Common Bean Germplasm Research Articles

Mapping yield and yield-related traits using diverse common bean germplasm.

Common bean (bean) is one of the most important legume crops, and mapping genes for yield and yield-related traits is essential for its improvement. However, yield is a complex trait that is typically controlled by many loci in crop genomes. The objective of this research was to identify regions in the bean genome associated with yield and a number of yield-related traits using a collection of 121 diverse bean genotypes with different yields. The beans were evaluated in replicated trials at two locations, over two years. Significant variation among genotypes was identified for all traits analyzed in the four environments. The collection was genotyped with the BARCBean6K_3 chip (5,398 SNPs), two yield/antiyield gene-based markers, and seven markers previously associated with resistance to common bacterial blight (CBB), including a Niemann-Pick polymorphism (NPP) gene-based marker. Over 90% of the single-nucleotide polymorphisms (SNPs) were polymorphic and separated the panel into two main groups of small-seeded and large-seeded beans, reflecting their Mesoamerican and Andean origins. Thirty-nine significant marker-trait associations (MTAs) were identified between 31 SNPs and 15 analyzed traits on all 11 bean chromosomes. Some of these MTAs confirmed genome regions previously associated with the yield and yield-related traits in bean, but a number of associations were not reported previously, especially those with derived traits. Over 600 candidate genes with different functional annotations were identified for the analyzed traits in the 200-Kb region centered on significant SNPs. Fourteen SNPs were identified within the gene model sequences, and five additional SNPs significantly associated with five different traits were located at less than 0.6Kb from the candidate genes. The work confirmed associations between two yield/antiyield gene-based markers (AYD1m and AYD2m) on chromosome Pv09 with yield and identified their association with a number of yield-related traits, including seed weight. The results also confirmed the usefulness of the NPP marker in screening for CBB resistance. Since disease resistance and yield measurements are environmentally dependent and labor-intensive, the three gene-based markers (CBB- and two yield-related) and quantitative trait loci (QTL) that were validated in this work may be useful tools for simplifying and accelerating the selection of high-yielding and CBB-resistant bean cultivars.

Sampling strategies for genotyping common bean (Phaseolus vulgaris L.) Genebank accessions with DArTseq: a comparison of single plants, multiple plants, and DNA pools.

Genotyping large-scale gene bank collections requires an appropriate sampling strategy to represent the diversity within and between accessions. A panel of 44 common bean (Phaseolus vulgaris L.) landraces from the Alliance Bioversity and The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) gene bank was genotyped with DArTseq using three sampling strategies: a single plant per accession, 25 individual plants per accession jointly analyzed after genotyping (in silico-pool), and by pooling tissue from 25 individual plants per accession (seq-pool). Sampling strategies were compared to assess the technical aspects of the samples, the marker information content, and the genetic composition of the panel. The seq-pool strategy resulted in more consistent DNA libraries for quality and call rate, although with fewer polymorphic markers (6,142 single-nucleotide polymorphisms) than the in silico-pool (14,074) or the single plant sets (6,555). Estimates of allele frequencies by seq-pool and in silico-pool genotyping were consistent, but the results suggest that the difference between pools depends on population heterogeneity. Principal coordinate analysis, hierarchical clustering, and the estimation of admixture coefficients derived from a single plant, in silico-pool, and seq-pool successfully identified the well-known structure of Andean and Mesoamerican gene pools of P. vulgaris across all datasets. In conclusion, seq-pool proved to be a viable approach for characterizing common bean germplasm compared to genotyping individual plants separately by balancing genotyping effort and costs. This study provides insights and serves as a valuable guide for gene bank researchers embarking on genotyping initiatives to characterize their collections. It aids curators in effectively managing the collections and facilitates marker-trait association studies, enabling the identification of candidate markers for key traits.

Release of multiple virus and bruchid resistant Mesoamerican bean germplasm lines PR1303‐129 and PR1743‐44

AbstractPR1303‐129 (Reg. no. GP‐317, PI 702998) and PR1743‐44 (Reg. no. GP‐318, PI 702999) are multiple virus‐ and bruchid‐resistant common bean (Phaseolus vulgaris L.) germplasm lines developed and released cooperatively by the University of Puerto Rico Agricultural Experiment Station, the USDA‐ARS, the Instituto Dominicano de Investigaciones Agropecuarias y Forestales, the Instituto de Ciencia y Tecnología Agrícola, and Zamorano University. The black bean PR1303‐129 and small dark red bean PR1743‐44 combine resistance to Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), Bean golden yellow mosaic virus (BGYMV) and the common bean weevil [Acanthoscelides obtectus (Say)] with partial resistance to the Mexican bean weevil [Zabrotes subfasciatus (Boheman)]. Marker‐assisted selection was used to identify the presence of the bgm‐1 gene and the SW12 quantitative trait locus (QTL) for BGYMV resistance and the I and bc‐3 genes for resistance to BCMV and BCMNV. The parents of PR1303‐129 and PR1743‐44 were reported to possess the I gene for resistance to BCMV. Greenhouse inoculations were used to confirm the presence of the bc‐3 gene. Lines were screened in the laboratory and field for resistance to bruchids. Mean seed yields of PR1303‐129 and PR1743‐44 in six trials conducted in Puerto Rico were comparable to the check cultivar ‘Verano’. The release of these germplasm lines should contribute to the development of Mesoamerican cultivars for Central America and the Caribbean with enhanced levels of resistance to viral diseases and pests.

High Genetic Diversity in the Himalayan Common Bean (Phaseolus vulgaris) Germplasm with Divergence from Its Center of Origin in the Mesoamerica and Andes.

The common bean is found in the Himalayan region of Pakistan with substantial morphological variability. Genetic diversity within any crop species is a precursor for genetic improvement; however, little is known about common bean genetic diversity in this region. We explored the genetic diversity in the common bean from the Himalayan region (Khyber Pakhtunkhwa, Gilgit-Baltistan, Kashmir) of Pakistan. Microsatellite genotyping was carried out for 147 samples with 40 simple sequence repeat (SSR) markers. The results revealed a clear divergence of the Pakistani population from the primary gene pool (with FST values of 0.2 with Andes and 0.27 with Mesoamerica). However, within the Himalayan germplasm, no clear evidence of spatial structure was observed (with the maximum FST values of only 0.025), probably due to the dispersal of seeds by human activity within the region. This was further elucidated by the discriminant analyses of principal components. Considering the diversity parameters, high genotypic diversity was observed for the indigenous lines (0.990), comparable to the primary gene pool (0.976 for Mesoamerica and 0.976 for Andes populations). A high genotypic diversity was observed within the Himalayan population (ranging from 0.500 for Upper Dir to 0.952 for Mansehra). Gene diversity across loci varied between 0.28 for Chitral to 0.38 for Kurram. Our results suggested a divergent and independent evolution of the Himalayan population, which might have led to the diversification of the common bean germplasm in the region postintroduction into the region. The diversity observed could also be exploited in future breeding programs for the development and introduction of climate-resilient varieties.

Genetic divergence in common bean genotypes from the IRAD gene bank: morpho-agronomic characteristics, fungal and bacterial disease resistance, and opportunities for genetic improvement

For successful plant breeding in any crop species, the importance of diversity in the available germplasm population is known and established. Thirty-two common bean (Phaseolus vulgaris) genotypes from the IRAD gene bank in Cameroon were evaluated for divergence in terms of their morpho-agronomic traits, fungal disease resistance, and bacterial disease resistance to assess the opportunity for genetic improvement of the crop. The trait associations were estimated using correlation coefficients and genotypes were classified into groups using cluster and principal component analyses. Seven qualitative and 16 quantitative traits comprising growth, phenological, yield, and disease variables were evaluated in this study. The qualitative markers revealed the degree of polymorphism among the 32 common bean genotypes. The number of phenotypic classes per character (Na) ranged from 2 to 18, with an average of 5.14. The expected gene diversity (He) ranged from 0.37 to 0.93 (mean = 0.56). The number of effective phenotypic classes (Ne) ranged from 1.82 to 14.22, with a mean of 3.85. An extensive range of variation was evident for the majority of traits, highlighting their utility for characterizing common bean germplasm. Many qualitative traits, including seed coat color, seed shape, and seed size, and also some quantitative traits of economic importance including seed yield, were found to be highly variable within the collection, with the MAC55 genotype displaying the highest yield (32.65 g per plant). Four genotypes, namely MAC55, BOA-5-1M6, FEB 192, and Banguem showed resistance to the two main common bean diseases, angular leaf spot and common blight. We detected highly significant correlations among several traits related to yield. A high broad-sense heritability was found for most of the quantitative traits. We carried out two-dimensional principal component analysis and used hierarchical clustering to group the analyzed germplasm according to their phenotypic similitudes. The evidence of agro-morphological diversity in the present collection and the identification of discriminant characters between the available germplasm through the use of PCA analysis have significant implications for establishing breeding schemes in common bean.

Release of UPR‐Mp‐37 and UPR‐Mp‐48 white common bean germplasm with improved resistance to ashy stem blight

AbstractWhite common bean (Phaseolus vulgaris L.) breeding lines (BL) UPR‐Mp‐37 (Reg. no. GP‐315, PI 703030), and UPR‐Mp‐48 (Reg. no. GP‐316, PI 703031) with improved resistance to ashy stem blight [caused by Macrophomina phaseolina (Tassi) Goidanich] were developed at the University of Puerto Rico. Both these BL had lower severity (mean scores of 4.1–4.7) to PRI21 M. phaseolina isolate compared with white common bean genotypes ‘Bella’, ‘Beníquez’, NY6020‐4, and ‘Verano’ that had a susceptible response (scores >7.0). UPR‐Mp‐37 was selected from the cross NY6020‐4/A 195//SEA 5 while UPR‐Mp‐48 was derived from the common bean population BAT 477/NY6020‐4//PRA154. UPR‐Mp‐37 has an indeterminate growth habit type III, initiates flowering at 30 days after planting, reaches harvesting maturity at 89 days, and has an average weight of 27.4 g per 100 seed. UPR‐Mp‐48 has a determinate growth habit type I, initiates flowering and matures at 33 and 85 days after planting, respectively, and has an average weight of 29.6 g per 100 seed. Both BL had over 800 kg ha−1 seed yields in Isabela, Puerto Rico. The resistance of UPR‐Mp‐37 and UPR‐Mp‐48 BL can be introgressed into susceptible white beans to reduce the disease severity.

Oligogenic control of quantitative resistance against powdery mildew revealed in Portuguese common bean germplasm.

Common bean (Phaseolus vulgaris L.) is one of the most important food legumes worldwide, being its production severely affected by fungal diseases such as powdery mildew. Portugal has a diverse germplasm, with accessions of Andean, Mesoamerican, and admixed origin, making it a valuable resource for common bean genetic studies. In this work, we evaluated the response of a Portuguese collection of 146 common bean accessions to Erysiphe diffusa infection, observing a wide range of disease severity and different levels of compatible and incompatible reactions, revealing the presence of different resistance mechanisms. We identified 11 incompletely hypersensitive resistant, and 80 partially resistant accessions. We performed a genome-wide association study to clarify its genetic control, resulting in the identification of eight disease severity-associated single-nucleotide polymorphisms, spread across chromosomes Pv03, Pv09, and Pv10. Two of the associations were unique to partial resistance, and one to incomplete hypersensitive resistance. The proportion of variance explained by each association varied between 15 and 86%. The absence of a major locus, together with the relatively small number of loci controlling disease severity (DS), suggested an oligogenic inheritance of both types of resistance. Seven candidate genes were proposed including a disease resistance protein (TIR-NBS-LRR class), an NF-Y transcription factor complex component, and an ABC-2 type transporter family protein. This work contributes with new resistance sources and genomic targets valuable to develop selection molecular tools and support powdery mildew resistance precision breeding in common bean.

Genome-wide Association Studies revealed DArTseq loci associated with seed traits in Turkish common bean germplasm

Genome-wide Association Studies revealed DArTseq loci associated with seed traits in Turkish common bean germplasm

Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean.

Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.

High-density DArTSeq SNP markers revealed wide genetic diversity and structured population in common bean (Phaseolus vulgaris L.) germplasm in Ethiopia

IntroductionCommon bean is one of the widely consumed food security crop in Africa, Asia, and South America. Understanding genetic diversity and population structure is crucial for designing breeding strategies.MaterialsTwo hundred and eighty-nine germplasm were recently collected from different regions of Ethiopia and introduced from CIAT to estimate genetic diversity and population structure using 11,480 DArTSeq SNP markers.ResultsThe overall mean genetic diversity and polymorphic information content (PIC) were 0.38 and 0.30, respectively, suggested the presence of adequate genetic diversity among the genotypes. Among the geographical regions, landraces collected from Oromia showed the highest diversity (0.39) and PIC (0.30). The highest genetic distance was observed between genotypes collected from SNNPR and CIAT (0.49). In addition, genotypes from CIAT were genetically more related to improved varieties than the landraces which could be due to sharing of parents in the improvement process. The analysis of molecular variance revealed that the largest proportion of variation was due to within the population both in geographical region (63.67%) and breeding status (61.3%) based classification. Model-based structure analysis delineated the 289 common bean genotypes into six hypothetical ancestoral populations.ConclusionsThe genotypes were not clustered based on geographical regions and they were not the main drivers for the differentiation. This indicated that selection of the parental lines should be based on systematic assessment of the diversity rather than geographical distance. This article provides new insights into the genetic diversity and population structure of common bean for association studies, designing effective collection and conservation for efficient utilization for the improvement of the crop.

Evaluation of phenological development and agronomic traits in exotic common bean germplasm across multiple environments

AbstractTwenty-nine exotic common bean germplasms and three elite cultivars were examined for phenotypic diversity in two bean-producing environments (Kanpur and Shimla) across three winter seasons and one rainy season. The estimate of genetic variability parameters revealed that the exotic bean germplasm has enough diversity for all the evaluated features. The highest genotypic and phenotypic coefficients of variation were found in seed yield, followed by 100-seed weight, pods per plant and pod length. Furthermore, seed yield was the most heritable and genetically advanced quantitative feature, followed by 100-seed weight, pod length and pods per plant. According to a trait association study, the days to maturity of phenological traits have a strong positive correlation with the days to initial flowering and the days to 50% flowering. Pods per plant and seeds per pod most strongly influence increased grain yield. The first two principal components accounted for 63.3% of the variation and demonstrated significant diversity among exotic bean lines for the traits studied, according to the principal component analysis. According to the hierarchical clustering analysis, 29 accessions and three cultivars were divided into three groups. Cluster I contains early flowering and maturing accessions, while cluster III contains high pods per plant and an increased grain yield of germplasms. The fundamental source of phenological fluctuations in both environmental circumstances is temperature. This study found four genetically divergent and stable performance accessions, including EC932021, EC932189 (earliness), and EC931452, EC931971 (high grain yield), which may aid in the establishment of a bean breeding programme.

Registration of UPR‐Mp‐34 and UPR‐Mp‐42 common bean germplasm with enhanced resistance to ashy stem blight

AbstractCommon bean (Phaseolus vulgaris L.) breeding lines (BL) UPR‐Mp‐34 (Reg no. CV‐313, PI 701379) and UPR‐Mp‐42 (Reg no. CV‐314, PI 701380) were developed at the University of Puerto Rico. UPR‐Mp‐34 was derived from A 195/‘PC 50’//SEA 5, and UPR‐Mp‐42 was developed from BAT 477/NY6020‐4//PRA154 common bean populations. Both BL have intermediate levels of resistance (mean scores, 4–6) to two inoculations of the PRI21 Macrophomina phaseolina (Tassi) Goidanich isolate (the causal agent of ashy stem blight) compared with BAT 477, SEA 5, TARS‐MST1, and XAN 176, which mostly had susceptible scores (7–9) in the greenhouse and field evaluations. UPR‐Mp‐34 has an indeterminate growth habit Type III, has a cream seed (average weight, 26.5 g per 100 seeds), initiates flowering at 32 d after planting, and reaches harvesting maturity at 86 d. Mean seed yield was 730 and 340 kg ha−1 in Isabela and Lajas, respectively. UPR‐Mp‐42 possesses black seed (23.8 g per 100 seeds), has a determinate growth habit Type I, initiates flowering at 30 d, and matures at 76 d. Mean seed yield was 750 kg ha−1 in both locations. The intermediate levels of ashy stem blight resistance from both BL could be combined with other sources of resistance and introgressed into common bean cultivars from different market classes.

Stem, leaf and cotyledon resistance responses to a prevalent Sclerotinia sclerotiorum pathotype in Australia highlight new opportunities to improve white mould resistance in common bean

Context White mould (Sclerotinia sclerotiorum) inflicts major yield losses on common bean (Phaseolus vulgaris); yet, commercial cultivars known for their high yields and market-adapted grains lack physiological resistance to this disease. Aims This study aimed to test diverse common bean genotypes for resistance in stem, leaf and cotyledon tissues. Methods Thirty-four common bean genotypes with a wide range of agronomic traits and grain types, including genotypes noted previously for susceptible and resistant responses to white mould, were inoculated with the prevalent S. sclerotiorum isolate MBRS-1. Then they were assessed for resistance in stem, leaf and cotyledon tissues under controlled environment conditions, by inoculating plants with a 105 mL−1 hyphal fragment concentration. Key results There was significant (P < 0.001) variation in resistance responses in stem, leaf and cotyledon tissues across the genotypes. Contender, ICA Bunsi, XAN 280 and Taisho-Kintoki showed the highest resistance in stems, whereas Norvell 2558, Pico de Oro, Sanilac, Othelo and Negro Argel exhibited notable resistance in leaves. Metis, Canario 107, Pico de Oro, Pogonion and Jubilejnaja 287 displayed the most resistance in cotyledons. Conclusions This is the first reported attempt to determine the response of common bean germplasm to a prevalent pathotype of S. sclerotiorum in Australia. Bean genotypes exhibiting high-level resistance to white mould identified in this study can be used as parental lines for crosses in common bean breeding programs and/or directly as improved cultivars. Implications The study highlighted both the value of screening under controlled environmental conditions to reliably locate new stem, leaf and/or cotyledon resistances and the possibility of using rapid cotyledon screening to indicate stem resistances because the expression of resistances in cotyledons generally correlated strongly with those in stems.

Screening a newly developed common bean germplasm with improved resistance to ashy stem blight in multiple environments.

Ashy stem blight (ASB) caused by the necrotrophic fungus Macrophomina phaseolina (Tassi) Goidanich is an important disease in common bean (Phaseolus vulgaris L.) in the Americas and worldwide. Low to intermediate levels of ASB resistance exist in cultivated and landrace genotypes of the common bean and the tertiary gene pool. However, cultivars with higher levels of resistance are not yet available. Our objectives were to 1) pyramid higher levels of resistance from multiple parent populations within the primary gene pool and 2) compare the response of the newly developed breeding lines (BL) with known sources of resistance. The BL UPR-Mp-22, UPR-Mp-34, UPR-Mp-42, and UPR-Mp-48, known sources of resistance, and susceptible checks were inoculated twice per plant with the PRI21 M. phaseolina isolate in the greenhouse and field trials conducted in Isabela and Lajas, Puerto Rico. None of the genotypes tested were resistant (mean scores 1-3). However, the new black UPR-Mp-42 and white UPR-Mp-48 BL had an intermediate response (mean scores 4-6) compared to white common bean genotypes 'Bella,' NY6020-4, and 'Verano' and black bean TARS-MST1 that were susceptible (scores ≥7) in all environments. Andean genotypes A 195, PRA154, PRA155, and UPR-Mp-22 were intermediate in the greenhouse. In contrast, UPR-Mp-34 had significantly lower scores than BAT 477 that had a susceptible reaction in the greenhouse in Isabela and in the field in Lajas and SEA 5 that was susceptible in all environments. These new BL possess an enhanced ASB resistance and may be used to improve common bean cultivars or germplasms of different market classes.

Canning quality of popular common bean germplasm in Eastern and Central Africa

Common bean (Phaseolus vulgaris L.) genotypes popular in eastern and central Africa were evaluated to determine their suitability for the canning industry. The genotypes were planted at the National Agricultural Research Laboratories (NARL), Kawanda-Uganda in the second rainy seasons (July-September) of 2015, 2016 and off season of 2017 (November- February). Two samples per genotype were evaluated at the canning facilities at Kawanda and Michigan State University (MSU) using a protocol based on home canning. One sample per genotype from the 2017 harvest was evaluated at Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre (AAFC-LRDC) using the industry canning protocol. Data (n=134) was collected on seed moisture content, dry and soaked bean weight, hydration coefficient (HC) and visual quality, including colour retention, appearance, brine clarity, bean splitting and freedom starch/clumps on replicated samples. Additional data on unreplicated samples were collected on 100-seed weight, seed solids for canning, hydration coefficient after soaking (HCS), hydration coefficient after blanching (HCB), drain weight (%), matting, appearance, seed color, texture, and cooking quality traits including hard seed and partially hydrated seed (%) and HC after cooking. Analysis of variance of data from MSU and Kawanda showed significant (P≤0.01) differences among genotypes for the assessed parameters. Majority of the genotypes expressed good soaking ability considering that their HC were above the 1.8 recommended for canning and 28% combined the two mentioned traits with good overall canning quality visual rating. Apart from 26, all other varieties had good HC based on data from Canada. About 24% of genotypes belonging to various market classes consistently combined this trait with good visual quality. The most outstanding genotypes based on these traits included SAB659 (red mottled), MAC44 (red mottled), NABE21 (cream), NABE12C (cream) and VAX5 (cream), KK8 (red mottled), Bihogo (yellow) and VAX4 (black). These genotypes were superior to the white beans: MEXICO 142, Awash1, and Awash Melka, that were considered as high-quality controls. Results indicated that genotypes of diverse backgrounds, with good canning quality traits exist among the currently utilised varieties and breeding lines. This diversity could be exploited for breeding and varietal promotion in the canning industry. Key words: Common bean, canning, hydration coefficient, visual quality, drained weight

Exogenous melatonin enhances cell wall response to salt stress in common bean (Phaseolus vulgaris) and the development of the associated predictive molecular markers.

Common bean (Phaseolus vulgaris) is an important food crop; however, its production is affected by salt stress. Salt stress can inhibit seed germination, promote senescence, and modify cell wall biosynthesis, assembly, and architecture. Melatonin, an indole heterocycle, has been demonstrated to greatly impact cell wall structure, composition, and regulation in plants under stress. However, the molecular basis for such assumptions is still unclear. In this study, a common bean variety, "Naihua" was treated with water (W), 70 mmol/L NaCl solution (S), and 100 μmol/L melatonin supplemented with salt solution (M+S) to determine the response of common bean to exogenous melatonin and explore regulatory mechanism of melatonin against salt stress. The results showed that exogenous melatonin treatment alleviated salt stress-induced growth inhibition of the common bean by increasing the length, surface area, volume, and diameter of common bean sprouts. Moreover, RNA sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) indicated that the cell wall regulation pathway was involved in the salt stress tolerance of the common bean enhanced by melatonin. Screening of 120 germplasm resources revealed that melatonin treatment improved the salt tolerance of more than 65% of the common bean germplasm materials. Melatonin also up-regulated cell wall pathway genes by at least 46%. Furthermore, we analyzed the response of the common bean germplasm materials to melatonin treatment under salt stress using the key genes associated with the synthesis of the common bean cell wall as the molecular markers. The results showed that two pairs of markers were significantly associated with melatonin, and these could be used as candidate markers to predict whether common bean respond to exogenous melatonin and then enhance salt tolerance at the sprouting stage. This study shows that cell wall can respond to exogenous melatonin and enhance the salt tolerance of common bean. The makers identified in this study can be used to select common bean varieties that can respond to melatonin under stress. Overall, the study found that cell wall could response melatonin and enhance the salt tolerance and developed the makers for predicting varieties fit for melatonin under stress in common bean, which may be applied in the selection or development of common bean varieties with abiotic stress tolerance.

Enviromic prediction is useful to define the limits of climate adaptation: A case study of common bean in Brazil

Ongoing changes in the global environmental conditions foster plant breeding research to develop climate-smart cultivars as fast as possible. Data analytics are essential for achieving this goal, especially the so-called science of enviromics (large-scale environmental characterization of crop growing conditions) that could be used to pinpoint the relevant environment impacts driving the adaptation of a certain specie in a breeding framework. Here we quantified the effects of diverse climate factors on the current adaptation of elite common bean germplasm in Brazil. To capture the non-linearity of those impacts across a wide range of environments, we developed an “enviromic prediction” approach by combining Generalized Additive Models (GAM), environmental covariates (EC), and grain yield (GY) from 18 years of historical breeding trials. Then, we predicted the optimum limits for ECs at each production scenario (four regions, three seasons, and two grain types) and its respective predictions of GY adaptation. Our results indicate that the nonlinear influence of air temperature, solar radiation, and rainfall led to a huge interaction of the impacts among the development stages, seasons, and regions. This revealed that seasonality differently affected the vegetative and reproductive stages, which its impact drastically vary according to the region and season, which makes unfeasible the development of a breeding strategy for selecting for broad adaptation. Conversely, with our approach it was possible to pinpoint the effects of the region- or season-specific impacts, which helped identify the “climate limits” and critical development phases for each possible production scenario. This could allow breeders to design crop ideotypes while directing efforts to develop climate-smart varieties. Furthermore, enviromics prediction is a cost-effective way to use EC as a data analytics tool to support the visualization of regional breeding gaps for specific growing conditions. • We verified the ability of GAM-based models to determine climate drivers that explain grain yield variation. • Climatic limitations for cropping common bean in Brazil were identified across diverse seasons and regions. • “Optimum” predicted values for climate variables in different common bean production regions were obtained.

Genetic transformation of common beans (Phaseolus vulgaris L.) through Agrobacterium tumefaciens carrying Cry1Ab gene.

Seed beetles are one of the most important causes of yield loss in bean production. It is essential to develop resistant varieties in the fight against these pests. Agrobacterium-based gene transformation is the most widely used breeding method worldwide to develop insect-resistant varieties. Embryonic axes and plumule explants were obtained from Agrobacterium tumefciens treated mature zygotic embryos of low and high raw protein-based common bean cultivars Akman 98 and Karacaşehir 90. Agrobacterium tumefaciens contained a synthetic Bacillus thuringiensis insecticidal crystal protein gene (Bt Cry1Ab) controlled by the 35S promoter and NOS terminator sequences. The transformation event was genotype and explant dependent. The plumule explants could not withstand kanamycin-based selection pressure and died. It was possible to get two transgenic plants using embryonic axis explants of low protein cultivar Akman 98. These results were validated using GUS analysis, PCR, RT-PCR, bioassay analysis, and ELISA test from the samples taken from T0 and T1 generations. Bioassay tests showed that these plants were protected from the damage of legume seed insects (Bruchus spp.). The results are very encouraging and may help in producing better transgenic common bean germplasm leading to safe agriculture and reducing environmental pollutions.

GENETIC DIVERSITY ANALYSIS OF COMMON BEAN (PHASEOLUS VULGARIS L.) GENOTYPES USING SCOT POLYMORPHISM

Common bean (Phaseolus vulgaris L.) is legume crop of worldwide importance and due to optimal content of proteins and other essential compounds it has a potential as a functional food. Genetic diversity studies are significant from the point of obtaining information important for breeding process. The goal of present work was to analyze genetic diversity among 34 genotypes of common bean from different countries using 5 SCoT (Start Codon Targeted) markers. Altogether 82 DNA fragments were amplified, out of which 66 fragments were polymorphic with an average of 11 polymorphic fragments per primer. The highest number of polymorphic fragments was detected by marker SCoT 59 (15). The percentage of polymorphism ranged from 57.17% (SCoT 2) to 78.57% (SCoT 19) with an average of 67.3%. PIC values varied from 0.719 (SCoT 19) to 0.886 (SCoT 3) and average PIC value was 0.802. The DI values varied between 0.722 (SCoT 19) and 0.888 (SCoT3), with an average of 0.804. The dendrogram of 34 genotypes of common bean, constructed based on hierarchical cluster analysis separated genotypes into two clusters (I and II). Cluster I was formed by two subclusters. Thirty-three genotypes were included in cluster I and genotype Albena (Slovak Republic), which significantly differed from other genotypes in seed size was included in cluster II. Obtained results support the effectiveness of SCoT markers in the analysis of common bean useful for genotypes differentiating and assessment of genetic diversity in the set of common bean germplasm.

Development of a Model for Genomic Prediction of Multiple Traits in Common Bean Germplasm, Based on Population Structure

Due to insufficient identification and in-depth investigation of existing common bean germplasm resources, it is difficult for breeders to utilize these valuable genetic resources. This situation limits the breeding and industrial development of the common bean (Phaseolus vulgaris L.) in China. Genomic prediction (GP) is a breeding method that uses whole-genome molecular markers to calculate the genomic estimated breeding value (GEBV) of candidate materials and select breeding materials. This study aimed to use genomic prediction to evaluate 15 traits in a collection of 628 common bean lines (including 484 landraces and 144 breeding lines) to determine a common bean GP model. The GP model constructed by landraces showed a moderate to high predictive ability (ranging from 0.59–0.88). Using all landraces as a training set, the predictive ability of the GP model for most traits was higher than that using the landraces from each of two subgene pools, respectively. Randomly selecting breeding lines as additional training sets together with landrace training sets to predict the remaining breeding lines resulted in a higher predictive ability based on principal components analysis. This study constructed a widely applicable GP model of the common bean based on the population structure, and encouraged the development of GP models to quickly aggregate excellent traits and accelerate utilization of germplasm resources.