Plant Gene最新文献

{"title":"Integrative leaf transcriptomic and physiological insights into salt stress responses in Eucalyptus: A comparative analysis of two contrasting clones","authors":"Ravita Tadiya ,&nbsp;Santan Barthwal ,&nbsp;Harish Singh Ginwal ,&nbsp;Hukum Singh ,&nbsp;Fateh Singh","doi":"10.1016/j.plgene.2025.100551","DOIUrl":"10.1016/j.plgene.2025.100551","url":null,"abstract":"<div><div>Salinity severely limits forest productivity; however, the molecular basis of tolerance in <em>Eucalyptus</em> remains unclear. We investigated the physiological and transcriptomic responses of a salt-tolerant clone (B-112) and a salt-sensitive clone (W-12) subjected to 80 days of severe salinity (EC ≥ 20 dS/m). Both clones showed reductions in photosynthesis, stomatal conductance, internal CO₂ concentration, and transpiration; however, the extent of decline was considerably smaller in B-112, indicating superior physiological resilience. RNA-seq profiling revealed the targeted reprogramming of 1025 genes in B-112, compared with a broad, less coordinated response involving 14,994 genes in W-12. In B-112, enrichment analyses highlighted the strong activation of abscisic acid (ABA) and ethylene signaling, mitogen-activated protein kinases (MAPKs) cascades, carbohydrate metabolism, antioxidant defense, and protein folding pathways. Key salt-responsive genes included Dehydrins (DHN1), Ethylene Response Factors (ERFs), cupredoxins, and expansins, indicating coordinated osmotic adjustment, cell-wall modification, and stress signaling. Conversely, W-12 displayed extensive upregulation of ubiquitination and vesicle trafficking genes, alongside repression of photosynthesis and chloroplast-related processes, consistent with a damage-induced rather than adaptive program. qRTPCR validation confirmed high concordance with RNAseq results. Together, these findings reveal that B-112 sustains salt tolerance through proactive and focused transcriptomic reprogramming, while W-12 exhibits reactive stress-triggered responses, providing candidate targets for breeding and genetic improvement of <em>Eucalyptus</em> in saline environments.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100551"},"PeriodicalIF":1.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145157959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EG-net: A gene regulatory network to serve as a blueprint for tailored and precise oil palm (Elaeis guineensis Jacq.) breeding.","authors":"Thalliton Luiz Carvalho da Silva ,&nbsp;Wellington Rangel dos Santos ,&nbsp;Roberto Coiti Togawa ,&nbsp;Manoel Teixeira Souza Júnior","doi":"10.1016/j.plgene.2025.100548","DOIUrl":"10.1016/j.plgene.2025.100548","url":null,"abstract":"<div><div>Conventional breeding of oil palm, a perennial with a protracted lifespan conducive to sustained production, is significantly hampered by two primary factors: its extended juvenile phase and a substantial time period required to reach peak productivity. These constraints significantly delay the development of improved cultivars through traditional breeding techniques. Plant genetic engineering and genome editing techniques, although unable to directly address these constraints, offer an alternative approach for introducing desirable traits in a more precise and expeditious manner. However, careful gene selection for targeted modifications is imperative. In long-lived crops, breeding precision is paramount. The selection of the most suitable gene for modification, and the assurance of its intended trait expression without disrupting others, becomes even more critical. This is where Gene Regulatory Networks (GRNs) come in. This study identified key regulatory molecules and constructed EG_Net, a GRN for the African oil palm (<em>Elaeis guineensis</em> Jacq.). EG_Net elucidates gene-regulatory interactions and guides precise genetic engineering strategies, offering valuable insights into oil palm biology. Three case studies validated the efficacy of EG-Net in identifying genes for engineering resistance to biotic (red ring and fatal yellowing diseases) and abiotic (drought and salinity) stresses. The identification of candidate genes and analysis of regulatory elements within GRNs facilitate future investigations into sustainable stress tolerance strategies in oil palm, ultimately promoting the long-term sustainability of the palm oil industry. This study provides a framework for optimizing genetic engineering approaches to enhance disease resistance, abiotic stress tolerance, and, consequently, the sustainability of the oil palm production system.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100548"},"PeriodicalIF":1.6,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145157956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide analysis of SWEET and TST sugar transporters in sugarbeet: Structural characterization and expression during development and postharvest storage","authors":"Karen K. Fugate ,&nbsp;Fernando L. Finger ,&nbsp;Melvin D. Bolton","doi":"10.1016/j.plgene.2025.100549","DOIUrl":"10.1016/j.plgene.2025.100549","url":null,"abstract":"<div><div>SWEET (Sugars Will Eventually be Exported Transporter) and TST (Tonoplast Sugar Transporter) genes are implicated in sucrose accumulation and sucrose loss during sugarbeet root production and postharvest storage, although information regarding their identities, structures and expression is limited. Research, therefore, was conducted to identify and structurally characterize sugarbeet SWEET and TST gene families and determine their organ-specific, developmental, and storage-related expression. Sixteen SWEET genes and four TST genes were found in the sugarbeet genome. SWEET genes were notably diverse in genomic and transcriptomic structure, yet shared similarities in protein motifs and structure, whilst TST genes were generally uniform in genomic, transcriptomic, and protein size and structure. Expression analysis revealed high expression of two SWEET genes (SWEET 1, SWEET12) in leaves, relatively low levels of SWEET gene expression in roots throughout all but the earliest stages of development, and a dramatic upregulation of four SWEET genes (SWEET1, SWEET12, SWEET14/N3, SWEET17b) during storage, including a greater than 17,000-fold increase in SWEET14/N3 expression. TST genes were expressed in all tissue types, with most TST expression derived from a single gene (TST2.1) which was highly expressed in roots, minimally expressed in leaves, and elevated in expression during root storage. Overall, these results point to the likely importance of SWEET1 and SWEET12 in leaves and TST2.1 in roots during development when sucrose is actively being accumulated and the likely importance of SWEET14/N3, and possibly SWEET1, SWEET12, SWEET17b, and TST2.1 during storage when vacuolar sequestered sucrose is remobilized and catabolized.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100549"},"PeriodicalIF":1.6,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145094903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Flower development in Brassica rapa: Linking anatomy, physiology, transcriptomics, and metabolomics","authors":"Waseem Ahmad Lone,&nbsp;Rayees Ahmad Rather,&nbsp;Tahira Akhtar Bhat,&nbsp;Umer Majeed Wani,&nbsp;Riffat John","doi":"10.1016/j.plgene.2025.100545","DOIUrl":"10.1016/j.plgene.2025.100545","url":null,"abstract":"<div><div>Flowering is essential to most plants, and is regulated by environmental and internal signals. This study investigates the molecular mechanisms regulating flower development in <em>Brassica rapa</em> L. by performing, anatomical studies, RNA sequencing, analysis of photosynthetic parameters and metabolomics at different developmental stages. We conducted RNA sequencing and analysed 47,135 genes across three pairwise comparisons: Vegetative vs. Pre-Bolting, Pre-Bolting vs. Bolting, and Bolting vs. Post-Bolting. The greatest differential gene expression was observed between the vegetative and pre-bolting stages, with significant changes in 3618 genes. Functional enrichment analysis revealed that photosynthesis, circadian rhythm regulation, response to environmental stimuli, and glucosinolate biosynthesis were the most enriched biological processes during floral transition. Photosynthetic parameters showed a significant increase from the vegetative to bolting stages, peaking from pre-bolting to bolting, and decreasing post-bolting. Metabolomic analysis identified 23 metabolites with significant changes during development. Key metabolites such as campesterol and gamma sitosterol increased during bolting, indicating a role in promoting floral meristem formation. Our study identified several key regulatory genes involved in the photoperiod, circadian clock, and gibberellin pathways, such as <em>GIGANTEA (GI), SOC1,</em> and <em>ELF3</em>. Upregulation of these genes from pre-bolting to bolting stages correlated with enhanced photosynthetic activity and gene expression related to light signaling, carbohydrate metabolism, carbon metabolism, and glucosinolate biosynthesis. These findings provide a comprehensive view of the transcriptional changes and regulatory networks governing the transition from vegetative growth to flowering in <em>B. rapa</em> L., highlighting the integration of environmental and internal cues in this complex process.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100545"},"PeriodicalIF":1.6,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145094902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and transcriptome-based expression analysis of hybrid sugarcane calmodulin-binding transcription activators under drought","authors":"Vitor Luciano Costa da Silva ,&nbsp;Ana Maria Martinez ,&nbsp;Maqsood Alam ,&nbsp;Muhammad Noman ,&nbsp;Antonio Chalfun-Junior","doi":"10.1016/j.plgene.2025.100547","DOIUrl":"10.1016/j.plgene.2025.100547","url":null,"abstract":"<div><div>As the highly demanding complex genome of the hybrid sugarcane cultivar became publicly available recently (2023), it opened avenues to further study this important crop at molecular level. We are interested in digging the multiple stress responsive transcription factors family, the Calmodulin-Binding Transcription Activator (CAMTA) of sugarcane. This manuscript presents a comprehensive study of <em>ScCAMTA</em> family based on the latest sugarcane genome sequence information. Within the 10 gb genome, through HMM model prepared from sorghum <em>CAMTA</em> common domains, we found 48 genes, 46 out of which carry all the <em>CAMTA</em>-associated domains including CG-1, TIG, IQ and Ank. The phylogenetic analysis clustered then into seven classes. Keeping sorghum as reference, we named them as <em>ScCAMTA1</em> – <em>ScCAMTA7</em>, while each one representing a class having 5–7 copies such as <em>ScCAMTA1A</em> – <em>ScCAMTA1E</em>, present in each sub-genome (chromosome) within the hybrid sugarcane. In parallel to determining their physico-chemical attributes, miRNA targets, protein interaction network and genome collinearity, we observed evolutionary conservation in gene structures, protein domains, and motif organization across the phylogenetic classes. Promoter analysis revealed the presence of multiple stress-responsive cis-regulatory elements, such as MBS (drought) and MYB (salinity), suggesting their direct involvement in stress adaptation. MicroRNA target analysis predicted 20 unique miRNAs targeting <em>ScCAMTA</em> transcripts, highlighting potential post-transcriptional regulation. Additionally, protein-protein interaction networks indicated functional connections to stress signaling pathways. Finally, their expression patterns under drought stress were determined using RNA-seq data, which revealed that <em>ScCAMTA7</em> is highly active under drought conditions, underscoring its potential role in drought response. This study furthers the insights into complex sugarcane genome and will assist in developing its drought-tolerant varieties.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100547"},"PeriodicalIF":1.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145157957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive genome-wide study of Glutaredoxin (GRX) gene family in the liverwort Marchantia polymorpha and exploring their roles in abiotic stress tolerance","authors":"Shivani Singh ,&nbsp;Garima Saxena ,&nbsp;Prachi Mishra ,&nbsp;Monica Kumari ,&nbsp;Prasanna Dutta ,&nbsp;Mehar Hasan Asif ,&nbsp;Debasis Chakrabarty","doi":"10.1016/j.plgene.2025.100550","DOIUrl":"10.1016/j.plgene.2025.100550","url":null,"abstract":"<div><div>Glutaredoxins (GRXs) are thiol-disulfide oxidoreductases that function as key regulators of redox homeostasis, development, and stress responses in plants. Despite their functional importance, little is known about the GRX gene family in early diverging land plants. In this study, we performed a comprehensive genome-wide identification of GRX genes in the liverwort <em>Marchantia polymorpha</em> and their role in abiotic stresses. A total of 17 <em>MpGRX</em> genes with 2 isoforms (19 <em>MpGRX</em>) containing the conserved Glutaredoxin domain (PF00462) were identified using BLAST, HMMER, and SMART approaches. Gene structure analysis revealed that six <em>MpGRX</em> genes contained a single intron, whereas the remaining genes exhibited more complex structures with three or more introns, suggesting gene expansion and functional diversification. Evolutionary analysis was conducted using non-synonymous (Ka) and synonymous (Ks) substitution rates between <em>MpGRX</em> genes and homologous genes from <em>Physcomitrella patens</em>, <em>Ceratopteris richardii</em>, <em>Pinus taeda</em>, <em>Arabidopsis thaliana</em>, and <em>Oryza sativa</em>. The results indicated generally low Ka values, except in one <em>MpGRX–PtGRX</em> pair with Ka = 1.59, suggesting potential functional divergence in gymnosperms. Ks-based divergence time estimates were consistent with known evolutionary separations. Selection pressure analysis based on Ka/Ks ratios revealed that most GRX gene pairs were under purifying selection, particularly those between <em>M. polymorpha</em> and mosses, ferns, and angiosperms.</div><div>This study provides novel insights into the structural diversity, evolutionary history, and selective constraints acting on the GRX gene family in <em>M. polymorpha</em>, offering a foundation for future functional and comparative studies in early land plant lineages.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100550"},"PeriodicalIF":1.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145095065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene expression analysis of four Solanum tuberosum L. varieties in vitro induced with Alternaria alternata and Streptomyces werraensis extracts","authors":"Izdihar Ferhat ,&nbsp;Wahiba Harrat ,&nbsp;Emre Yörük ,&nbsp;Boualem Harfi","doi":"10.1016/j.plgene.2025.100546","DOIUrl":"10.1016/j.plgene.2025.100546","url":null,"abstract":"<div><div>Potato (<em>Solanum tuberosum</em> L.) is one of the major tuber food crops worldwide. However, its culture is threatened by several diseases like potato brown leaf spot which is related to <em>Alternaria</em> fungi. This study addresses the challenge of inducing resistance in four potato varieties against brown spot disease by <em>in vitro</em> culture. The approach relies on combining <em>Streptomyces werraensis</em> extracts, reported as potential biocontrol agents, and <em>Alternaria alternata</em> pathogen extracts in the potato culture medium. Initially, potato micropropagation and microtuberization media were optimized, followed by an acclimatization phase and a pathogenicity test on the four varieties (Arizona, Désirée, Spunta and Synergy). Subsequently, potato microtubers were produced <em>in vitro</em>, with <em>microorganisms'</em> extracts included in the culture medium. To assess for induced resistance, qRT-PCR analysis was conducted to evaluate gene expression levels, targeting the most relevant genes (<em>ChtA1</em>, <em>ChtB3</em>, <em>PR1b</em>, <em>PRa1-like</em>, <em>WRKY31</em> and <em>WRKY75-like</em>). Gene expression analysis revealed significant differences between varieties, with Arizona variety showing the most vigorous response. These distinct varietal responses indicate genotype-specific reactions to the combined treatment of <em>A. alternata</em> and <em>S. werraensis</em> extracts. This research highlights the <em>S. werraensis</em> potential as a biocontrol agent to induce resistance in potatoes to <em>A. alternata</em>. The results support the integration of <em>in vitro</em> culture media supplemented with microorganism extracts for large-scale standardized potato production.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100546"},"PeriodicalIF":1.6,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145048782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and characterization of the CONSTANS-like gene family and its expression profiling under salt treatment in alfalfa (Medicago sativa L.)","authors":"Shuzhi Ma,&nbsp;Yiping Wei,&nbsp;Qinyan Bao,&nbsp;Zhaozhu Wen,&nbsp;Mengli Luo,&nbsp;Wenxuan Du","doi":"10.1016/j.plgene.2025.100544","DOIUrl":"10.1016/j.plgene.2025.100544","url":null,"abstract":"<div><div>Alfalfa (<em>Medicago sativa</em> L.) is a globally cultivated, high-quality forage crop. The CONSTANS-LIKE (COL) genes play crucial roles in regulating flowering time and stress responses in plants. However, the functional characterization of <em>COL</em> genes in alfalfa remain largely unexplored. In this study, we conducted a genome-wide analysis of the Xinjiang Daye alfalfa genome and identified 36 <em>MsCOL</em> genes. Multiple sequence alignment confirmed that all <em>MsCOL</em> genes contain conserved B-box and CCT (CO, CO-like and TOC1) domains. Phylogenetic analysis and gene structure analyses classified the <em>MsCOL</em> genes into two subclades, exhibiting similar exon-intron organization and conserved motif distributions. Chromosomal mapping revealed that these genes are distributed across 22 chromosomes. Expression profiling under salt stress demonstrated that <em>MsCOL</em> genes exhibit expression patterns, indicating their potential involvement in abiotic stress responses. These findings enhance our understanding of <em>MsCOL</em> gene function in alfalfa and provide a theoretical basis for breeding salt-tolerant alfalfa cultivars.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100544"},"PeriodicalIF":1.6,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144920283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Induced genetic diversity through EMS mutagenesis in Davana (Artemisia pallens Bess.) and use of ISSR markers to underpin agronomical and chemical traits","authors":"Arun J. Ganiger ,&nbsp;Channayya Hiremath ,&nbsp;K. Madhusudan ,&nbsp;Manoj kumar Chandrasekaran ,&nbsp;V.S. Pragadheesh","doi":"10.1016/j.plgene.2025.100543","DOIUrl":"10.1016/j.plgene.2025.100543","url":null,"abstract":"<div><div>Davana (<em>Artemisia pallens</em> Bess.) is an annual aromatic herb that belongs to the <em>Asteraceae</em> family. The current research was attempted to identify elite high essential oil yielding davana mutants with high davanone content. To determine the LD₅₀ value of EMS, seeds of the local davana cultivar “Bangalore” were treated with the chemical mutagen ethyl methane sulphonate (EMS) at varying concentrations of 0.10 %, 0.2 %, 0.3 %, 0.40 %, and 0.50 % for 16 h. The LD₅₀ value was (0.40 % for 16 h) determined by probit analysis. In the M₁ generation, 3000 davana plants were evaluated and forwarded to M₂. Based on visual observation of 1500 M₂ plants, 250 mutants were chosen, and their essential oil and davanone content was assessed. In the M₂ generation, the quantitative traits evaluated and chemical constituents assessed had higher mean and moderate to high phenotypic co-efficient of variation, in comparison to the control. Essential oil yield had a strong and significantly positive correlation to the number of flowers per plant, flower head diameter, and fresh herb yield traits. Based on superiority over control and Mean + 1 SD of M₂ population, 22 and 14 mutants were identified for essential oil yield and davanone content, respectively. Molecular diversity analysis of 16 high essential oil yielding M₂ plants and two check cultivars using ISSR markers revealed an average 79 % polymorphism, with the primer UBC-845 having the highest polymorphic information content. We identified several superior mutants including DM2158 (essential oil content-0.5 %) and DM2103 (Davanone content-70.92 %), indicating that mutation breeding can be an effective strategy to develop novel davana cultivars with higher essential oil and davanone content.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100543"},"PeriodicalIF":1.6,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144886341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the genetic diversity of common bean germplasm: insights into Andean gene pool variability","authors":"Cecilia Luvizutti Ferreira Silva ,&nbsp;Dario Grattapaglia ,&nbsp;Paula Arielle Mendes Ribeiro Valdisser ,&nbsp;Paula Pereira Torga ,&nbsp;Alessandra da Cunha Moraes Rangel ,&nbsp;Claudio Brondani ,&nbsp;Alexandre Siqueira Guedes Coelho ,&nbsp;Tereza Cristina de Oliveira Borba ,&nbsp;Rosana Pereira Vianello","doi":"10.1016/j.plgene.2025.100540","DOIUrl":"10.1016/j.plgene.2025.100540","url":null,"abstract":"<div><div>Common bean (<em>Phaseolus vulgaris</em>) is among the most widely consumed legumes globally, with Brazil playing a crucial role in preserving and expanding its existing genetic diversity. This study aimed to characterize a subset of 863 common bean accessions from Brazil's Gene Banks, mainly of Andean origin. A germplasm collection was genotyped with 4275 SNPs using the EMBRAPA Multispecies 65KChip. Population structure analysis revealed two main groups: Andean (<em>n</em> = 558) and Middle American (<em>n</em> = 267), along with 38 admixed accessions. Andean group exhibited lower gene diversity (GD = 0.086), and allelic richness (A_R = 1.83) compared to the Middle American group (GD = 0.270, A_R = 1.98). Brazilian landraces in the Andean and Middle American groups showed potentially lower overall diversity, emphasizing the need for conservation efforts to preserve these genetic resources. The Andean Brazilian core collection (<em>n</em> = 221; GD = 0.095) encompasses the active collection diversity evaluated (<em>n</em> = 337; GD = 0.093). A total of 26 SNPs potentially under selection, mainly associated with plant development and defense, were identified. Georeferencing landraces using climate maps identified potentially valuable varieties adapted to drought (e.g., BGF0011779, BGF0012528, BGF0013826) and high temperatures and low-fertility soils (e.g., BGF0016128, BGF0013871), highlighting their relevance for conservation and sustainable use in breeding programs. Accessions' photographs showcased a wide range of morphological diversity, colors, types, shapes, and sizes of beans. Our findings reveal a significant genetic diversity among common bean germplasm, offering practical breeding opportunities and enhancing the value of gene bank collections. Certain landraces show potential for adapting to challenging climatic conditions, making them promising subjects for further adaptation studies.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100540"},"PeriodicalIF":1.6,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144908858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}