uncover the molecular mechanisms of drought tolerance in response to terminal drought stress in the field. Further, genome-wide transcriptomic analysis of both tolerant and sensitive genotypes will assist us in identifying potential genes that may contribute to improving drought tolerance in the common bean.

Exogenous Application of Ascorbic Acid to Induce Tolerance Against Salt Stress in Common Bean Plants

Common beans have an important place in the world due to its high nutritional values in the human diet and with the largest cropping area among the legumes. Besides, they are named as quite sensitive to salt stress. Salinity is one of the utmost abiotic stress factors limiting agricultural production, which affects plant growth and development at different levels. Lately, exogenous applications of signalling and/or protective molecules to various parts of plants are used to combat salt stress before or at the time of stress. In this context, this research was conducted to assess the influence of foliar-applied ascorbic acid (AsA) on electrolyte leakage (EL), activity of antioxidative enzymes, total protein (TSP) content and protein profiles in the two common bean genotypes (salt-sensitive “Local Genotype” and salt-tolerant “Şeker Fasulye”) at early growth stage under salinity (0, 50, 100, 150 mM NaCl). The genotypes were exposed to salt stress from fully developed true leaf at the third nodes emerged stage for two weeks, meanwhile 3 mM AsA was foliar-applied every three days. Salt stress increased EL in both genotypes and exogenous AsA application decreased EL value especially in “Local Genotype”. Foliar-applied AsA generally reduced the adverse effects of NaCl on AsA content of both genotypes. Exogenous AsA application also increased the activities of catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) in the salt-stressed common bean plants and did not play a role in the TSP content. However, it has been determined that SDS-PAGE protein profiles represent adaptive mechanisms for dealing with excess salt in common bean genotypes. The results suggested that foliar-applied AsA was effective in reducing the adverse effects of salinity especially in relatively salt sensitive common bean genotype.

Number of experiments necessary to more accurately differentiate common bean genotypes for grain physical traits and minerals in cluster analysis

The number of experiments that provides greater detail in the differentiation of common bean genotypes for grain physical traits and minerals in cluster analysis is not known. This study was undertaken to determine the number of experiments necessary to more accurately differentiate common bean genotypes for grain physical traits and minerals in cluster analyses. Seven traits of grain physical quality and the concentration of six minerals were evaluated in 17 common bean genotypes with carioca (9) and black (8) grains. Statistical analyses were performed in data obtained from one, two, three and four experiments. A significant genotype × experiment interaction occurred for all traits, except for the potassium concentration. Tocher’s and the unweighted pair group method with arithmetic mean (UPGMA) cluster analyses were efficient in differentiating common bean genotypes by grain type when the data obtained from one experiment were considered. However, the use of data obtained from four experiments made it possible to recognize differences regarding grain lightness and brightness as well as the other traits. Four experiments are need for the Tocher’s and the UPGMA cluster analyses to more accurately differentiate carioca and black bean genotypes for grain physical traits and minerals.

Study of genetic diversity and search for anthracnose resistance alleles in common bean (Phaseolus vulgaris L.) genotypes cultivated in Azerbaijan

Common bean has become very popular and widespread among the population since its introduction to Azerbaijan in the second half of the 18th century. The paper represents for the first time the genetic diversity and anthracnose resistance of 37 common bean accessions cultivated in Azerbaijan. ISSR marker characterization in the present study revealed a total of 47 bands, with 33.6% of average polymorphism. The polymorphism information content (PIC) and genetic diversity index (GDI) for each primer were in the range of 0.25-0.48 (mean 0.35) and 0.45-0.73 (mean 0.59), respectively, indicating a moderate level of genetic diversity in the current collection. UNJ tree showed that the common bean accessions tended to cluster according to the local and introduced gene pools, indicating the same original sources of these accessions, which is also supported by PCo analysis. Screening with linked SCAR markers revealed the existence of common bean genotypes with single or multiple Co resistance alleles. Among studied genes Co-4 locus and its alleles were found in all samples, followed by Co-6 (40.5%) and Co-34 (16%). Three genotypes had all studies resistance loci, while 12 had Co-4 and Co-6, and 3 had Co-4 and Co-34. The results could provide valuable information for future common bean breeding activities and conservation. The use of genotypes with two or more resistance genes as donor parents can accelerate the development of new common bean cultivars with durable resistance to anthracnose.