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Tepary bean ( Phaseolus acutifolius A. Gray) is a diploid legume species (2 n = 2 x = 22). It is the most drought- and heat-tolerant crop of the genus Phaseolus . Tepary bean is native to the northern part of Mexico and the south-western part of the U.S. The lack of molecular markers associated with agronomic traits such as 100-seed weight and seed yield limit the development of elite tepary bean cultivars. Therefore, the objectives of this study were to evaluate tepary bean for 100-seed weight and yield, and identify single-nucleotide polymorphism (SNP) markers associated with these traits. A total of 230,000 high-quality SNPs obtained from the whole-genome resequencing of 153 tepary bean accessions were used for this study. For 100-seed weight, a total of 5 and 20 SNPs were found using a mixed linear model (MLM) and compressed mixed linear model (cMLM), respectively. A candidate gene, Phacu.CVR.002G320800.13 , encoding the squamosa promoter-binding protein-like (SBP domain) transcription factor family protein was found to be associated with 100-seed weight. For seed yield, a total of one and eight SNPs were identified using an MLM and cMLM, respectively. Phacu.CVR.009G294200.1 , encoding for peroxidase family protein, was identified as a candidate gene for seed yield. Both Phacu.CVR.002G320800.13 and Phacu.CVR.009G294200.1 are likely to be involved in seed development of tepary bean. This is one of the few studies investigating the genetics of 100-seed weight and seed yield in tepary bean.

Flavonoids are secondary metabolites associated with plant seed coat and flower color. These compounds provide health benefits to humans as anti-inflammatory and antioxidant compounds. The expression of the late biosynthetic genes in the flavonoid pathway is controlled by a ternary MBW protein complex consisting of interfacing MYB, beta-helix-loop-helix (bHLH), and WD40 Repeat (WDR) proteins. P, the master regulator gene of the flavonoid expression in common bean (Phaseolus vulgaris L.), was recently determined to encode a bHLH protein. The T and Z genes control the distribution of color in bean seeds and flowers and have historically been considered regulators of the flavonoid gene expression. T and Z candidates were identified using reverse genetics based on genetic mapping, phylogenetic analysis, and mutant analysis. Domain and AlphaFold2 structure analyses determined that T encodes a seven-bladed β-propeller WDR protein, while Z encodes a R2R3 MYB protein. Deletions and SNPs in T and Z mutants, respectively, altered the 3D structure of these proteins. Modeling of the Z MYB/P bHLH/T WDR MBW complex identified interfacing sequence domains and motifs in all three genes that are conserved in dicots. One Z MYB motif is a possible beta-molecular recognition feature (β-MoRF) that only appears in a structured state when Z MYB is modeled as a component of a MBW complex. Complexes containing mutant T and Z proteins changed the interaction of members of the complex in ways that would alter their role in regulating the expression of genes in the flavonoid pathway., Competing Interests: Conflicts of interest The authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

The Andean domesticated common beans (Phaseolus vulgaris) are significant sources of phenolic compounds associated with health benefits. However, the regulation of biosynthesis of these compounds during bean seed development remains unclear. To elucidate the gene expression patterns involved in the regulation of the flavonoid pathway, we conducted a transcriptome analysis of two contrasting Chilean varieties, Negro Argel (black bean) and Coscorron (white bean), at three developmental stages associated with seed color change, as well as different flavonoid compound accumulations. Our study reveals that phenolic compound synthesis initiates during seed filling, although it exhibits desynchronization between both varieties. We identified 10,153 Differentially Expressed Genes (DEGs) across all comparisons. The KEGG pathway 'Flavonoid biosynthesis' showed enrichment of induced DEGs in Negro Argel (PV172), consistent with the accumulation of delphinidin, petunidin, and malvidin hexosides in their seeds, while catechin glucoside, procyanidin and kaempferol derivatives were predominantly detected in Coscorrón (PV24). Furthermore, while the flavonoid pathway was active in both varieties, our results suggest that enzymes involved in the final steps, such as ANS and UGT, were crucial, inducing anthocyanin formation in Negro Argel. Additionally, during active anthocyanin biosynthesis, the accumulation of reserve proteins or those related to seed protection and germination was induced. These findings provide valuable insights and serve as a guide for plant breeding aimed at enhancing the health and nutritional properties of common beans., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Virus-induced drought tolerance presents a fascinating facet of biotic-abiotic interaction in plants, yet its molecular intricacies remain unclear. Our study shows that cowpea mild mottle virus (CPMMV) infection enhances drought tolerance in common bean (Phaseolus vulgaris) plants through a virus-derived small interfering RNA (vsiRNA)-activated autophagy pathway. Specifically, a 21 nt vsiRNA originating from the CPMMV Triple Gene Block1 (TGB1) gene targeted the 5' untranslated region (UTR) of the host Teosinte branched 1, Cycloidea, Proliferating Cell Factor (TCP) transcription factor gene PvTCP2, independent of the known role of TGB1 as an RNA silencing suppressor. This targeting attenuated the expression of PvTCP2, which encodes a transcriptional repressor, and in turn upregulated the core autophagy-related gene (ATG) PvATG8c, leading to activated autophagy activity surpassing the level induced by drought or CPMMV infection alone. The downstream EARLY RESPONSIVE TO DEHYDRATION (ERD) effector PvERD15 is a homologue of Arabidopsis thaliana AtERD15, which positively regulates stomatal aperture. PvERD15 was degraded in PvATG8c-mediated autophagy. Therefore, we establish a TGB1-PvTCP2-PvATG8c-PvERD15 module as a trans-kingdom fine-tuning mechanism that contributes to virus-induced drought tolerance in plant-drought-virus interactions., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Genetic information of bean seed traits can be an immense help to the breeder in selection of suitable genotypes and the appropriate breeding strategies. Therefore, the investigation aims to assess the genetic variability and to elucidate the genetic analysis of seed dietary fibre, carbohydrate, seed calcium and phosphorus contents of Phaseolus vulgaris in the high Guinean Savannah zone conditions. 5 × 5 half-diallel crosses of these traits were conducted in randomized complete block design with three replications. Results revealed high differences between five lines beans (p < 0.05), suggesting the sufficient genetic diversity for these traits. High broad sense heritability values were recorded for seed dietary fibre, carbohydrate and seed calcium content, attesting a strong implication of the genetic factors in the control of these traits; thereby, these traits can be improved through regular selection. The ratio GCA/SCA was greater than unity only for seed phosphorus content. It indicates the prevalence of additive gene effect in the involvement of the genetic control for this trait. The combining ability analysis revealed highly significant differences between parental GCA effects and F 1 cross SCA effects. The PB, BI, CT and PR lines beans will prove useful in common bean breeding programmes as donor genotypes, in the development of bean genetic resources for betterment improvement of nutritional traits., (© 2024. The Author(s).)

Background: Common bean (Phaseolus vulgaris) is one of the main nutritional resources in the world, and a low environmental impact source of protein. However, the majority of its cultivation areas are affected by drought and this scenario is only expected to worsen with climate change. Stomatal closure is one of the most important plant responses to drought and the MYB60 transcription factor is among the key elements regulating stomatal aperture. If targeting and mutating the MYB60 gene of common bean would be a valuable strategy to establish more drought-tolerant beans was therefore investigated., Results: The MYB60 gene of common bean, with orthology to the Arabidopsis AtMYB60 gene, was found to have conserved regions with MYB60 typical motifs and architecture. Stomata-specific expression of PvMYB60 was further confirmed by q-RT PCR on organs containing stomata, and stomata-enriched leaf fractions. Further, function of PvMYB60 in promoting stomata aperture was confirmed by complementing the defective phenotype of a previously described Arabidopsis myb60-1 mutant., Conclusions: Our study finally points PvMYB60 as a potential target for obtaining more drought-tolerant common beans in the present context of climate change which would further greatly contribute to food security particularly in drought-prone countries., (© 2024. The Author(s).)

The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture., (© 2024. The Author(s).)

Understanding the complex interactions between plants and herbivores is essential for improving crop resistance. Aiming to expand the role of cyanogenesis in plant defence, we investigated the response of the cyanogenic Phaseolus lunatus (lima bean) and the non-cyanogenic Phaseolus vulgaris (common bean) to Tetranychus urticae (spider mite) infestation. Despite mite infesting both legumes, leaf damage infringed by this feeder was reduced in lima bean. Comparative transcriptome analyses revealed that both species exhibited substantial metabolic and transcriptional changes upon infestation, although alterations in P. lunatus were significantly more pronounced. Specific differences in amino acid homeostasis and key genes associated with the cyanogenic pathway were observed in these species, as well as the upregulation of the mandelonitrile lyase gene (PlMNL1) following T. urticae feeding. Concomitantly, the PIMNL1 activity increased. Lima bean plants also displayed an induction of β-cyanoalanine synthase (PlCYSC1), a key enzyme for cyanide detoxification, suggesting an internal regulatory mechanism to manage the toxicity of their defence responses. These findings contribute to our understanding of the legume-herbivore interactions and underscore the potential role of cyanogenesis in the elaboration of specific defensive responses, even within the same genus, which may reflect distinctive evolutionary adaptations or varying metabolic capabilities between species., Competing Interests: Declaration of Competing Interest Cyanogenesis is an efficient plant metabolic process against phytophagous species based on the cyanohydrin production and the release of toxic hydrogen cyanide, but its mechanism is poorly studied in the context of plant-pest interactions. In this work we investigate the underlying factors contributing to the defence response displayed by the cyanogenic Phaseolus lunatus and the non-cyanogenic Phaseolus vulgaris to Tetranychus urticae infestation, and the potential of the cyanogenesis as a strategy of pest control., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The common bean ( Phaseolus vulgaris L.) is an economically important food crop grown worldwide; however, its production is affected by various environmental stresses, including cold, heat, and drought stress. The plant U-box (PUB) protein family participates in various biological processes and stress responses, but the gene function and expression patterns of its members in the common bean remain unclear. Here, we systematically identified 63 U-box genes, including 8 tandem genes and 55 non-tandem genes, in the common bean. These PvPUB genes were unevenly distributed across 11 chromosomes, with chromosome 2 holding the most members of the PUB family, containing 10 PUB genes. The analysis of the phylogenetic tree classified the 63 PUB genes into three groups. Moreover, transcriptome analysis based on cold-tolerant and cold-sensitive varieties identified 4 differentially expressed PvPUB genes, suggesting their roles in cold tolerance. Taken together, this study serves as a valuable resource for exploring the functional aspects of the common bean U-box gene family and offers crucial theoretical support for the development of new cold-tolerant common bean varieties.

Background: Laccase (LAC) gene family plays a pivotal role in plant lignin biosynthesis and adaptation to various stresses. Limited research has been conducted on laccase genes in common beans., Results: 29 LAC gene family members were identified within the common bean genome, distributed unevenly in 9 chromosomes. These members were divided into 6 distinct subclades by phylogenetic analysis. Further phylogenetic analyses and synteny analyses indicated that considerable gene duplication and loss presented throughout the evolution of the laccase gene family. Purified selection was shown to be the major evolutionary force through Ka / Ks. Transcriptional changes of PvLAC genes under low temperature and salt stress were observed, emphasizing the regulatory function of these genes in such conditions. Regulation by abscisic acid and gibberellins appears to be the case for PvLAC3, PvLAC4, PvLAC7, PvLAC13, PvLAC14, PvLAC18, PvLAC23, and PvLAC26, as indicated by hormone induction experiments. Additionally, the regulation of PvLAC3, PvLAC4, PvLAC7, and PvLAC14 in response to nicosulfuron and low-temperature stress were identified by virus-induced gene silence, which demonstrated inhibition on growth and development in common beans., Conclusions: The research provides valuable genetic resources for improving the resistance of common beans to abiotic stresses and enhance the understanding of the functional roles of the LAC gene family., (© 2024. The Author(s).)

Common beans ( Phaseolus vulgaris L.), besides being an important source of nutrients such as iron, magnesium, and protein, are crucial for food security, especially in developing countries. Common bean cultivation areas commonly face production challenges due to drought occurrences, mainly during the reproductive period. Dry spells last approximately 20 days, enough time to compromise production. Hence, it is crucial to understand the genetic and molecular mechanisms that confer drought tolerance to improve common bean cultivars' adaptation to drought. Sixty six RNASeq libraries, generated from tolerant and sensitive cultivars in drought time sourced from the R5 phenological stage at 0 to 20 days of water deficit were sequenced, generated over 1.5 billion reads, that aligned to 62,524 transcripts originating from a reference transcriptome, as well as 6673 transcripts obtained via de novo assembly. Differentially expressed transcripts were functionally annotated, revealing a variety of genes associated with molecular functions such as oxidoreductase and transferase activity, as well as biological processes related to stress response and signaling. The presence of regulatory genes involved in signaling cascades and transcriptional control was also highlighted, for example, LEA proteins and dehydrins associated with dehydration protection, and transcription factors such as WRKY, MYB, and NAC, which modulate plant response to water deficit. Additionally, genes related to membrane and protein protection, as well as water and ion uptake and transport, were identified, including aquaporins, RING-type E3 ubiquitin transferases, antioxidant enzymes such as GSTs and CYPs, and thioredoxins. This study highlights the complexity of plant response to water scarcity, focusing on the functional diversity of the genes involved and their participation in the biological processes essential for plant adaptation to water stress. The identification of regulatory and cell protection genes offers promising prospects for genetic improvement aiming at the production of common bean varieties more resistant to drought. These findings have the potential to drive sustainable agriculture, providing valuable insights to ensure food security in a context of climate change.

MADS-box genes are known to play important roles in diverse aspects of growth/devolopment and stress response in several plant species. However, no study has yet examined about MADS-box genes in P. vulgaris. In this study, a total of 79 PvMADS genes were identified and classified as type I and type II according to the phylogenetic analysis. While both type I and type II PvMADS classes were found to contain the MADS domain, the K domain was found to be present only in type II PvMADS proteins, in agreement with the literature. All chromosomes of the common bean were discovered to contain PvMADS genes and 17 paralogous gene pairs were identified. Only two of them were tandemly duplicated gene pairs (PvMADS-19/PvMADS-23 and PvMADS-20/PvMADS-24), and the remaining 15 paralogous gene pairs were segmentally duplicated genes. These duplications were found to play an important role in the expansion of type II PvMADS genes. Moreover, the RNAseq and RT-qPCR analyses showed the importance of PvMADS genes in response to drought stress in P. vulgaris., (© 2024. The Author(s).)

Common bean provides diet rich in vitamins, fiber, minerals, and protein, which could contribute into food security of needy populations in many countries. Developing genotypes that associate favorable agronomic and grain quality traits in the common bean crop could increase the chances of adopting new cultivars black bean. In this context, the present study aimed at selection of superior black bean lines using multi-variate indexes, Smith-Hazel-index, and genotype by yield*trait biplot analysis. These trials were conducted in Campos dos Goytacazes - RJ, in 2020 and 2021. The experimental design used was randomized blocks, with 28 treatments and three replications. The experimental unit consisted of four rows 4.0 m long, spaced at 0.50 m apart, with a sowing density of 15 seeds per meter. The two central rows were used for the evaluations. The selection of superior genotypes was conducted using the multiple trait stability index (MTSI), multi-trait genotype-ideotype distance index (MGIDI), multi-trait index based on factor analysis and genotype-ideotype distance (FAI-BLUP), Smith-Hazel index, and Genotype by Yield*Trait Biplot (GYT). The multivariate indexes efficiently selected the best black bean genotypes, presenting desirable selection gains for most traits. The use of multivariate indexes and GYT enable the selection of early genotypes with higher grain yields. These lines G9, G13, G17, G23, and G27 were selected based on their performance for multiple traits closest to the ideotype and could be recommended as new varieties., (© 2024. The Author(s).)

Background: Disease can drastically impair common bean (Phaseolus vulgaris L.) production. Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc. and Magnus) Briosi and Cavara, is one of the diseases that are widespread and cause serious economic loss in common bean., Results: Transcriptome analysis of the early response of common bean to anthracnose was performed using two resistant genotypes, Hongyundou and Honghuayundou, and one susceptible genotype, Jingdou. A total of 9,825 differentially expressed genes (DEGs) responding to pathogen infection and anthracnose resistance were identified by differential expression analysis. By using weighted gene coexpression network analysis (WGCNA), 2,051 DEGs were found to be associated with two resistance-related modules. Among them, 463 DEGs related to anthracnose resistance were considered resistance-related candidate genes. Nineteen candidate genes were coexpressed with three resistance genes, Phvul.001G243600, Phvul.001G243700 and Phvul.001G243800. To further identify resistance genes, 46 candidate genes were selected for experimental validation using salicylic acid (SA) and methyl jasmonate (MeJA). The results indicated that 38 candidate genes that responded to SA/MeJA treatment may be involved in anthracnose resistance in common bean., Conclusions: This study identified 38 resistance-related candidate genes involved in the early response of common bean, and 19 resistance-related candidate genes were coexpressed with anthracnose resistance genes. This study identified putative resistance genes for further resistance genetic investigation and provides an important reference for anthracnose resistance breeding in common bean., (© 2024. The Author(s).)

Key Message: Association analysis, colocation study with previously reported QTL, and differential expression analyses allowed the identification of the consistent QTLs and main candidate genes controlling seed traits. Common beans show wide seed variations in shape, size, water uptake, and coat proportion. This study aimed to identify consistent genomic regions and candidate genes involved in the genetic control of seed traits by combining association and differential expression analyses. In total, 298 lines from the Spanish Diversity Panel were genotyped with 4,658 SNP and phenotyped for seven seed traits in three seasons. Thirty-eight significant SNP-trait associations were detected, which were grouped into 23 QTL genomic regions with 1,605 predicted genes. The positions of the five QTL regions associated with seed weight were consistent with previously reported QTL. HCPC analysis using the SNP that tagged these five QTL regions revealed three main clusters with significantly different seed weights. This analysis also separated groups that corresponded well with the two gene pools described: Andean and Mesoamerican. Expression analysis was performed on the seeds of the cultivar 'Xana' in three seed development stages, and 1,992 differentially expressed genes (DEGs) were detected, mainly when comparing the early and late seed development stages (1,934 DEGs). Overall, 91 DEGs related to cell growth, signaling pathways, and transcriptomic factors underlying these 23 QTL were identified. Twenty-two DEGs were located in the five QTL regions associated with seed weight, suggesting that they are the main set of candidate genes controlling this character. The results confirmed that seed weight is the sum of the effects of a complex network of loci, and contributed to the understanding of seed phenotype control., (© 2024. The Author(s).)

The NAC family of transcription factors includes no apical meristem (NAM), Arabidopsis thaliana transcription activator 1/2 (ATAF1/2), and cup-shaped cotyledon (CUC2) proteins, which are unique to plants, contributing significantly to their adaptation to environmental challenges. In the present study, we observed that the PvNAC52 protein is predominantly expressed in the cell membrane, cytoplasm, and nucleus. Overexpression of PvNAC52 in Arabidopsis strengthened plant resilience to salt, alkali, osmotic, and ABA stresses. PvNAC52 significantly ( p < 0.05) reduced the degree of oxidative damage to cell membranes, proline content, and plant water loss by increasing the expression of MSD1 , FSD1 , CSD1 , POD , PRX69 , CAT , and P5CS2 . Moreover, the expression of genes associated with abiotic stress responses, such as SOS1 , P5S1 , RD29A , NCED3 , ABIs , LEAs , and DREBs , was enhanced by PvNAC52 overexpression. A yeast one-hybrid assay showed that PvNAC52 specifically binds to the cis-acting elements ABRE (abscisic acid-responsive elements, ACGTG) within the promoter. This further suggests that PvNAC52 is responsible for the transcriptional modulation of abiotic stress response genes by identifying the core sequence, ACGTG. These findings provide a theoretical foundation for the further analysis of the targeted cis-acting elements and genes downstream of PvNAC52 in the common bean.

This study aimed to investigate the availability of flavonoids, anthocyanins, and phenolic acids in mutant bean seeds, focusing on M 7 mutant lines, and their corresponding initial and local cultivars. HPLC-DAD-MS/MS and HPLC-MS/MS were used to analyze twenty-eight genotypes of common bean. The obtained results suggest that the mutations resulted in four newly synthesized anthocyanins in the mutant bean seeds, namely, delphinidin 3- O -glucoside, cyanidin 3- O -glucoside, pelargonidin 3- O -glucoside, and petunidin 3- O -glucoside, in 20 accessions with colored seed shapes out of the total of 28. Importantly, the initial cultivar with white seeds, as well as the mutant white seeds, did not contain anthocyanins. The mutant lines were classified into groups based on their colors as novel qualitative characteristics. Five phenolic acids were further quantified: ferulic, p -coumaric, caffeic, sinapic, and traces of chlorogenic acids. Flavonoids were represented by epicatechin, quercetin, and luteolin, and their concentrations in the mutant genotypes were several-fold superior compared to those of the initial cultivar. All mutant lines exhibited higher concentrations of phenolic acids and flavonoids. These findings contribute to the understanding of the genetics and biochemistry of phenolic accumulation and anthocyanin production in common bean seeds, which is relevant to health benefits and might have implications for common bean breeding programs and food security efforts.

High-throughput phenotyping brings new opportunities for detailed genebank accessions characterization based on image-processing techniques and data analysis using machine learning algorithms. Our work proposes to improve the characterization processes of bean and peanut accessions in the CIAT genebank through the identification of phenomic descriptors comparable to classical descriptors including methodology integration into the genebank workflow. To cope with these goals morphometrics and colorimetry traits of 14 bean and 16 forage peanut accessions were determined and compared to the classical International Board for Plant Genetic Resources (IBPGR) descriptors. Descriptors discriminating most accessions were identified using a random forest algorithm. The most-valuable classification descriptors for peanuts were 100-seed weight and days to flowering, and for beans, days to flowering and primary seed color. The combination of phenomic and classical descriptors increased the accuracy of the classification of Phaseolus and Arachis accessions. Functional diversity indices are recommended to genebank curators to evaluate phenotypic variability to identify accessions with unique traits or identify accessions that represent the greatest phenotypic variation of the species (functional agrobiodiversity collections). The artificial intelligence algorithms are capable of characterizing accessions which reduces costs generated by additional phenotyping. Even though deep analysis of data requires new skills, associating genetic, morphological and ecogeographic diversity is giving us an opportunity to establish unique functional agrobiodiversity collections with new potential traits., Competing Interests: he authors have declared that no competing interests exist., (Copyright: © 2024 Conejo-Rodríguez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Common bean (Phaseolus vulgaris L.) is one of the most important grain legumes consumed globally, especially in Ethiopia, for its edible seeds, cash crops, and supply of protein for farmers. Efficient statistical methods must be employed for the evaluation of common bean varieties to accurately select superior varieties that contribute to agricultural productivity. The objective of this study was to identify promising large mottled bean varieties through analysis of multi-environment trials (MET) data using multiplicative spatial mixed models. In this study, 16-18 large mottled common bean varieties, including one check, were sown across nine growing environments in Ethiopia using lattice and alpha lattice designs, with three replications laid out in a square or rectangular (row by column) array of plots, respectively during the main cropping season from 2015 to 2018. We present a linear mixed model analysis that integrates spatial and factor analytic (FA) models, and the heritability measure was used to evaluate the efficiency of these models with the conventional analysis. The analysis of the spatial model, and more significantly, the spatial+FA model, revealed a notable enhancement in heritability. With the exception of a trial conducted at Kobo, a genotype DAP 292, found to be good performing for days to flowering and maturity, but for yield only across four clusters of trials, C2, C3, C5 and C7, formed with trials of relatively high genetic variance. Across these clusters, the yield advantage of this variety over the check ranged from 10-32%. This genotype also has a yield that is somewhat comparable to the check across the remaining clusters. Overall, both the spatial and factor analytic models proved to be effective approaches for analyzing the data in this study. The analysis of multi-environment trial data through the use of more efficient statistical models can provide a more robust platform for evaluating common bean varieties with greater confidence in selecting superior varieties across a range of environments. Hence, scaling up the use of this efficient analysis method is indispensable for enhancing the selection of superior varieties., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Argaw et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The GATA transcription factors (TFs) have been extensively studied for its regulatory role in various biological processes in many plant species. The functional and molecular mechanism of GATA TFs in regulating tolerance to abiotic stress has not yet been studied in the common bean. This study analyzed the functional identity of the GATA gene family in the P. vulgaris genome under different abiotic and phytohormonal stress. The GATA gene family was systematically investigated in the P. vulgaris genome, and 31 PvGATA TFs were identified. The study found that 18 out of 31 PvGATA genes had undergone duplication events, emphasizing the role of gene duplication in GATA gene expansion. All the PvGATA genes were classified into four significant subfamilies, with 8, 3, 6, and 13 members in each subfamily (subfamilies I, II, III, and IV), respectively. All PvGATA protein sequences contained a single GATA domain, but subfamily II members had additional domains such as CCT and tify. A total of 799 promoter cis-regulatory elements (CREs) were predicted in the PvGATAs. Additionally, we used qRT-PCR to investigate the expression profiles of five PvGATA genes in the common bean roots under abiotic conditions. The results suggest that PvGATA01/10/25/28 may play crucial roles in regulating plant resistance against salt and drought stress and may be involved in phytohormone-mediated stress signaling pathways. PvGATA28 was selected for overexpression and cloned into N. benthamiana using Agrobacterium-mediated transformation. Transgenic lines were subjected to abiotic stress, and results showed a significant tolerance of transgenic lines to stress conditions compared to wild-type counterparts. The seed germination assay suggested an extended dormancy of transgenic lines compared to wild-type lines. This study provides a comprehensive analysis of the PvGATA gene family, which can serve as a foundation for future research on the function of GATA TFs in abiotic stress tolerance in common bean plants., (© 2024. The Author(s).)

The domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of 281 common bean landraces from Chile was analyzed using a 12K-SNP microarray. Additionally, 401 accessions representing the rest of the five common bean races were analyzed. A total of 2543 SNPs allowed us to differentiate a genetic group of 165 accessions that corresponds to the race Chile, 90 of which were classified as pure accessions, such as the bean types 'Tórtola', 'Sapito', 'Coscorrón', and 'Frutilla'. Our genetic analysis indicates that the race Chile has a close relationship with accessions from Argentina, suggesting that nomadic ancestral peoples introduced the bean seed to Chile. Previous archaeological and genetic studies support this hypothesis. Additionally, the low genetic diversity (π = 0.053; uHe = 0.53) and the negative value of Tajima' D (D = -1.371) indicate that the race Chile suffered a bottleneck and a selective sweep after its introduction, supporting the hypothesis that a small group of Argentine bean genotypes led to the race Chile. A total of 235 genes were identified within haplotype blocks detected exclusively in the race Chile, most of them involved in signal transduction, supporting the hypothesis that intracellular signaling pathways play a fundamental role in the adaptation of organisms to changes in the environment. To date, our findings are the most complete investigation associated with the origin of the race Chile of common bean.

Background: Morphological plasticity is one of the capacities of plants to modify their morphological appearance in response to external stimuli. A plant's morphology and physiology are constantly tuned to its variable surroundings by complex interactions between environmental stimuli and internal signals. In most of plant species,, such phenotypic and physiological expression varies among different varieties based on their levels of particular environmental stress conditions. However, the morphological and yield responses of common bean varieties to different environmental conditions are not well known. The purpose of the study was to evaluate morphological and yield response of common bean to soil moisture stress and to investigate the morphological mechanism by which common bean varieties tolerate fluctuations in moisture stress., Methods: A pot experiment was carried out to investigate the effects of different moisture levels on the phenotypic and yield responses of common bean varieties. A factorial combination of five common bean varieties (Hirna, kufanzik, Awash-1, Ado, and Chercher) and three moisture levels (control, waterlogging stress, and moisture deficit stress) was used in three replications. Moisture stress treatments were started 20 days after planting, at the trifoliate growth stage. To evaluate the response of each variety, morphological and yield data were collected at week intervals., Main Results: The results indicated that moisture levels and varieties had a significant influence on all growth parameters. Crop phenology was significantly influenced by the interaction effect of moisture level and variety. Exposing Hirna variety to moisture stress led to extended flowering and pod setting by 23 and 24 days, respectively, compared to the other treatments. The results showed that the phenotypic responses to moisture deficit and waterlogging stress varied between varieties. Waterlogging stress had a stronger reduction effect on the fresh weight, dry weight and leaf area of common bean varieties than moisture deficit and the control. Pods per plant, seeds per plant, grain yield per plant, and harvest index were significantly influenced by the varieties, moisture stress levels and their interaction. Except for Chercher and Hirna. However, varieties Ado, kufanzik and Awasha-1 did not show significant differences on the time of flower initiation due to moisture level. Biomass and growth in leaf fresh weight, leaf dry weight, leaf area, leaf number and plant height were significantly influenced by moisture level. When moisture deficit and waterlogging stress occurred, Ado and Awash-1 were more responsive to moisture stress than Hirna, Chercher, and Kufanzik., Conclusion: Hence, Hirna and Kufanzik varieties were found to be tolerant because they produced higher yields than the Chercher, Awash-1, and Ado varieties., (© 2024. The Author(s).)

Salinity poses a significant challenge to global crop productivity, affecting approximately 20% of cultivated and 33% of irrigated farmland, and this issue is on the rise. Negative impact of salinity on plant development and metabolism leads to physiological and morphological alterations mainly due to high ion concentration in tissues and the reduced water and nutrients uptake. Common bean (Phaseolus vulgaris L.), a staple food crop accounting for a substantial portion of consumed grain legumes worldwide, is highly susceptible to salt stress resulting in noticeable reduction in dry matter gain in roots and shoots even at low salt concentrations. In this study we screened a common bean panel of diversity encompassing 192 homozygous genotypes for salt tolerance at seedling stage. Phenotypic data were leveraged to identify genomic regions involved in salt stress tolerance in the species through GWAS. We detected seven significant associations between shoot dry weight and SNP markers. The candidate genes, in linkage with the regions associated to salt tolerance or harbouring the detected SNP, showed strong homology with genes known to be involved in salt tolerance in Arabidopsis. Our findings provide valuable insights onto the genetic control of salt tolerance in common bean and represent a first contribution to address the challenge of salinity-induced yield losses in this species and poses the ground to eventually breed salt tolerant common bean varieties., (© 2024. The Author(s).)

Amino acid transporters (AATs) are essential integral membrane proteins that serve multiple roles, such as facilitating the transport of amino acids across cell membranes. They play a crucial role in the growth and development of plants. Phaseolus vulgaris, a significant legume crop, serves as a valuable model for studying root symbiosis. In this study, we have conducted an exploration of the AAT gene family in P. vulgaris. In this research, we identified 84 AAT genes within the P. vulgaris genome sequence and categorized them into 12 subfamilies based on their similarity and phylogenetic relationships with AATs found in Arabidopsis and rice. Interestingly, these AAT genes were not evenly distributed across the chromosomes of P. vulgaris . Instead, there was an unusual concentration of these genes located toward the outer edges of chromosomal arms. Upon conducting motif analysis and gene structural analysis, we observed a consistent presence of similar motifs and an intron-exon distribution pattern among the subfamilies. When we analyzed the expression profiles of PvAAT genes, we noted tissue-specific expression patterns. Furthermore, our investigation into AAT gene expression under rhizobial and mycorrhizal symbiotic conditions revealed that certain genes exhibited high levels of expression. Specifically, ATLa5 and LHT2 was notably upregulated under both symbiotic conditions. These findings point towards a potential role of AATs in the context of rhizobial and mycorrhizal symbiosis in P. vulgaris, in addition to their well-established regulatory functions., (© 2024. The Author(s).)

Bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) have a damaging impact on global common bean (Phaseolus vulgaris L.) cultivation, causing potential yield losses of over 80%. The primary strategy for controlling these viruses is through host plant resistance. This research aimed to identify and validate structural variations for the bc-u d gene as revealed by long-read sequencing, develop an efficient DNA marker to assist selection of bc-u d in snap and dry beans, and examine the interactions between the bc-u d allele and other BCMV resistance genes. A gene (Phvul.005G125100) model on chromosome Pv05, encoding a vacuolar protein-sorting 4 (Vps4) AAA+ ATPase endosomal sorting complexes required for transport (ESCRT) protein, was identified as the best candidate gene for bc-u d . An 84-bp repetitive insertion variant within the gene, exhibited 100% co-segregation with the bc-u d resistance allele across 264 common bean accessions. The 84-bp repetitive insertion was labeled with an indel marker IND&#95;05&#95;36225873 which was useful for tracking the bc-u d allele across diverse germplasm. A different single nucleotide polymorphism variant within the same candidate gene was associated with the bc-4 gene. Segregation in F 2 populations confirmed bc-u d and bc-4 were alleles, so bc-4 was renamed bc-u r to fit gene nomenclature guidelines. The interactions of bc-u d and bc-u r with other resistance genes, such as bc-1 (receptor-like kinase on Pv03) and bc-2 (Vps4 AAA+ ATPase ESCRT protein on Pv11), validated gene combinations in the differential "host groups" effective against specific BCMV/BCMNV "pathogroups." These findings increase our understanding of the Bc-u locus, and enhance our ability to develop more resilient bean varieties through marker-assisted selection, reducing the impact of BCMV and BCMNV., (© 2023 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

The aim of this study was to evaluate the accuracy of the ridge regression best linear unbiased prediction model across different traits, parent population sizes, and breeding strategies when estimating breeding values in common bean (Phaseolus vulgaris). Genomic selection was implemented to make selections within a breeding cycle and compared across five different breeding strategies (single seed descent, mass selection, pedigree method, modified pedigree method, and bulk breeding) following 10 breeding cycles. The model was trained on a simulated population of recombinant inbreds genotyped for 1010 single nucleotide polymorphism markers including 38 known quantitative trait loci identified in the literature. These QTL included 11 for seed yield, eight for white mold disease incidence, and 19 for days to flowering. Simulation results revealed that realized accuracies fluctuate depending on the factors investigated: trait genetic architecture, breeding strategy, and the number of initial parents used to begin the first breeding cycle. Trait architecture and breeding strategy appeared to have a larger impact on accuracy than the initial number of parents. Generally, maximum accuracies (in terms of the correlation between true and estimated breeding value) were consistently achieved under a mass selection strategy, pedigree method, and single seed descent method depending on the simulation parameters being tested. This study also investigated model updating, which involves retraining the prediction model with a new set of genotypes and phenotypes that have a closer relation to the population being tested. While it has been repeatedly shown that model updating generally improves prediction accuracy, it benefited some breeding strategies more than others. For low heritability traits (e.g., yield), conventional phenotype-based selection methods showed consistent rates of genetic gain, but genetic gain under genomic selection reached a plateau after fewer cycles. This plateauing is likely a cause of faster fixation of alleles and a diminishing of genetic variance when selections are made based on estimated breeding value as opposed to phenotype., (© 2024 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Generating transgenic hairy roots has been the preferred strategy for molecular studies in common bean (Phaseolus vulgaris L.), since generating stable knockout lines in this species is challenging. However, the number of plants producing hairy roots following the original protocol published in 2007 is usually low, which has impeded progress. Since its initial publication, the original protocol has been extensively modified, but these modifications have not been adequately or systematically reported, making it difficult to assess the reproducibility of the method. The protocol presented here is an update and expansion of the original method. Importantly, it includes new, critical steps for generating transgenic hairy roots and using them in molecular analyses based on reverse-genetics approaches. Using this protocol, the expression of two different genes, used as an example, was significantly increased or decreased in approximately 30% of the transformed plants. In addition, the promoter activity of a given gene was observed, and the infection process of rhizobia in transgenic hairy roots was monitored successfully. Thus, this improved protocol can be used to upregulate, downregulate, and perform promoter activity analysis of various genes in common bean transgenic hairy roots as well as to track rhizobia infection., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Pacheco et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The effect of plant domestication on plant-microbe interactions remains difficult to prove. In this study, we provide evidence of a domestication effect on the composition and abundance of the plant microbiota. We focused on the genus Phaseolus, which underwent four independent domestication events within two species (P. vulgaris and P. lunatus), providing multiple replicates of a process spanning thousands of years. We targeted Phaseolus seeds to identify a link between domesticated traits and bacterial community composition as Phaseolus seeds have been subject to large and consistent phenotypic changes during these independent domestication events. The seed bacterial communities of representative plant accessions from subpopulations descended from each domestication event were analyzed under controlled and field conditions. The results showed that independent domestication events led to similar seed bacterial community signatures in independently domesticated plant populations, which could be partially explained by selection for common domesticated plant phenotypes. Our results therefore provide evidence of a consistent effect of plant domestication on seed microbial community composition and abundance and offer avenues for applying knowledge of the impact of plant domestication on the plant microbiota to improve microbial applications in agriculture., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Ashy stem blight (ASB) caused by Macrophomina phaseolina (Tassi) Goidanich affects the common bean ( Phaseolus vulgaris L.) at all growing stages. Higher levels of resistance were observed in Andean common beans, but specific resistant quantitative trait loci (QTLs) conferring resistance to this pathogen have not been reported in this gene pool. The objectives of this research were to: (i) conduct a genome-wide association study (GWAS) and QTL mapping for resistance in the Andean breeding line PRA154; and (ii) identify single nucleotide polymorphism (SNP) markers and candidate genes for ASB resistance. Phenotyping was conducted under greenhouse conditions by inoculating the 107 F 6:7 recombinant inbred lines (RILs) derived from the cross between the susceptible cultivar 'Verano' and the partial-resistant breeding line PRA154 twice with the M. phaseolina isolate PRI21. Genotyping was performed with 109,040 SNPs distributed across all 11 P. vulgaris chromosomes. A novel major QTL was located between 28,761,668 and 31,263,845 bp, extending 2.5 Mbp on chromosome Pv 07, and the highest significant SNP markers were Chr07&#95;28761668&#95;A&#95;G, Chr07&#95;29131720&#95;G&#95;A, and Chr07&#95;31263845&#95;C&#95;T with the highest LOD (more than 10 in most of the cases) and R-squared values, explaining 40% of the phenotypic variance of the PRI21 isolate. The gene Phvul.007G173900 (methylcrotonyl-CoA carboxylase alpha chain and mitochondrial 3-methylcrotonyl-CoA carboxylase 1 [MCCA]) with a size of 10,891 bp, located between 29,131,591 and 29,142,481 bp on Pv 07, was identified as one candidate for ASB resistance in PRA154, and it contained Chr07&#95;29131720&#95;G&#95;A. The QTL and genetic marker information could be used to assist common bean breeders to develop germplasm and cultivars with ASB resistance through molecular breeding., Competing Interests: The author(s) declare no conflict of interest.

Background: The common bean (Phaseolus vulgaris) has become the food of choice owing to its wealthy nutritional profile, leading to a considerable increase in its cultivation worldwide. However, anthracnose has been a major impediment to production and productivity, as elite bean cultivars are vulnerable to this disease. To overcome barriers in crop production, scientists worldwide are working towards enhancing the genetic diversity of crops. One way to achieve this is by introducing novel genes from related crops, including landraces like KRC 8. This particular landrace, found in the North Western Himalayan region, has shown adult plant resistance against anthracnose and also possesses a recessive resistance gene., Methods and Results: In this study, a population of 179 F 2:9 RIL individuals (Jawala × KRC 8) was evaluated at both phenotypic and genotypic levels using over 830 diverse molecular markers to map the resistance gene present in KRC 8. We have successfully mapped a resistance gene to chromosome Pv01 using four SSR markers, namely IAC 238, IAC 235, IAC 259, and BM 146. The marker IAC 238 is closely linked to the gene with a distance of 0.29 cM, while the other markers flank the recessive resistance gene at 10.87 cM (IAC 259), 17.80 cM (BM 146), and 25.22 cM (IAC 235). Previously, a single recessive anthracnose resistance gene (co-8) has been reported in the common bean accession AB 136. However, when we performed PCR amplification with our tightly linked marker IAC 238, we got different amplicons in AB 136 and KRC 8. Interestingly, the susceptible cultivar Jawala produced the same amplicon as AB 136. This observation indicated that the recessive gene present in KRC 8 is different from co-8. As the gene is located far away from the Co-1 locus, we suggest naming the recessive gene co-Indb/co-19. Fine mapping of co-Indb in KRC 8 may provide new insights into the cloning and characterization of this recessive gene so that it can be incorporated into future bean improvement programs. Further, the tightly linked marker IAC 238 can be utilized in marker assisted introgression in future bean breeding programs., Conclusion: The novel co-Indb gene present in Himalayan landrace KRC 8, showing adult plant resistance against common bean anthracnose, is independent from all the resistance genes previously located on chromosome Pv01., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Key Message: Mapping and fine mapping of bean anthracnose resistance genes is a continuous process. We report fine mapping of anthracnose resistance gene Co-18 which is the first anthracnose gene mapped to Pv10. The discovery of resistance gene is a major gain in the bean anthracnose pathosystem research. Among the Indian common bean landraces, KRC-5 exhibit high levels of resistance to the bean anthracnose pathogen Colletotrichum lindemuthianum. To precisely map the anthracnose resistance gene, we used a Recombinant Inbred Line (F 2:9 RIL) population (KRC-5 × Jawala). The inheritance test revealed that KRC-5 carries a dominant resistance gene temporarily designated as Co-18. We discovered two RAPD markers linked to Co-18 among 287 RAPD markers. These RAPD markers were eventually developed into SCARs (Sc-OPR15 and Sc-OPF6) and flank Co-18 on chromosome Pv10 at a distance of 5.3 and 4.2 cM, respectively. At 4.0-4.1 Mb on Pv10, we detected a SNP (single-nucleotide polymorphism) signal. We synthesized 58 SSRs and 83 InDels from a pool of 135 SSRs and 1134 InDels, respectively. Five SSRs, four InDels, and two SCARs were used to generate the high-density linkage map, which led to the identification of two SSRs (SSR24 and SSR36) that are tightly linked to Co-18. These two SSRs flank the Co-18 to 178 kb genomic region with 13 candidate genes including five NLR (nucleotide-binding and leucine-rich repeat) genes. The closely linked markers SSR24 and SSR36 will be used in cloning and pyramiding of the Co-18 gene with other R genes to develop durable resistant bean varieties., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Melatonin plays important roles in multiple stress responses; however, the downstream signaling pathway and molecular mechanism remain unclear. This study aimed to elucidate the transcriptional regulation of melatonin-induced salt stress tolerance in Phaseolus vulgaris L. and identify the key downstream transcription factors of melatonin through transcriptomic and metabolomic analyses. The melatonin-induced transcriptional network of hormones, transcription factors, and functional genes was established under both control and stress conditions. Among these, eight candidate transcription factors were identified via gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, one gene related to transmembrane transport of salts (Phvul.004G177300). These genes may play a role in maintaining the cell structure and excreting sodium ions outside the cell or transporting them to the vacuoles for storage. Melatonin regulates the Phvul.009G210332 gene and metabolites C05642 (N-acetyl-N-2-formyl-5-methoxycanurine), C05643 (6-hydroxymelatonin), C05660 (5-methoxyindoleacetic acid) involved in tryptophan metabolism. The metabolites C05642 and C05643 were identified as decomposition products of tryptophan, indicating that exogenous melatonin entered the P. vulgaris tissue and was metabolized. Melatonin promotes the synthesis and metabolism of tryptophan, which is crucial to plant metabolism, growth, maintenance, and repair., (© 2024. The Author(s).)

Key Message: Inversions and translocations are the major chromosomal rearrangements involved in Vigna subgenera evolution, being Vigna vexillata the most divergent species. Centromeric repositioning seems to be frequent within the genus. Oligonucleotide-based fluorescence in situ hybridization (Oligo-FISH) provides a powerful chromosome identification system for inferring plant chromosomal evolution. Aiming to understand macrosynteny, chromosomal diversity, and the evolution of bean species from five Vigna subgenera, we constructed cytogenetic maps for eight taxa using oligo-FISH-based chromosome identification. We used oligopainting probes from chromosomes 2 and 3 of Phaseolus vulgaris L. and two barcode probes designed from V. unguiculata (L.) Walp. genome. Additionally, we analyzed genomic blocks among the Ancestral Phaseoleae Karyotype (APK), two V. unguiculata subspecies (V. subg. Vigna), and V. angularis (Willd.) Ohwi & Ohashi (V. subg. Ceratotropis). We observed macrosynteny for chromosomes 2, 3, 4, 6, 7, 8, 9, and 10 in all investigated taxa except for V. vexillata (L.) A. Rich (V. subg. Plectrotropis), in which only chromosomes 4, 7, and 9 were unambiguously identified. Collinearity breaks involved with chromosomes 2 and 3 were revealed. We identified minor differences in the painting pattern among the subgenera, in addition to multiple intra- and interblock inversions and intrachromosomal translocations. Other rearrangements included a pericentric inversion in chromosome 4 (V. subg. Vigna), a reciprocal translocation between chromosomes 1 and 5 (V. subg. Ceratotropis), a potential deletion in chromosome 11 of V. radiata (L.) Wilczek, as well as multiple intrablock inversions and centromere repositioning via genomic blocks. Our study allowed the visualization of karyotypic patterns in each subgenus, revealing important information for understanding intrageneric karyotypic evolution, and suggesting V. vexillata as the most karyotypically divergent species., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Bean common mosaic virus (BCMV) was detected on common bean ( Phaseolus vulgaris ) plants showing wrinkled and/or narrow leaves, curling, shrinking and chlorosis of leaves, dwarfing of plants, and mottled pods in Inner Mongolia and named BCMV-22Huhe. Its genome has a size of 10,062 bp and was deposited in GenBank under the accession number OR778613. It is closely related to BCMV-Az (GenBank accession no. KP903372, in China) in the lineage of AzBMV. A recombination event was detected for BCMV-22Huhe among the 99 BCMV isolates published in the NCBI GenBank database, showing that BCMV-CJ25 (MK069986, found in Mexico) was a potential major parent, and the minor parent is unknown. This work is the first description of the occurrence of BCMV in Inner Mongolia, China.

This study identified proteomic changes in the seeds of two tolerant (SB-DT3 and SB-DT2) and two sensitive (Merlot and Stampede) common bean genotypes in response to terminal drought stress. Differentially expressed proteins (DEPs) were abundant in the susceptible genotype compared to the tolerant line. DEPs associated with starch biosynthesis, protein-chromophore linkage, and photosynthesis were identified in both genotypes, while a few DEPs and enriched biological pathways exhibited genotype-specific differences. The tolerant genotypes uniquely showed DEPs related to sugar metabolism and plant signaling, while the sensitive genotypes displayed more DEPs involved in plant-pathogen interaction, proteasome function, and carbohydrate metabolism. DEPs linked with chaperone and signal transduction were significantly altered between both genotypes. In summary, our proteomic analysis revealed both conserved and genotype-specific DEPs that could be used as targets in selective breeding and developing drought-tolerant common bean genotypes.

The mechanisms underlying susceptibility to and defense against Pseudomonas syringae (Pph) of the common bean (Phaseolus vulgaris) have not yet been clarified. To investigate these, 15-day-old plants of the variety Riñón were infected with Pph and the transcriptomic changes at 2 h and 9 h post-infection were analysed. RNA-seq analysis showed an up-regulation of genes involved in defense/signaling at 2 h, most of them being down-regulated at 9 h, suggesting that Pph inhibits the transcriptomic reprogramming of the plant. This trend was also observed in the modulation of 101 cell wall-related genes. Cell wall composition changes at early stages of Pph infection were associated with homogalacturonan methylation and the formation of egg boxes. Among the cell wall genes modulated, a pectin methylesterase inhibitor 3 (PvPMEI3) gene, closely related to AtPMEI3, was detected. PvPMEI3 protein was located in the apoplast and its pectin methylesterase inhibitory activity was demonstrated. PvPMEI3 seems to be a good candidate to play a key role in Pph infection, which was supported by analysis of an Arabidopsis pmei3 mutant, which showed susceptibility to Pph, in contrast to resistant Arabidopsis Col-0 plants. These results indicate a key role of the degree of pectin methylesterification in host resistance to Pph during the first steps of the attack., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Color can be an indicator of plant health, quality, and productivity, and is useful to researchers to understand plant nutritional content in their studies. Color may be related to chlorophyll content and photosynthetic activity and provides information for those studying diseases and mineral nutrition because every nutrient deficiency and many diseases produce symptoms that affect color. In order to identify significant loci related to both leaf and pod color in a snap bean ( Phaseolus vulgaris L.) diversity panel, a genome-wide association study (GWAS) was carried out. Leaf color in one and pod traits in multiple environments were characterized using a colorimeter. L*a*b* color data were recorded and used to calculate chroma (C*) and hue angle (H°). Leaves were evaluated at three positions (lower, middle, and upper) in the canopy and both pod exterior and interior colors were obtained. GWAS was conducted using two reference genomes that represent the Andean (G19833) and Middle American (5-593) domestication centers. Narrow sense heritabilities were calculated using the mixed linear model (MLM) method in genome association and prediction integrated tool (GAPIT), and significant single nucleotide polymorphisms (SNPs) for each color parameter were obtained using the Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) GWAS model with two principal components (PCAs). In comparison to pod color traits, narrow sense heritabilities of leaf traits were low and similar for both reference genomes. Generally, narrow sense heritability for all traits was highest in the lower, followed by middle, and then upper leaf positions. Heritability for both pod interior and exterior color traits was higher using the G19833 reference genome compared to 5-593 when evaluated by year and means across years. Forty-five significant SNPs associated with leaf traits and 872 associated with pods, totaling 917 significant SNPs were identified. Only one SNP was found in common for both leaf and pod traits on Pv03 in the 5-593 reference genome. One-hundred thirteen significant SNPs, 30 in leaves and 83 in pods had phenotypic variation explained (PVE) of 10% or greater. Fourteen SNPs (four from G19833 and ten from 5-593) with ≥10 PVE%, large SNP effect, and largest p -value for L* and H° pod exterior was identified on Pv01, Pv02, Pv03, and Pv08. More SNPs were associated with pod traits than with leaf traits. The pod interior did not exhibit colors produced by anthocyanins or flavonols which allowed the differentiation of potential candidate genes associated with chloroplast and photosynthetic activity compared to the pod exterior where candidate genes related to both flavonoids and photosynthesis affected color. Several SNPs were associated with known qualitative genes including the wax pod locus ( y ), persistent color ( pc ), purple pods ( V ), and two genes expressed in seeds but not previously reported to affect other plant tissues ( B and J ). An evaluation of significant SNPs within annotated genes found a number, within a 200 kb window, involved in both flavonoid and photosynthetic biosynthetic pathways.

Common bean (Phaseolus vulgaris L.) is a major legume crop worldwide, but its growth and development frequently face challenges due to abiotic stresses, particularly drought. Proper supplement of copper could mitigate the adverse effects of drought, but excessive accumulation of this metal in plants can be harmful. The suppressor of MAX2 1-like (SMXL) gene family, which plays important roles in various plant processes, including stress responses, remains poorly understood in common bean. In this study, we identified nine orthologues of SMXL genes in common bean, which are located on six chromosomes and classified into four subgroups. Basic molecular properties, including theoretical isoelectric point (PI), molecular weight (MW), grand average of hydropathicity (GVIO), gene structure, and conserved motifs were characterized, and numerous cis-elements in promoters were predicted. The expression patterns of PvSMXL genes were found to be distinct under 10% polyethylene glycol (PEG)-induced drought stress and 200 μM Cu treatments. Most PvSMXLs showed reduced expression in response to Cu treatment, whereas nearly half PvSMXLs exhibited inducible expression under drought stress. PvSMXL2, which exhibited a rapid response to karrikin 1 (KAR 1 ), an active form of the plant growth regulators newly found in the smoke of burning plant material, was down-regulated by both PEG-induced drought and Cu stresses. Transient silencing of PvSMXL2 resulted in enhanced drought stress tolerance without conferring Cu tolerance. These findings provide valuable insights into the functions of SMXL genes in common bean under abiotic stress conditions., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

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., Competing Interests: No The authors have declared that no competing interests exist., (Copyright: © 2023 Mwale et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Key Message: R-BPMV is located within a recently expanded TNL cluster in the Phaseolus genus with suppressed recombination and known for resistance to multiple pathogens including potyviruses controlled by the I gene. Bean pod mottle virus (BPMV) is a comovirus that infects common bean and legumes in general. BPMV is distributed throughout the world and is a major threat on soybean, a closely related species of common bean. In common bean, BAT93 was reported to carry the R-BPMV resistance gene conferring resistance to BPMV and linked with the I resistance gene. To fine map R-BPMV, 182 recombinant inbred lines (RILs) derived from the cross BAT93 × JaloEEP558 were genotyped with polymerase chain reaction (PCR)-based markers developed using genome assemblies from G19833 and BAT93, as well as BAT93 BAC clone sequences. Analysis of RILs carrying key recombination events positioned R-BPMV to a target region containing at least 16 TIR-NB-LRR (TNL) sequences in BAT93. Because the I cluster presents a suppression of recombination and a large number of repeated sequences, none of the 16 TNLs could be excluded as R-BPMV candidate gene. The evolutionary history of the TNLs for the I cluster were reconstructed using microsynteny and phylogenetic analyses within the legume family. A single I TNL was present in Medicago truncatula and lost in soybean, mirroring the absence of complete BPMV resistance in soybean. Amplification of TNLs in the I cluster predates the divergence of the Phaseolus species, in agreement with the emergence of R-BPMV before the separation of the common bean wild centers of diversity. This analysis provides PCR-based markers useful in marker-assisted selection (MAS) and laid the foundation for cloning of R-BPMV resistance gene in order to transfer the resistance into soybean., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Key Message: QTL mapping, association analysis, and colocation study with previously reported QTL revealed three main regions controlling pod morphological traits and two loci for edible pod characteristics on the common bean chromosomes Pv01 and Pv06. Bean pod phenotype is a complex characteristic defined by the combination of different traits that determine the potential use of a genotype as a snap bean. In this study, the TUM RIL population derived from a cross between 'TU' (dry) and 'Musica' (snap) was used to investigate the genetic control of pod phenotype. The character was dissected into pod morphological traits (PMTs) and edible pod characteristics (EPC). The results revealed 35 QTL for PMTs located on seven chromosomes, suggesting a strong QTL colocation on chromosomes Pv01 and Pv06. Some QTL were colocated with previously reported QTL, leading to the mapping of 15 consensus regions associated with bean PMTs. Analysis of EPC of cooked beans revealed that two major loci with epistatic effect, located on chromosomes Pv01 and Pv06, are involved in the genetic control of this trait. An association study using a subset of the Spanish Diversity Panel (snap vs. non-snap) detected 23 genomic regions, with three regions being mapped at a position similar to those of two loci identified in the TUM population. The results demonstrated the relevant roles of Pv01 and Pv06 in the modulation of bean pod phenotype. Gene ontology enrichment analysis revealed a significant overrepresentation of genes regulating the phenylpropanoid metabolic process and auxin response in regions associated with PMTs and EPC, respectively. Both biological functions converged in the lignin biosynthetic pathway, suggesting the key role of the pathway in the genetic control of bean pod phenotype., (© 2023. The Author(s).)

Common bean (Phaseolus vulgaris) is one of the legume crops most consumed worldwide and bean rust is one of the most severe foliar biotrophic fungal diseases impacting its production. In this work, we searched for new sources of rust resistance (Uromyces appendiculatus) in a representative collection of the Portuguese germplasm, known to have accessions with an admixed genetic background between Mesoamerican and Andean gene pools. We identified six accessions with incomplete hypersensitive resistance and 20 partially resistant accessions of Andean, Mesoamerican, and admixed origin. We detected 11 disease severity-associated single-nucleotide polymorphisms (SNPs) using a genome-wide association approach. Six of the associations were related to partial (incomplete non-hypersensitive) resistance and five to incomplete hypersensitive resistance, and the proportion of variance explained by each association varied from 4.7 to 25.2%. Bean rust severity values ranged from 0.2 to 49.1% and all the infection types were identified, reflecting the diversity of resistance mechanisms deployed by the Portuguese germplasm.The associations with U. appendiculatus partial resistance were located in chromosome Pv08, and with incomplete hypersensitive resistance in chromosomes Pv06, Pv07, and Pv08, suggesting an oligogenic inheritance of both types of resistance. A resolution to the gene level was achieved for eight of the associations. The candidate genes proposed included several resistance-associated enzymes, namely β-amylase 7, acyl-CoA thioesterase, protein kinase, and aspartyl protease. Both SNPs and candidate genes here identified constitute promising genomics targets to develop functional molecular tools to support bean rust resistance precision breeding., (© 2023. The Author(s).)

Iron and zinc deficiencies are the most prevalent cause of global hidden hunger. Rice, being one of the most consumed crops worldwide, is suitable to target for Fe and Zn biofortification. In present study, we generated rice transgenic lines to meet the recommended dietary requirement of iron and zinc through endosperm specific expression of dicot (kidney bean) and monocot (pearl millet) Ferritins along with constitutive expression of rice nicotianamine synthase 2 (OsNAS2) gene. Visualization through perls' prussian staining and quantification by ICP-MS showed significant improvement in grain iron content in all the transgenic lines. The transgenic lines expressing any of the three selected gene combinations (PvFerrtin-OsNAS2, feedPgFerrtin-OsNAS2 and foodPgFerritin-OsNAS2), showed the potential to surpass the 30% of the estimated average requirement (13 μg/g Fe and 28 μg/g Zn) proposed for rice in HarvestPlus breeding program. Though the expression of PvFerritin along with OsNAS2 gene in IET10364 (indica) variety showed the best result, providing up to 4.2- and 3.5-fold increase in iron (30.56 μg/g) and zinc (60.1 μg/g) content, respectively; in polished grains compared to non-transgenic control. Thus, the lines developed in our study can be used for further breeding purpose to enhance the iron and zinc content in commercial rice varieties., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Background: High-Affinity Potassium ions represent one of the most important and large group of potassium transporters. Although HAK genes have been studied in a variety of plant species, yet, remain unexplored in common bean., Results: In the current study, 20 HAK genes were identified in common bean genome. Super-family "K&#95;trans" domain was found in all PvHAK genes. Signals for localization of PvHAK proteins were detected in cell membrane. Fifty three HAKs genes, across diverse plant species, were divided into 5 groups based on sequential homology. Twelve pairs of orthologs genes were found in various plant species. PvHAKs genes were distributed unequally on 7 chromosomes with maximum number (7) mapped on chromosome 2 while only 1 PvHAK found on each chromosome 1, 4, and 6. Tandem gene duplication was witnessed in 2 paralog pairs while 1 pair exhibited segmental gene duplication. Five groups were made in PvHAK gene family based on Phylogeny. Maximum PvHAKs (10) were detected in Group-V while group-II composed of only 1 PvHAK gene. Variation was witnessed in number and size of motifs, and structure of PvHAKs associated with different groups. Light and hormone responsive elements contributed 57 and 24% share, respectively, to cis regulatory elements. qRT-PCR based results revealed significant increase in expression of all 4 PvHAK genes under low-potassium stress., Conclusion: The current study provides valuable information for further functional characterization and uncovering the molecular mechanism associated with Potassium transportation in plants., (© 2023. The Author(s).)

Anthracnose caused by Colletotrichum lindemuthianum is a major disease of common bean (Phaseolus vulgaris) worldwide. Yellow beans are a major market class of common bean especially in eastern and southern Africa. The Yellow Bean Collection (YBC), which is comprised of 255 genotypes, and has not been used previously in genetic studies on anthracnose, is an excellent genetic resource for understanding the extent of anthracnose resistance and its genetic architecture in the yellow bean market class. The objectives of this study were i) evaluate the YBC for resistance to races 5, 19, 39, 51, 81, 183, 1050 and 1105 of C. lindemuthianum. and ii) conduct genome-wide association analysis to identify genomic regions and candidate genes associated with resistance to C. lindemuthianum. The YBC was genotyped with 72,866 SNPs, and genome-wide association analysis was conducted using Mixed Linear Model in TASSEL. Andean and Middle American genotypes with superior levels of resistance to the eight races were identified. YBC278 was the only one among 255 genotypes that was highly resistant to all eight races. Resistance to anthracnose in the YBC was controlled by major-effect loci on chromosomes Pv01, Pv03, Pv04, Pv05 and Pv07. The genomic region on Pv01, which overlapped with the Andean locus Co-1 provided resistance to races 81, 1050 and 1105. Significant SNPs for resistance to race 39 were identified on Pv02. The genomic region on Pv04, which overlapped with known major-effect loci Co-3, Co-15, Co-16, Co-y and Co-z, provided resistance to races 5, 19, 51 and 183. Novel genomic regions for resistance to race 39 were identified on Pv05 and Pv07. Plant resistance genes (R genes) with NB-ARC and LRR domains, which occurred in clusters, were identified as positional candidate genes for genomic regions on Pv02 and Pv04., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Anthracnose (ANT) and angular leaf spot (ALS) are significant diseases in common bean, leading to considerable yield losses under specific environmental conditions. The California Dark Red Kidney (CDRK) bean cultivar is known for its resistance to multiple races of both pathogens. Previous studies have identified the CoPv01 CDRK /PhgPv01 CDRK resistance loci on chromosome Pv01. Here, we evaluated the expression levels of ten candidate genes near the CoPv01 CDRK /PhgPv01 CDRK loci and plant defense genes using quantitative real-time PCR in CDRK cultivar inoculated with races 73 of Colletotrichum lindemuthianum and 63-39 of Pseudocercospora griseola . Gene expression analysis revealed that the Phvul.001G246300 gene exhibited the most elevated levels, showing remarkable 7.8-fold and 8.5-fold increases for ANT and ALS, respectively. The Phvul.001G246300 gene encodes an abscisic acid (ABA) receptor with pyrabactin resistance, PYR1-like (PYL) protein, which plays a central role in the crosstalk between ABA and jasmonic acid responses. Interestingly, our results also showed that the other defense genes were initially activated. These findings provide critical insights into the molecular mechanisms underlying plant defense against these diseases and could contribute to the development of more effective disease management strategies in the future.

The common bean ( Phaseolus vulgaris L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. phaseoli ( Fop ), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for Fop race 1 and race 4 were matched with genotypic data from 4740 SNPs of BARCBean6K&#95;3 Infinium Bea Chips. After ranking the 157-accession panel and revealing 21 Fusarium wilt-resistant accessions, the GWAS pinpointed 16 SNPs on chromosomes Pv04, Pv05, Pv07, Pv8, and Pv09 linked to Fop race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with Fop race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both Fop race 1 and race 4 resistances. Furthermore, within a 30 kb flanking region of these associated SNPs, a total of 17 candidate genes were identified. Some of these genes were annotated as classical disease resistance protein/enzymes, including NB-ARC domain proteins, Leucine-rich repeat protein kinase family proteins, zinc finger family proteins, P-loopcontaining nucleoside triphosphate hydrolase superfamily, etc. Genomic prediction (GP) accuracy for Fop race resistances ranged from 0.26 to 0.55. This study advanced common bean genetic enhancement through marker-assisted selection (MAS) and genomic selection (GS) strategies, paving the way for improved Fop resistance.

Key Message: Quantitative Trait Loci "hotspots" for drought tolerance were identified on chromosomes Pv06, Pv07 and Pv10 of common bean. Drought is a major production constraint of common bean (Phaseolus vulgaris L.) worldwide. The objective of this study was to identify the Quantitative Trait Loci (QTL) for drought tolerance in an Andean population of Recombinant Inbred Lines (RILs). A total of 155 F 5:7 RILs derived from a cross between Kijivu (drought tolerant) and Bukoba (drought susceptible) were evaluated for drought tolerance in field and pot experiments. Four field experiments were conducted at three locations in Zambia in 2020 and 2021. All field trials were conducted in the dry season under irrigation. The 155 RILs were genotyped with 11,292 SNPs, and composite interval mapping was conducted to identify QTL for drought tolerance. Seed yield for Kijivu under drought stress was consistently higher than for Bukoba across all four field trials. A total of 60 QTL were identified for morphological, agronomic, and physiological traits under drought stress and non-stress conditions. However, the majority of these QTL were specific to drought stress. QTL "hotspots" for drought tolerance were identified on chromosomes Pv06, Pv07, and Pv10. Extensive co-localizations for agronomic and morpho-physiological traits under drought stress were observed at the three drought-tolerance QTL hotspots. Additionally, these three QTL hotspots overlapped with previously identified QTL for drought tolerance, while several others identified QTL are novel. The three identified QTL hotspots could be used in future marker-assisted selection for drought tolerance in common bean., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

In most legumes, the rhizobial symbionts exhibit diversity across different environments. Although common bean (Phaseolus vulgaris L.) is one of the important legumes in southern Africa, there is no available information on the genetic diversity and N 2 -fixing effectiveness of its symbionts in Malkerns, Eswatini. In this study, we assessed the phylogenetic positions of rhizobial microsymbionts of common bean from Malkerns in Eswatini. The isolates obtained showed differences in morpho-physiology and N 2 -fixing efficiency. A dendrogram constructed from the ERIC-PCR banding patterns, grouped a total of 88 tested isolates into 80 ERIC-PCR types if considered at a 70% similarity cut-off point. Multilocus sequence analysis using 16S rRNA, rpoB, dnaK, gyrB, and glnII and symbiotic (nifH and nodC) gene sequences closely aligned the test isolates to the type strains of Rhizobium muluonense, R. paranaense, R. pusense, R. phaseoli and R. etli. Subjecting the isolates in this study to further description can potentially reveal novel species. Most of the isolates tested were efficient in fixing nitrogen and elicited greater stomatal conductance and photosynthetic rates in the common bean. Relative effectiveness (RE) varied from 18 to 433%, with 75 (85%) out of the 88 tested isolates being more effective than the nitrate fed control plants., (© 2023. Springer Nature Limited.)