Plant Gene最新文献

{"title":"Genome-wide identification and expression analysis of the OVATE gene family in melon (Cucumis melo L.)","authors":"Zixuan Li ,&nbsp;Shuaidong Wu ,&nbsp;Wenxi Liu ,&nbsp;Jiyuan Wang ,&nbsp;Yanliang Guo ,&nbsp;Congsheng Yan ,&nbsp;Yan Wang ,&nbsp;Huijun Zhang ,&nbsp;Jie Liu","doi":"10.1016/j.plgene.2025.100532","DOIUrl":"10.1016/j.plgene.2025.100532","url":null,"abstract":"<div><div>The OVATE gene family (OFP) is widely present in plants and plays a crucial role in regulating growth, development, and plant morphology, particularly in shaping fruit morphology. However, limited research has been conducted on the <em>OFP</em> gene in melon. In this study, we systematically identified and analyzed the entire <em>OFP</em> gene family in the melon genome. By comparing with 20 AtOFP protein sequences, 16 <em>CmOFP</em> genes were identified from the melon genome, and their physicochemical properties were characterized. Phylogenetic relationship analysis revealed that CmOFP and AtOFP could be classified into five subfamilies. Syntenic analysis demonstrated high synteny between Arabidopsis and melon <em>OFP</em>. Additionally, the gene structure and conserved domains of CmOFP were determined, and its predicted tertiary protein structure was elucidated. Through promoter analysis of <em>CmOFP</em>, a total of 30 regulatory elements were identified, showing significant differences in both number and classification among these elements. Expression pattern analysis indicated that the relative expression of <em>CmOFP</em> in the ovary was high and decreased post-pollination. Transcriptome analysis of different melon fruit pulps revealed that plant hormone signal transduction pathways were closely associated with fruit shape determination. Notably, four <em>CmOFP</em> genes exhibited significant differential expression across various fruit shapes, suggesting potential applications in fruit shape improvement. This study provides a theoretical foundation for further exploring the functional roles of <em>CmOFP</em> and their utilization in melon breeding programs.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100532"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144704123","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 of medicinal plant Solanum procumbens Lour. using DNA barcodes and morphology","authors":"Lieu Thi Thuy Nguyen ,&nbsp;Quyen Thi Thao Tran ,&nbsp;Dan Thai Vo ,&nbsp;Tri Minh Bui ,&nbsp;Biet Van Huynh ,&nbsp;Dung Minh Ha-Tran","doi":"10.1016/j.plgene.2025.100517","DOIUrl":"10.1016/j.plgene.2025.100517","url":null,"abstract":"<div><h3>Background</h3><div>This study employed DNA barcoding to identify and differentiate <em>Solanum procumbens</em>, a potential medicinal plant used from other species in Solanaceae family. Eleven plant samples of <em>Solanum</em> spp. with morphological characteristics similar with those of <em>S. procumbens</em> and <em>S. trilobatum</em> were collected from various locations across Vietnam. Five DNA barcode markers were analyzed for identifying <em>Solanum procumbens</em> and its morphologically cryptic species <em>Solanum trilobatum</em>.</div></div><div><h3>Results</h3><div>Ten putative <em>S. procumbens</em> samples displayed a high identity (99.6–99.7 %) with the reference sequence within the transfer RNA leucine-transfer RNA phenylalanine <em>(trnL</em>–<em>trnF)</em> region. DNA sequences of the Internal Transcribed Spacer (ITS) region exhibited lower identity with the reference sequence, ranging from 94 % to 97.25 %. Despite this difference, DNA barcoding effectively differentiated these individuals, with both chloroplast <em>trnL</em>–<em>trnF</em> and nuclear ITS barcodes achieving high identification accuracy. The precision of <em>trnL</em>–<em>trnF</em> and ITS in species identification was validated using dried leaf samples of the putative <em>S. procumbens</em> and <em>S. trilobatum</em>. The consistency between fresh and dried samples confirms that our results are reliable and applicable in the pharmaceutical industry.</div></div><div><h3>Conclusions</h3><div>Phylogenetic analysis based on barcoding data aligned with morphology-based phenogram. These findings demonstrate the effectiveness of DNA barcoding for accurate identification of <em>S. procumbens</em>, particularly when morphological traits are ambiguous.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100517"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144166991","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":"Genetic diversity analysis in cytoplasmic male sterile ‘A’ lines and restorer ‘R’ lines of Indian mustard using SSR markers","authors":"K.H. Singh,&nbsp;Lal Singh,&nbsp;Nehanjali Parmar,&nbsp;Deepika Sharma,&nbsp;J. Nanjundan,&nbsp;Ajay Kumar Thakur","doi":"10.1016/j.plgene.2025.100518","DOIUrl":"10.1016/j.plgene.2025.100518","url":null,"abstract":"<div><div>Indian mustard (<em>Brassica juncea</em> L. Czern &amp; Coss.) is a highly economically important oilseed crop of India. An accurate estimation of genetic diversity inherent in breeding material is a pre-requisite for the success of any hybrid breeding programme, as it leads to identification of genetically divergent parents for exploiting high heterotic levels. In the present study, 200 genome-wide spanned simple sequence repeat (SSR) markers were used for estimation of genetic diversity and identification of genetically divergent parental combinations in a panel of 28 parental lines of Indian mustard comprising of 21 cytoplasmic male sterile (CMS) ‘A' lines and 7 restrorer ‘R' lines. A total of 179 SSR markers resulted in positive amplification with 155 (81.57 %) SSRs producing polymorphic amplicons and 24 (13.41 %) SSRs resulted into monomorphic products. Allele number varied from 2 to 6 with a mean value of 3.27 alleles per SSR marker. PIC values ranged from 0.23 to 0.7 with a mean value of 0.38 per SSR marker. Gene diversity values were in the range of 0.27–0.75 with average value of 0.47, inferring the presence of a moderate level of genetic diversity in the plant material. Neighbor-Joining dendrogram could not exactly differentiate ‘A' and ‘R' lines into different groups. This study led to identification of few genetically diverse A and R lines, suitable for making crosses for heterotic hybrid development in Indian mustard. On the basis of Euclidean distances, various cross-combinations viz. MJA10 &amp; MJR3/EC597313, MJA 14 &amp; MJR3/EC597313, and MH 12–12/EC597313S &amp; MJR9 were designated as genetically diverse genotypes. These cross-combinations may be used in hybrid breeding program to exploit heterosis in Indian mustard improvement.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100518"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144068341","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":"Chloroplast genomes of six Aloe species: Insights into genetic variation and evolutionary patterns","authors":"Dede Kurniawan ,&nbsp;Linzhou Li ,&nbsp;Min Liu ,&nbsp;Jose Marie Wynne Aquavita ,&nbsp;Martha Britany Napitupulu ,&nbsp;Manik Prabhu Narsing Rao ,&nbsp;Turhadi Turhadi ,&nbsp;Shouzhou Zhang ,&nbsp;Tong Wei ,&nbsp;Sunil Kumar Sahu","doi":"10.1016/j.plgene.2025.100530","DOIUrl":"10.1016/j.plgene.2025.100530","url":null,"abstract":"<div><div><em>Aloe</em> is a highly diverse genus of succulent plants with important pharmacological, medicinal, and commercial importance. However, the limited availability of genomic resources has constrained evolutionary and comparative genomics studies of this genus. To address this problem, we sequenced and assembled the first comprehensive chloroplast genome sequences of six <em>A</em><em>loe</em> species (<em>Aloe barberae, Aloe excelsa, Aloe marlothii, Aloe perfoliata, Aloe glauca</em>, and <em>Aloe tenuifolia</em>) using a high-throughput whole-genome sequencing approach. The total length of the assembled chloroplast genomes varied from 152,383 to 154,127 bp, exhibiting a conserved quadripartite structure comprising 131 genes. Comparative genomic analyses revealed the loss of the <em>rpl32</em> and <em>infA</em> genes across all the sampled species except for <em>Aloe arborescens</em>, suggesting lineage-specific gene retention. Furthermore, we identified eight protein-coding genes under positive selection and five intergenic regions with significant variability, which hold potential for molecular species identification (DNA barcoding) and phylogenetic studies. Phylogenetic reconstruction revealed robust branch support values, validating the monophyletic status of the <em>Aloe</em> genus and updating the sister clade of <em>Aloe vera</em>, which was previously close to <em>Aloe maculata</em>. These findings offer insights into genetic variation, gene loss, and potential evolutionary patterns, contributing to future phylogenetic and conservation research.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100530"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655442","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":"Segregation distortion and linkage analysis in F2 populations of pumpkin (C.Moschata Duch)","authors":"Zixia Zhang,&nbsp;Yanfang Jiang,&nbsp;Hailong Zhu,&nbsp;Ziyao Chen,&nbsp;Zefa Liu","doi":"10.1016/j.plgene.2025.100508","DOIUrl":"10.1016/j.plgene.2025.100508","url":null,"abstract":"<div><div>F₂ materials derived from a cross between introgression lines B-5 × A-3 were used as mapping population in <em>C. moschata.</em> Duch. Among the 89 genetic markers (ls, yf, and 87 marker alleles) analyzed, 5 markers (5.6 % P&lt;0.01) and 12 markers (13.5 % P&lt;0.01) showed genetic distortion in the F₂ population. Among these segregation distortion genetic markers, 11 genetic markers were skewed to the male parent B-5(64.70 %), 3 genetic markers were skewed to the heterozygote (17.65 %), and 3 genetic markers were skewed to both parents (17.65 %). These segregation distortion genetic markers were in the clusters of tight loci or single markers, which were distributed in 9 different chromosomes with 3 (SDR1, SDR2, and SDR3) hot regions in 3 (LGP2, LGP6, and LGP10) of them. In this research, reasons for segregation distortion were discussed, and the gametophyte selection may be the result of segregation distortion of genetic polymorphic loci.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100508"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835254","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":"The 14-3-3 gene family in Nicotiana tabacum: Genome-wide identification, expression profiling, subcellular localization, and protein interaction analysis in response to cadmium stress","authors":"Tengfei Ma ,&nbsp;Kunjian Yang ,&nbsp;Fang Yang ,&nbsp;Li Chen ,&nbsp;Ji Chen ,&nbsp;Shunqin Zhu ,&nbsp;Wanhong Liu","doi":"10.1016/j.plgene.2025.100525","DOIUrl":"10.1016/j.plgene.2025.100525","url":null,"abstract":"<div><div>Plant 14-3-3 proteins play a crucial role in the fine-tuning of growth and development, stress resistance, and nutrient metabolism. Tobacco is recognized as a hyperaccumulator of cadmium (Cd), yet the understanding of the <em>Nt14-3-3</em> gene family remains limited in tobacco (<em>Nicotiana tabacum</em> L.). This study systematically identified 28 members (designated as NtGRF1 through NtGRF28) of the <em>Nt14-3-3</em> family in the cultivated variety TN90 and categorized them into ε and non-ε groups. Genes within the same evolutionary branch exhibited similar conserved motif patterns and intron-exon structures. Promoter <em>cis</em>-acting element analysis indicated that the expression of <em>NtGRF</em> genes is regulated by plant hormones, particularly abscisic acid (ABA) and jasmonic acid (JA), as well as various stress factors. RNA-seq-based analysis revealed three expression patterns for the <em>Nt14-3-3</em> family genes: constitutively high-expressing, low-expressing, and tissue-specific expression groups, corroborating these findings with qPCR results. Cd stress significantly enhanced the expression levels of six out of eight randomly screened <em>NtGRF</em> genes (<em>NtGRF8, NtGRF15, NtGRF16, NtGRF21, NtGRF22,</em> and <em>NtGRF28</em>). Subcellular localization analysis showed that <em>NtGRF8, NtGRF16,</em> and <em>NtGRF22</em> were expressed in the cytoplasm and nucleus, while <em>NtGRF26</em> was restricted to the cytoplasm. Yeast two-hybrid assays demonstrated that <em>NtGRF16</em> and <em>NtGRF22</em> formed homodimers, with heterodimer formation also prevalent. These results offer important insights into the potential biological functions of the <em>Nt14-3-3</em> gene family, emphasizing their role in various biological processes, particularly in the response of tobacco to cadmium stress.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100525"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144279366","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":"Computational interference of gene regulatory networks on the growth and development of millets","authors":"Lipsa Leena Panigrahi ,&nbsp;Gayatri Mishra ,&nbsp;Dhaneswar Swain ,&nbsp;Gyana Ranjan Rout","doi":"10.1016/j.plgene.2025.100531","DOIUrl":"10.1016/j.plgene.2025.100531","url":null,"abstract":"<div><div>Millets are among the cereal crops cultivated for nutrient-rich food. They are generally considered as resilient crops in terms of growth requirements, as they can withstand harsh climatic factors such as unpredictable climate change and nutrient-depleted soils. The present review highlighted that gene regulatory networks are rewired to control the adaptable traits and to understand the transcriptional regulatory system against environmental stress. By combining machine learning, predictive modeling, and multi-omics data to unravel intricate regulatory relationships, computational methods have entirely changed the study of GRNs (gene regulatory networks), making and identifying important transcription factors, co-regulators, and signaling networks. Recent developments in artificial intelligence, systems biology, and bioinformatics have made reconstructing and analyzing millet GRNs, providing new information on blooming mechanisms, nutrient absorption,and drought resistance. Data scarcity, species-specific heterogeneity, and the requirement for high-throughput functional validation. Computational models incorporating transcriptomics, proteomics, and metabolomics help to improve crop improvement by enabling targeted genetic alterations and increasing predictive accuracy. This study discusses critical approaches, accessible datasets, and new developments in computational GRN investigations in millets. Deep learning, CRISPR-based gene editing, and synthetic biology in millet research are among the opportunities to develop new genotypes. By using computational methods to gain a thorough understanding of millet GRNs, it will be possible to create millet varieties that are more nutritious and climate-robust, promoting sustainable agriculture.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100531"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655443","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 receptor-like 2 kinase 1-like genes reveals involvement of a RLK1L member in tolerance to salt stress in Medicago sativa","authors":"Yiping Wei ,&nbsp;Tian Zhang ,&nbsp;Qinyan Bao,&nbsp;Zhaozhu Wen,&nbsp;Shuzhi Ma,&nbsp;Yanbo Zhang,&nbsp;Wenxuan Du","doi":"10.1016/j.plgene.2025.100520","DOIUrl":"10.1016/j.plgene.2025.100520","url":null,"abstract":"<div><div>The <em>Catharanthus roseus</em> receptor-like kinase 1-like (CrRLK1L) family constitutes a specialized group within plant receptor-like protein kinases that has been detected in numerous plant varieties. However, <em>RLK1L</em> members have not been characterized in alfalfa. Through systematic analysis, this study examined the features and identification of <em>RLK1L</em> genes within alfalfa based on known gene sequences from the model plants within the Arabidopsis genus, specifically <em>Arabidopsis thaliana</em>, and those in the Medicago genus, such as <em>Medicago truncatula</em>. Phylogenetic analysis of <em>AtCrRLK1Ls</em>, <em>MtCrRLK1Ls</em>, and <em>MsCrRLK1Ls</em> led to the classification of 19 <em>MsCrRLK1L</em> genes in alfalfa into eight distinct clusters<em>.</em> Bioinformatic analyses revealed that the molecular masses of MsCrRLK1L proteins spanned from 29.17 to 167.36 kDa. Subcellular targeting predictions indicated predominant cell membrane localization for these polypeptides Conserved domain profiling demonstrated the ubiquitous presence of a malectin-like domain across all MsCrRLK1L members. Chromosome localization and collinearity analysis showed that the 19 <em>MsCrRLK1L</em> genes were unevenly distributed across five alfalfa chromosomes, with four gene pairs exhibiting intra-species collinearity. <em>Cis</em>-Acting element analysis identified stress- and hormone-responsive motifs, suggesting that <em>MsCrRLK1Ls</em> are involved in abiotic stress signaling. Gene expression profiling under salt stress (200 mM NaCl) demonstrated tissue-specific induction patterns, with six <em>MsCrRLK1L</em> genes significantly upregulated in aerial and root tissues. Furthermore, <em>MsCrRLK1L2</em> overexpression in <em>Arabidopsis</em> improved the germination rate and growth status under salt stress. This study comprehensively profiles the <em>MsCrRLK1L</em> family in alfalfa, confirming its role in salt tolerance and suggesting genetic targets to boost crop resilience.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100520"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144139563","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":"Effectiveness of KASP-SNP markers in selecting for grain quality traits in rice","authors":"Maxwell Darko Asante ,&nbsp;Kirpal Agyemang Ofosu ,&nbsp;Felix Frimpong ,&nbsp;Deladem Kwami Alphonso ,&nbsp;Elizabeth Nartey ,&nbsp;Agyei Elvis Obeng ,&nbsp;Ralph K. Bam ,&nbsp;Daniel D. Gamenyah ,&nbsp;Priscilla F. Ribeiro ,&nbsp;William Manilal","doi":"10.1016/j.plgene.2025.100503","DOIUrl":"10.1016/j.plgene.2025.100503","url":null,"abstract":"<div><div>Grain quality is a crucial factor for rice consumers, and as such, it is a major focus for breeders. Phenotyping for grain quality traits can be a laborious and costly process. In this study, we evaluated the effectiveness of KASP-SNP markers in selecting for grain quality traits, including aroma, gelatinization temperature, grain length, grain width, and grain length: width ratio. We phenotyped 300 diverse rice genotypes for these four traits and genotyped them using their respective KASP-SNP markers. A regression analysis of the phenotype on the genotype was performed. The markers associated with the <em>fgr-1</em> and <em>GS3</em> genes explained 97 % and 94 % of the phenotypic variation for aroma and grain length, respectively. Two SNP markers (snpOS00440 and snpOS00441) associated with the <em>GW5/SW5</em> gene each explained 82 % of the phenotypic variation for grain width, which increased marginally to 85 % when combined. However, two markers, snpOS00036 and snpOS00450, for gelatinization temperature explained only 2 % and 25 % of the phenotypic variation, respectively, indicating that these markers were not efficient in predicting this trait. Our findings suggest that the markers associated with aroma (<em>fgr-1</em>), grain length (<em>GS3)</em>, and grain width (<em>GW5/SW5</em>) are highly efficient and reliable for marker-assisted selection.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100503"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844127","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":"Molecular network, structural and expression analyses of NHX genes in Phaseolus vulgaris in response to salt stress","authors":"Faten Mhadhbi,&nbsp;Hatem Boubakri","doi":"10.1016/j.plgene.2025.100526","DOIUrl":"10.1016/j.plgene.2025.100526","url":null,"abstract":"<div><div>Salt stress is one of the most serious abiotic stresses limiting plant productivity worldwide. Here, we identified and characterized Sodium/Hydrogen antiporter (NHX) family in <em>Phaseolus vulgaris</em> genome and studied their expression in response to salt stress, for the first time, using RT q-PCR. In total, we identified 9 <em>PvNHX</em> genes from the common bean genome. Phylogeny, gene structure, motif patterns were performed and allowed the classification of these genes according to their subcellular localization into three subfamilies termed vacuolar (Vac-class), plasma membrane (PM-class) and endosomal (Endo-class). Conserved motifs and gene structures showed that most of which had an amiloride-binding site (FFI/LY/FLLPPI). RT q-PCR analysis revealed that salt stress induced the expression of specific <em>PvNHX</em> genes in both leaves (<em>PvNHX1</em>, <em>PvNHX2</em>, Pv<em>NHX3</em>, and <em>PvNHX7</em>) and roots (<em>PvNHX1</em>, <em>PvNHX2</em>, <em>PvNHX3</em>, <em>PvNHX4</em> and <em>PvNHX7</em>), suggesting their potential role in regulating salinity tolerance in <em>P. vulgaris.</em> Protein-protein interaction (PPI) network indicated that several PvNHX proteins interact with CIPK24 (CBL-interacting serine/threonine-protein kinase 24), CBL4 (Calcineurin B-like protein 4) and KEA4 (K⁺ efflux antiporter 4) proteins, implying their involvement in CBL-CIPK pathway during salinity adaptation. These findings provide valuable targets within the <em>PvNHX</em> family for genetic engineering aimed at improving salinity tolerance in <em>Phaseolus vulgaris</em>.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100526"},"PeriodicalIF":2.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321044","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}