Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding

Phaseolus vulgaris mutants reveal variation in the nuclear genome

Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean.

Genetic differentiation of a southern Africa tepary bean (Phaseolus acutifolius A Gray) germplasm collection using high-density DArTseq SNP markers

Genetic resources of tepary bean (Phaseolus acutifolius A. Gray) germplasm collections are not well characterized due to a lack of dedicated genomic resources. There is a need to assemble genomic resources specific to tepary bean for germplasm characterization, heterotic grouping, and breeding. Therefore, the objectives of this study were to deduce the genetic groups in tepary bean germplasm collection using high-density Diversity Array Technology (DArT) based single nucleotide polymorphism (SNP) markers and select contrasting genotypes for breeding. Seventy-eight tepary bean accessions were genotyped using 10527 SNPs markers, and genetic parameters were estimated. Population structure was delineated using principal component and admixture analyses. A mean polymorphic information content (PIC) of 0.27 was recorded, indicating a relatively low genetic resolution of the developed SNPs markers. Low genetic variation (with a genetic distance [GD] = 0.32) existed in the assessed tepary bean germplasm collection. Population structure analysis identified five sub-populations through sparse non-negative matrix factorization (snmf) with high admixtures. Analysis of molecular variance indicated high genetic differentiation within populations (61.88%) and low between populations (38.12%), indicating high gene exchange. The five sub-populations exhibited variable fixation index (FST). The following genetically distant accessions were selected: Cluster 1:Tars-Tep 112, Tars-Tep 10, Tars-Tep 23, Tars-Tep-86, Tars-Tep-83, and Tars-Tep 85; Cluster 3: G40022, Tars-Tep-93, and Tars-Tep-100; Cluster 5: Zimbabwe landrace, G40017, G40143, and G40150. The distantly related and contrasting accessions are useful to initiate crosses to enhance genetic variation and for the selection of economic traits in tepary bean.

Whole-genome resequencing of common bean elite breeding lines

The expansion of bean genome technologies has prompted new perspectives on generating resources and knowledge essential to research and implementing biotechnological tools for the practical operations of plant breeding programs. This study aimed to resequence the entire genome (whole genome sequencing-WGS) of 40 bean genotypes selected based on their significance in breeding programs worldwide, with the objective of generating an extensive database for the identification of single nucleotide polymorphisms (SNPs). Over 6 million SNPs were identified, distributed across the 11 bean chromosomes. After quality variant filtering, 420,509 high-quality SNPs were established, with an average of 38,228 SNPs per chromosome. These variants were categorized based on their predicted effects, revealing that the majority exerted a modifier impact on non-coding genome regions (94.68%). Notably, a significant proportion of SNPs occurred in intergenic regions (62.89%) and at least one SNP was identified in 58.63% of the genes annotated in the bean genome. Of particular interest, 7841 SNPs were identified in 85% of the putative plant disease defense-related genes, presenting a valuable resource for crop breeding efforts. These findings provide a foundation for the development of innovative and broadly applicable technologies for the routine selection of superior genotypes in global bean improvement and germplasm characterization programs.

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

INTRODUCTION

Common 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.

MATERIALS

Two 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.

RESULTS

The 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.

CONCLUSIONS

The 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.

Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers

Genetic integrity of an accession should be preserved in the conservation of germplasm. Characterization of diverse germplasm based on a molecular basis enhances its conservation and use in breeding programs. The aim of this study was to assess the genetic diversity of 169 sorghum accessions using a total of 6977 SNP markers. The polymorphic information content of the markers was 0.31 which is considered to be moderately high. Structure analysis using ADMIXTURE program revealed a total of 10 subpopulations. Neighbor-joining tree revealed the presence of six main clusters among these subpopulations whereas in principal component analysis, seven clusters were identified. Cluster analysis grouped most populations depending on source of collection although other accessions originating from the same source were grouped under different clusters. Analysis of molecular variance (AMOVA) revealed 30% and 70% of the variation occurred within and among accessions, respectively. Gene flow within the populations was, however, limited indicating high differentiation within the subpopulation. Observed heterozygosity among accessions varied from 0.03 to 0.06 with a mean of 0.05 since sorghum is a self-pollinating crop. High genetic diversity among the subpopulations can be further explored for superior genes to develop new sorghum varieties.

Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA

Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10−3 ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.

Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean

Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.

Characterization of fungal pathogens and germplasm screening for disease resistance in the main production area of the common bean in Argentina

The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet, mainly in Africa and Latin America. Argentina is one of the five major producers of the common bean in the world, and the main cultivation areas are concentrated in the northwestern provinces of this country. Crop production of the common bean is often affected by biotic factors like some endemic fungal diseases, which exert a major economic impact on the region. The most important fungal diseases affecting the common bean in Argentina are white mold caused by Sclerotinia sclerotiorum, angular leaf spot caused by Pseudocercospora griseola, web blight and root rot caused by Rhizoctonia solani, which can cause production losses of up to 100% in the region. At the present, the most effective strategy for controlling these diseases is the use of genetic resistance. In this sense, population study and characterization of fungal pathogens are essential for developing cultivars with durable resistance. In this review we report diversity studies carried out on these three fungal pathogens affecting the common bean in northwestern Argentina, analyzing more than 200 isolates by means of molecular, morphological and pathogenic approaches. Also, the screening of physiological resistance in several common bean commercial lines and wild native germplasm is reviewed. This review contributes to the development of sustainable management strategies and cultural practices in bean production aimed to minimize yield losses due to fungal diseases in the common bean.

Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding

Introgression of bruchid (Zabrotes subfasciatus) resistance into small red common bean (Phaseolus vulgaris) background and validation of the BRU_00261 (snpPV0007) resistance marker

Bruchids are a major storage pest of common bean. Genetic resistance is a suitable method to avoid grain losses during storage. The objective of the study was to introgress the arcelin-based resistance locus into selected advanced breeding line and to validate the molecular marker BRU_00261. A total of 208 progeny F₄ families were phenotyped using a randomized complete block design, with three replications. Highly significant differences (P <  .001) among the entries, parents and offspring were recorded for almost all traits. There was no significant difference between the two parents in the number of eggs laid. The progenies were grouped as highly resistant (34.3%), resistant (11.9%), moderately resistant (21.4%) and susceptible (32.4%). The levels of broad sense heritability ranged from 68.5%-93.9% for all the traits. Eighty-three most resistant lines and the parental lines were genotyped with the marker BRU_00261 (snpPV0007). The marker segregation deviated significantly from the expected independent segregation towards a strong enrichment for the resistant marker in the selected families. This marker will be useful for selecting promising materials in early generations and phenotypic confirmation of positive lines in later generations.

DISTRIBUTION AND BIOLOGY OF INVASIVE SPECIES OF BEAN BRUCHID <i>ACANTHOSCELIDES OBTECTUS</i> (INSECTA, COLEOPTERA, BRUCHIDAE)

The review of literary sources on ecology, biology, distribution of bean bruchid ( Acanthoscelides obtectus ) and its main food plant - Phaseolus vulgaris in North and South America; Europe, Africa, Asia, Australia and more details in Russia; the influence of abiotic, biotic and anthropogenic factors on the invasive process, phytosanitary condition of common bean crops in Russia is presented. Some aspects of the invader management are shown. The main stages and areas of cultivation of common bean and invasion of bean bruchid from their primary habitat in South America and in the south of North America are traced; the vectors and reasons causing them are considered. In Russia, the economic importance of bean bruchid has increased since the mid-1980s, which coincided with the climate warming; there was an expansion of its distribution in the eastern and north-western directions. At the last decades of the 20th century, it had penetrated in Smolensk and in the south part of the Tver and the Tomsk regions. With the increase in production of beans in Russia, the lack of systemic protection from bean bruchid and further increase of climate warming will contribute to the extension of its range to the north in the European part of Russia and the Urals to 57-58° N. Lat., where the conditions of the summer period are favorable for development of common bean and bean bruchid. To the east, it may spread to Tyva, Buryatia, the Trans-Baikal territory, the Amur region, the Jewish Autonomous region, and the southern part of the Khabarovsk territory. With the introduction of strict internal quarantine and a system of protection of common bean from this pest, which prevents the spread of infected dry bean, on the contrary, it is possible to reduce the distribution range of the bean bruchid, with its disappearance in the Siberian, Ural districts, Bashkortostan and Tatarstan.

Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa

Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two-stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome-wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (-0.57 ± 0.21), and CKT and Zn (-0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high-yielding, biofortified, and rapid cooking African common bean cultivars.

Physiological and genetic characterization of heat stress effects in a common bean RIL population

Heat stress is a major abiotic stress factor reducing crop productivity and climate change models predict increasing temperatures in many production regions. Common bean (Phaseolus vulgaris L.) is an important crop for food security in the tropics and heat stress is expected to cause increasing yield losses. To study physiological responses and to characterize the genetics of heat stress tolerance, we evaluated the recombinant inbred line (RIL) population IJR (Indeterminate Jamaica Red) x AFR298 of the Andean gene pool. Heat stress (HS) conditions in the field affected many traits across the reproductive phase. High nighttime temperatures appeared to have larger effects than maximum daytime temperatures. Yield was reduced compared to non-stress conditions by 37% and 26% in 2016 and 2017 seasons, respectively. The image analysis tool HYRBEAN was developed to evaluate pollen viability (PolVia). A significant reduction of PolVia was observed in HS and higher viability was correlated with yield only under stress conditions. In susceptible lines the reproductive phase was extended and defects in the initiation of seed, seed fill and seed formation were identified reducing grain quality. Higher yields under HS were correlated with early flowering, high pollen viability and effective seed filling. Quantitative trait loci (QTL) analysis revealed a QTL for both pod harvest index and PolVia on chromosome Pv05, for which the more heat tolerant parent IJR contributed the positive allele. Also, on chromosome Pv08 a QTL from IJR improved PolVia and the yield component pods per plant. HS affected several traits during the whole reproductive development, from floral induction to grain quality traits, indicating a general heat perception affecting many reproductive processes. Identification of tolerant germplasm, indicator traits for heat tolerance and molecular tools will help to breed heat tolerant varieties to face future climate change effects.

Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean

The bean fly (Ophiomyia spp) is a key insect pest causing significant crop damage and yield loss in common bean (Phaseolus vulgaris L., 2n = 2x = 22). Development and deployment of agronomic superior and bean fly resistant common bean varieties aredependent on genetic variation and the identification of genes and genomic regions controlling economic traits. This study's objective was to determine the population structure of a diverse panel of common bean genotypes and deduce associations between bean fly resistance and agronomic traits based on single nucleotide polymorphism (SNP) markers. Ninety-nine common bean genotypes were phenotyped in two seasons at two locations and genotyped with 16 565 SNP markers. The genotypes exhibited significant variation for bean fly damage severity (BDS), plant mortality rate (PMR), and pupa count (PC). Likewise, the genotypes showed significant variation for agro-morphological traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield (GYD). The genotypes were delineated into two populations, which were based on the Andean and Mesoamerican gene pools. The genotypes exhibited a minimum membership coefficient of 0.60 to their respective populations. Eighty-three significant (P<0.01) markers were identified with an average linkage disequilibrium of 0.20 at 12Mb across the 11 chromosomes. Three markers were identified, each having pleiotropic effects on two traits: M100049197 (BDS and NPP), M3379537 (DTF and PC), and M13122571 (NPP and GYD). The identified markers are useful for marker-assisted selection in the breeding program to develop common bean genotypes with resistance to bean fly damage.

Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

Brazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.

Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

Brazilian germplasm of winter squash (Cucurbita moschata D.) displays vast genetic variability, allowing identification of promising genotypes for agro-morphological traits

Winter squash fruits (Cucurbita moschata D.) are among the best sources of vitamin A precursors and constitute sources of bioactive components such as phenolic compounds and flavonoids. Approximately 70% of C. moschata seed oil is made up of unsaturated fatty acids, with high levels of monounsaturated fatty acids and components such as vitamin E and carotenoids, which represent a promising nutritional aspect in the production of this vegetable. C. moschata germplasm expresses high genetic variability, especially in Brazil. We assessed 91 C. moschata accessions, from different regions of Brazil, and maintained at the Federal University of Viçosa (UFV) Vegetable Germplasm Bank, to identify early-flowering accessions with high levels of carotenoids in the fruit pulp and high yields of seed and seed oil. Results showed that the accessions have high variability in the number and mass of seeds per fruit, number of accumulated degree-days for flowering, total carotenoid content, and fruit productivity, which allowed selection for considerable gains in these characteristics. Analysis of the correlation between these characteristics provided information that will assist in selection to improve this crop. Cluster analysis resulted in the formation of 16 groups, confirming the variability of the accessions. Per se analysis identified accessions BGH-6749, BGH-5639, and BGH-219 as those with the earliest flowering. Accessions BGH-5455A and BGH-5598A had the highest carotenoid content, with averages greater than 170.00 μg g^-1 of fresh mass. With a productivity of 0.13 t ha^-1, accessions BGH-5485A, BGH-4610A, and BGH-5472A were the most promising for seed oil production. These last two accessions corresponded to those with higher seed productivity, averaging 0.58 and 0.54 t ha^-1, respectively. This study confirms the high potential of this germplasm for use in breeding for promotion of earlier flowering and increase in total content of fruit pulp carotenoids and in seed and seed oil productivity.

Induction of competent cells for Agrobacterium tumefaciens-mediated stable transformation of common bean (Phaseolus vulgaris L.)

Stable transformation of common bean (Phaseolus vulgaris L.) has been successful, to date, only using biolistic-mediated transformation and shoot regeneration from meristem-containing embryo axes. In this study, using precultured embryo axes, and optimal co-cultivation conditions resulted in a successful transformation of the common bean cultivar Olathe using Agrobacterium tumefaciens strain EHA105. Plant regeneration through somatic embryogenesis was attained through the preculture of embryo axes for 12 weeks using induced competent cells for A. tumefaciens-mediated gene delivery. Using A. tumefaciens at a low optical density (OD) of 0.1 at a wavelength of 600 nm for infection and 4-day co-cultivation, compared to OD₆₀₀ of 0.5, increased the survival rate of the inoculated explants from 23% to 45%. Selection using 0.5 mg L^-1 glufosinate (GS) was effective to identify transformed cells when the bialaphos resistance (bar) gene under the constitutive 35S promoter was used as a selectable marker. After an 18-week selection period, 1.5% -2.5% inoculated explants, in three experiments with a total of 600 explants, produced GS-resistant plants through somatic embryogenesis. The expression of bar was confirmed in first- and second-generation seedlings of the two lines through reverse polymerase chain reaction. Presence of the bar gene was verified through genome sequencing of two selected transgenic lines. The induction of regenerable, competent cells is key for the successful transformation, and the protocols described may be useful for future transformation of additional Phaseolus germplasm.