Bean Genome Research Articles

Chromosome-scale assembly of the African yam bean genome

Genomics-informed breeding of locally adapted, nutritious, albeit underutilised African crops can help mitigate food and nutrition insecurity challenges in Africa, particularly against the backdrop of climate change. However, utilisation of modern genome-assisted crop improvement tools including genomic selection and genome editing for many African indigenous crops is hampered by the scarcity of genomic resources. Here we report on the assembly of the genome of African yam bean (Sphenostylis stenocarpa), a tuberous legume crop that is indigenous to Africa. By combining Nanopore-based assembly with Hi-C scaffolding, we produced a high-quality chromosome-scale assembly with an N50 of 69.5 Mbp. Using transcriptome evidence from Nanopore RNASeq and protein homology evidence from related crops, we predicted and annotated 31,614 putative protein coding genes. We also show how this genome substantially improves anchoring of genetic markers from African yam bean, confirming its significance as a resource for genetic research in African yam bean.

Predicting the role of β-GAL genes in bean under abiotic stress and genome-wide characterization of β-GAL gene family members.

Β-Gals are a subgroup of the glycoside hydrolase (GH) family of enzymes, which possess the Glyco_hydro_35 (GH35) domain. Although studies have been conducted on the β-Gal gene family in numerous plant species, no such research has been conducted on beans. The purpose of this study was to determine the gene expression levels of β-Gal genes in the leaf tissue of P. vulgaris under salt and drought stress using quantitative real-time polymerase chain reaction (qRT-PCR) and to perform a comprehensive analysis of β-Gal gene family members using bioinformatics tools. In the bean genome, 25 Pvul-βGAL proteins with amino acid numbers ranging from 291 to 1119, molecular weights from 32.94 to 126.56kDa, and isoelectric points from 5.46 to 9.08 were identified. Both segmental and tandem duplication have occurred in β-Gal genes in the bean genome, and Pvul-BGAL genes have been subject to negative selection in the evolutionary process. For a deeper comprehension of the evolutionary proximity of Pvul-BGAL genes, a phylogenetic tree and synteny map were drawn together with Arabidopsis thaliana and Glycine max β-Gal genes. The expression profiles of β-Gal genes in different tissues of the bean were determined in silico. In addition, the expression profiles of β-Gal genes in the leaves of bean plants subjected to drought and salt stress were analyzed, and the role of β-Gal genes in salt and drought stress was estimated. In this study, the role of β-Gal gene family in abiotic stress response and the characterization of β-Gal genes in beans were determined for the first time and will provide a basis for future functional genomics studies.

The Jan Sjödin faba bean mutant collection: morphological and molecular characterization.

Plant mutagenesis creates novel alleles, thereby increasing genetic and phenotypic diversity. The availability of the faba bean (Vicia faba L.) reference genome and a growing set of additional genomic resources has increased the scientific and practical value of mutant collections. We aimed to genotype and morphologically phenotype a historical faba bean mutant collection developed and characterized by Jan Sjödin (1934-2023) over half a century ago in order to increase its value to researchers. The collection was genotyped using high-throughput single-primer enrichment technology (SPET) assays. We used 11,073 informative single nucleotide polymorphism (SNP) markers spanning the faba bean genome to genotype 52 mutant lines along with the background line, cv. Primus. A range of flower, seed, leaf, and stipule mutations were observed. The analysis of population structure revealed a shallow structure with no major subpopulations. Principal component and cluster analyses revealed, to a minor extent, that the mutants clustered by their phenotype. The mutants' phenotypic variation and shallow structure indicate that the Sjödin faba bean collection has the potential to play a significant role in faba bean breeding and in genetic and functional studies.

Exploring common bean's defense arsenal: Genome-wide characterization of PR-1 gene family and its transcriptional response to Colletotrichum lindemuthianum inoculation

Pathogenesis-related Protein 1 (PR-1) plays a crucial role in plant defense responses, particularly against fungal pathogens. Despite its significance, comprehensive studies characterizing this gene family in the common bean (Phaseolus vulgaris) are currently lacking. Therefore, the objective of this study was to conduct genomic mining and characterization of the PR-1 in common bean (PvPR-1) genome. Additionally, we assessed the transcriptional expression of all its isoforms in response to inoculation with the fungus Colletotrichum lindemuthianum. This evaluation was performed on leaf tissue samples obtained from both sensitive (Rosinha) and resistant (Africano 4) common bean varieties at 24-, 48-, and 96-hours post inoculation. Thirteen PvPR-1 genes were consistently identified, forming two major clusters across the clustering analyses. Physicochemical characterization indicated that the PvPR-1 proteins are predominantly basic, hydrophilic, and extracellularly localized. Moreover, their promoter regions contain putative cis-regulatory elements that respond to a broad spectrum of plant hormones, including jasmonic acid, gibberellin, and ethylene, which are key regulators of both biotic and abiotic stress responses. This discovery implies a multifaceted role for the studied proteins in common bean physiology. KEGG pathway analysis implicated PvPR-1 proteins in hormonal signaling (corroborating the anchored cis-regulatory elements) and plant-pathogen interaction networks. Secondary structure evaluation revealed the predominance of α-helices and coiled structures within these proteins. Subsequent 3D modeling demonstrated a conserved ‘α-β-α’ sandwich architecture characterized by a central cavity. This structural motif suggests potential functional versatility, particularly in pathogen recognition and responses. Additionally, the study provided insight into the potential interactions of PvPR-1 with Chitinase II (PR-3) and Rab-18, as suggested by the STRING platform. Temporal differences in PvPR-1 gene expression were observed between the common bean contrasting varieties following C. lindemuthianum inoculation. Africano-4, the resistant one, showed a higher abundance of up-regulated and constitutively expressed PvPR-1 transcripts compared to its sensitive counterpart (Rosinha), indicating a more effective role of this gene family against the pathogen. Furthermore, based on PCA analyses and interaction networks of differentially expressed genes, three key targets within the PvPR-1 family (PvPR-1-4, PvPR-1-5, and PvPR-1-10) emerged as promising candidates for future functional characterization. These molecular actors displayed differential transcriptional patterns between the studied varieties without compromising the transcript abundance of PvPR-1 protein synthesis in the resistant one. Consequently, they may represent key components of resistance mechanisms that contribute to the differentiation between the two organisms. These findings deepen our understanding of PvPR-1 genes and their roles in common bean defense responses. They also emphasized the potential of PvPR-1 genes as candidates for breeding stress-resistant common bean varieties, which are crucial for bolstering crop resilience to environmental adversities.

Characterization of α-hairpinin in the genome of lima bean (Phaseolus lunatus)

Antimicrobial α-Hairpinin peptides are sources of bioactive molecules with significant structural diversity and various biological activities. Phaseolus lunatus, known as lima bean, is a plant from the Fabaceae family, native to Central and South America. It is the second most important legume agronomically and economically in tropical regions, after the common bean. Due to its importance, several omics studies have been recently conducted on this species. The research aimed to characterize the antimicrobial peptides of the α-hairpinin family in the lima bean genome by analyzing their physicochemical properties, in silico biological activities, and three-dimensional structure. To this end, α-hairpinin sequences were identified according to the cysteine pattern characteristic of this protein family. After target identification, a search for conserved domains, signal peptides, and subcellular localization was conducted. Molecular mass, isoelectric point, grand average of hydropathicity (GRAVY), and biological activities were also analyzed, and a three-dimensional model of the candidate was generated. Following the mining process, an α-hairpinin sequence from P. lunatus (PlHrp1) was identified. PlHrp1 consisted of 41 amino acids, was predicted to be in the extracellular region, had an isoelectric point of 6.28, a mass of 4.81 kDa, and a gravy of -1.078. The alignment revealed that PlHrp1 contained the 4 conserved cysteine residues. In silico activity analyses demonstrated that PlHrp1 exhibited antifungal and antibacterial activities, with no antiviral activity. The secondary structure displayed two antiparallel α-helices connected by a loop. The model described 94.4% of amino acid residues in favorable positions. This study provides a comprehensive analysis of α-hairpinin peptides in the Phaseolus lunatus genome, highlighting the presence of this peptide family in the lima bean species and offering insights into their potential.

The impact of retrotransposons on castor bean genomes.

Castor bean (Ricinus communis L.) is an important oil crop. However, the influence of transposable elements (TEs) on the dynamics of castor bean evolution awaits further investigation. This study explored the role of transposable elements in the genomes of wild castor bean accessions from Ethiopia (Rc039) and Kenya (WT05) as well as in the cultivated variety (Hale). The distribution and composition of repeat sequences in these three lineages exhibited relative consistency, collectively accounting for an average of 36.7% of the genomic sequences. Most TE families displayed consistent lengths and compositions across these lineages. The dynamics of TEs significantly differed from those of genes, showing a lower correlation between the two. Additionally, the distribution of TEs on chromosomes showed an inverse trend compared to genes. Furthermore, Hale may have originated from the ancestor of Rc039. The divergent evolutionary paths of TEs compared to genes indicate the crucial role of TEs in shaping castor bean genetics and evolution, providing insights into the fields of castor bean and plant genomics research.

Genome-wide analysis of the common bean (Phaseolus vulgaris) laccase gene family and its functions in response to abiotic stress

BackgroundLaccase (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.Results29 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.ConclusionsThe 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.

In Silico Structural and Functional Characterization of the Thaumatin‐Like Gene Family in Phaseolus lunatus Reveals the Potential for Microbial and Antiviral Activity

ABSTRACTThaumatin‐like proteins (TLPs) are part of the pathogenesis‐related (PR) proteins that are important in host plant defense. TLPs have multiple defense functions against pathogens (bacteria, viruses, and fungi) and are involved in other biological processes of several living organisms. However, the biological role of TLPs must be elucidated for other species, such as Phaseolus lunatus, popularly known as lima bean. In this study, we propose to investigate the biological activity of TLPs in P. lunatus, which can help develop a detailed functional characterization of the TLP gene in other crop cultures. As a result, a total of 31 PlTPLs genes and 16 highly conserved cysteine residues for each family member were identified in the lima bean genome. Regarding phylogenetic analysis, 128 TLPs from different plant species, including P. lunatus, were used, and the phenetic tree revealed that the TLPs could be divided into six groups. The leading group was Group 4, containing 34 TLPs; the smallest was Group 7, containing only a single TLP. The analysis of antimicrobial and antiviral activity revealed that 27 PlTLPs have antimicrobial activity and 7 PlTLPs have potential antiviral activity. For chromosomal distribution of the PlTLPs, 8 of 11 chromosomes presented at least one PlTLs on one of the chromosomes. Finally, molecular modeling was carried out between two TLPs (PlTLP5 and PlTLP14), which presented antimicrobial and antiviral activity and did not have allergenic activity. The results showed that the two candidates presented ≥90% of their residues in the favorable regions and ∼10% in the permitted regions, demonstrating that the two PlTLPs are considered promising targets for biotechnological applications, especially those related to the genetic improvement of agricultural crops and the development of antimicrobial agents.

Genetic Diversity, Linkage Disequilibrium, and Population Structure in a Common Bean Reference Collection

An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture’s global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF < 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 < 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies.

Genome-wide characterization of MATE family members in common bean (Phaseolus vulgaris Linn.) and their expression profiles in response to abiotic stress

Multidrug and toxic compound extrusion (MATE) family plays an important role in the detoxification process of plants under various stresses. Nevertheless, a comprehensive study on MATE family members has thus far not been performed in common bean (Phaseolus vulgaris Linn.), limiting our understanding of its functions in common bean acclimation to stressful environments. In this study, a total of 56 PvMATEs members with uneven distribution on all chromosomes were identified from the common bean genome, with the most on chromosome 4 (10 members) and the least on chromosome 6 and 10 (1 members). Based on their orthologous relationship with those from Arabidopsis and rice, PvMATEs were classified into Clades I, II, III and Ⅳ, wherein 19, 15, 14, and 8 members were included, respectively. Gene ontology (GO) term and cis-regulatory element (CRE) analyses results indicated that the potential functions of PvMATEs were involved in hormonal response, developmental regulation and multiple stress response of common bean. The results of Phytozome and qRT-PCR analyze showed that the expression of PvMATEs in common bean are tissue specificity, with the most in root. Furthermore, 75 mM NaCl, 75 mM CuCl2, 0.35uM HgCl2, 16uM CdCl2, 4.38uM Benzo[c]-phenanthrene (C18H12) and 10 % PEG6000 treatments significantly up-regulated the expression levels of some PvMATEs in common bean roots, indicating that these genes are involved in multiple abiotic stresses respond of common bean. Taken together, these observations enriched our knowledge of MATE family in the common bean and benefit for breeding improved cultivars.

High-quality faba bean reference transcripts generated using PacBio and Illumina RNA-seq data

The genome of faba bean was first published in 2023. To promote future molecular breeding studies, we improved the quality of the faba genome based on high-density genetic maps and the Illumina and Pacbio RNA-seq datasets. Two high-density genetic maps were used to conduct the scaffold ordering and orientation of faba bean, culminating in an increased length (i.e., 14.28 Mbp) of chromosomes and a decrease in the number of scaffolds by 45. In gene model mining and optimisation, the PacBio and Illumina RNA-seq datasets from 37 samples allowed for the identification and correction 121,606 transcripts, and the data facilitated a prediction of 15,640 alternative splicing events, 2,148 lncRNAs, and 1,752 fusion transcripts, thus allowing for a clearer understanding of the gene structures underlying the faba genome. Moreover, a total of 38,850 new genes including 56,188 transcripts were identified compared with the reference genome. Finally, the genetic data of the reference genome was integrated and a comprehensive and complete faba bean transcriptome sequence of 103,267 transcripts derived from 54,753 uni-genes was formed.

Genome-Wide Analysis and Characterization of FBA (Fructose 1,6-bisphosphate aldolase) Gene Family of Phaseolus vulgaris L

Fructose-1,6-biphosphate aldolase (FBA) genes have important roles in plant stress responses. At the same time, these genes positively affect growth and development in plants. FBA is involved in gluconeogenesis, glycolysis, and the Calvin-Benson cycle, and it is an enzyme that plays an important role in signal transduction of these stages. This study aims to determine and characterize the FBA gene family in the bean genome. As a result of the study, 7 Pvul-FBA genes were determined in the bean (Phaseolus vulgaris L.) genome. The highest amino acid number of Pvul-FBA proteins was determined in the Pvul-FBA-1 gene (1374), and the highest molecular weight (43.03 kDa) was determined in the Pvul-FBA-7 gene. Again, the highest isoelectric point (8.03) was determined in the Pvul-FBA-3 gene. It has been determined that the Pvul-FBA-6/Pvul-FBA-7 genes are segmental duplicated genes. The main four groups were obtained according to the phylogenetic analysis consisting of FBA proteins of three plants (P. vulgaris, Glycine max, and Arabidopsis thaliana). As a result of interproscan analysis, Motif-1, 2, 3, 4 and 5 were found to contain the fructose-bisphosphate aldolase domain. According to in silico gene expression analysis, it was determined that the expression rates of Pvul-FBA genes increased or decreased under salt and drought stress conditions. Synteny analyses of FBA genes in common bean and A. thaliana plants showed that these three plants have a relationship in terms of FBA genes. The results of this research will allow a better designation of the molecular structure of the FBA gene family in common bean.

Genome-wide analysis of LOG family genes in castor and RcLOG5 enhances drought, salt, and cold stress tolerance in Arabidopsis thaliana

The gene encoding the specific phosphohydrolase LONELY GUY (LOG) plays an important role in the activation of cytokinin and the stress response in plant cells. However, the role of LOG genes in castor bean (Ricinus communis) has not been reported. In this study, we identified a total of nine members of the LOG gene family in the castor bean genome and investigated the upregulated expression of the RcLOG5 gene using transcriptome data analysis. We found that the RcLOG5 gene exhibited tissue-specific expression and was activated by polyethylene glycol, NaCl, low temperature, and abscisic acid stress. The subcellular localization results showed that the RcLOG5 gene is mainly located in the cytoplasm. Based on phenotypic and physiological indicators, namely root length, peroxidase activity, and malondialdehyde content, overexpression of the RcLOG5 gene not only improved the drought resistance, salt tolerance, and cold tolerance of transgenic Arabidopsis, but also shortened the dormancy period of the transgenic plants. Transcriptomic sequencing revealed that the overexpression of the RcLOG5 gene led to the enrichment of differentially expressed genes in the glutathione metabolism pathway in transgenic Arabidopsis. Moreover, the overexpression plants had higher levels of glutathione and a higher GSH/GSSG ratio under stress compared to the wild type. Therefore, we inferred that the RcLOG5 gene may be responsible for regulating cell membrane homeostasis by reducing the accumulation of reactive oxygen species through the glutathione pathway. Overall, the overexpression of the RcLOG5 gene positively regulated the stress resistance of transgenic Arabidopsis. This study provides valuable gene resources for breeding stress-tolerant castor bean varieties.

Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean.

Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.

A genomic toolkit for winged bean Psophocarpus tetragonolobus

A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed ‘the soybean for the tropics’. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.

Comprehensive analysis of the aldehyde dehydrogenase gene family in Phaseolus vulgaris L. and their response to saline-alkali stress.

Aldehyde dehydrogenase (ALDH) scavenges toxic aldehyde molecules by catalyzing the oxidation of aldehydes to carboxylic acids. Although ALDH gene family members in various plants have been extensively studied and were found to regulate plant response to abiotic stress, reports on ALDH genes in the common bean (Phaseolus vulgaris L.) are limited. In this study, we aimed to investigate the effects of neutral (NS) and basic alkaline (AS) stresses on growth, physiological and biochemical indices, and ALDH activity, ALDH gene expression of common bean. In addition, We used bioinformatics techniques to analyze the physical and chemical properties, phylogenetic relationships, gene replication, collinearity, cis-acting elements, gene structure, motifs, and protein structural characteristics of PvALDH family members. We found that both NS and AS stresses weakened the photosynthetic performance of the leaves, induced oxidative stress, inhibited common bean growth, and enhanced the antioxidative system to scavenge reactive oxygen species. Furthermore, we our findings revealed that ALDH in the common bean actively responds to NS or AS stress by inducing the expression of PvALDH genes. In addition, using the established classification criteria and phylogenetic analysis, 27 PvALDHs were identified in the common bean genome, belonging to 10 ALDH families. The primary expansion mode of PvALDH genes was segmental duplication. Cis-acting elemental analysis showed that PvALDHs were associated with abiotic stress and phytohormonal responses. Gene expression analysis revealed that the PvALDH gene expression was tissue-specific. For instance, PvALDH3F1 and PvALDH3H1 were highly expressed in flower buds and flowers, respectively, whereas PvALDH3H2 and PvALDH2B4 were highly expressed in green mature pods and young pods, respectively. PvALDH22A1 and PvALDH11A2 were highly expressed in leaves and young trifoliates, respectively; PvALDH18B2 and PvALDH18B3 were highly expressed in stems and nodules, respectively; and PvALDH2C2 and PvALDH2C3 were highly expressed in the roots. PvALDHs expression in the roots responded positively to NS-AS stress, and PvALDH2C3, PvALDH5F1, and PvALDH10A1 were significantly (P < 0.05) upregulated in the roots. These results indicate that AS stress causes higher levels of oxidative damage than NS stress, resulting in weaker photosynthetic performance and more significant inhibition of common bean growth. The influence of PvALDHs potentially modulates abiotic stress response, particularly in the context of saline-alkali stress. These findings establish a basis for future research into the potential roles of ALDHs in the common bean.

Dynamic Expressions of Yellow Stripe-Like (YSL) Genes During Pod Development Shed Light on Associations with Iron Distribution in Phaseolus vulgaris.

The global prevalence of iron deficiency-induced "hidden hunger" highlights a critical health concern, underscoring the pressing need to improve iron nutrition through safe and efficient means, such as increasing iron intake from plant-based foods. Yellow Stripe-Like (YSL) genes play a crucial role in long-distance iron transport between source and sink tissues in plants. Here, we report on the analysis of YSL family genes in the common bean (Phaseolus vulgaris L.), an iron-rich legume crop. We identified 9 YSL genes in the common bean genome using BLAST and HMM methods. Gene duplication analysis revealed that PvYSL7a and PvYSL7b originated through tandem duplication events. Structural analysis noted an absence of conservative motifs in PvYSL3b and PvYSL7a, which led to distinct predicted 3D protein structures. Leveraging publicly available RNA-seq data from developing bean pods, the expression patterns of PvYSL genes alongside pod and seed development were analyzed. Notably, PvYSL7a and PvYSL7b, as well as PvYSL1a and PvYSL1b, exhibited diverged expression patterns in seeds, signifying their functional divergence in this tissue. Moreover, PvYSL3a and PvYSL3b exhibited divergent expression patterns in both pod walls and seeds during pod development, underscoring their distinct roles in facilitating iron transportation between pods and seeds. This study provides valuable insights into the gene regulatory basis of iron accumulation in bean pods and seeds.

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

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

Transcriptomic analysis reveals candidate genes associated with salinity stress tolerance during the early vegetative stage in fababean genotype, Hassawi-2

Abiotic stresses are a significant constraint to plant production globally. Identifying stress-related genes can aid in the development of stress-tolerant elite genotypes and facilitate trait and crop manipulation. The primary aim of this study was to conduct whole transcriptome analyses of the salt-tolerant faba bean genotype, Hassawi-2, under different durations of salt stress (6 h, 12 h, 24 h, 48 h, and 72 h) at the early vegetative stage, to better understand the molecular basis of salt tolerance. After de novo assembly, a total of 140,308 unigenes were obtained. The up-regulated differentially expressed genes (DEGs) were 2380, 2863, 3057, 3484, and 4820 at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. Meanwhile, 1974, 3436, 2371, 3502, and 5958 genes were downregulated at 6 h, 12 h, 24 h, 48 h, and 72 h of salt stress, respectively. These DEGs encoded various regulatory and functional proteins, including kinases, plant hormone proteins, transcriptional factors (TFs) basic helix-loop-helix (bHLH), Myeloblastosis (MYB), and (WRKY), heat shock proteins (HSPs), late embryogenesis abundant (LEA) proteins, dehydrin, antioxidant enzymes, and aquaporin proteins. This suggests that the faba bean genome possesses an abundance of salinity resistance genes, which trigger different adaptive mechanisms under salt stress. Some selected DEGs validated the RNA sequencing results, thus confirming similar gene expression levels. This study represents the first transcriptome analysis of faba bean leaves subjected to salinity stress offering valuable insights into the mechanisms governing salt tolerance in faba bean during the vegetative stage. This comprehensive investigation enhances our understanding of precise gene regulatory mechanisms and holds promise for the development of novel salt-tolerant faba bean salt-tolerant cultivars.

Genome wide identification, structural characterization and phylogenetic analysis of High-Affinity potassium (HAK) ion transporters in common bean (Phaseolus vulgaris L.)

BackgroundHigh-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.ResultsIn the current study, 20 HAK genes were identified in common bean genome. Super-family “K_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.ConclusionThe current study provides valuable information for further functional characterization and uncovering the molecular mechanism associated with Potassium transportation in plants.