Functional & Integrative Genomics最新文献

{"title":"A curated tissue-specific proteome, phosphoproteome, and kinome map of Drosophila melanogaster with an integrated outlook in circadian physiology","authors":"Sandip Das,&nbsp;Arpita Kannihalli,&nbsp;Srishti Banerjee,&nbsp;Nikita Chakraborty,&nbsp;Sandipan Ray","doi":"10.1007/s10142-025-01554-9","DOIUrl":"10.1007/s10142-025-01554-9","url":null,"abstract":"<div><p>The fruit fly <i>Drosophila melanogaster</i> is a simple multicellular model system widely used in biomedical research. Here, we aimed to curate a comprehensive tissue and organ-specific proteome, phosphoproteome, and kinome atlas of <i>D. melanogaster.</i> Using information from published literature and databases, we have systematically curated the protein expression profiles, phosphorylation patterns, and the associated kinases and phosphatases in 11 tissue types across the different developmental stages and mature <i>D. melanogaster</i> and its derived cell lines. Gene annotation and pathway enrichment analysis were performed using the DAVID. Protein-protein interaction analysis was carried out using STRING, BioGrid, OmniPath, and InWeb-IM. <i>Drosophila</i> kinase and phosphatase gene orthologs in humans and mice were identified through the FlyBase database, utilizing the DRSC integrative ortholog prediction tool. We mapped a total of 18,377 proteins, 9021 phosphoproteins, 433 kinases, and 141 phosphatases in <i>D. melanogaster</i>. Subsequent categorization of the proteins into different tissue types indicated the enrichment of some tissue-specific pathways and expression clusters. We identified 295 and 289 <i>Drosophila</i> kinase orthologs in humans and mice through an ortholog screening. In the rhythmicity analysis, we observed 24-hour periodicity in 5289 transcripts, 678 proteins, 437 phosphoproteins, 166 kinases, and 89 phosphatases. The findings of our study are integrated as a convenient resource for understanding the proteome-level organizations in <i>Drosophila</i>, their oscillating expression, and their tissue-specific roles in maintaining cellular and physiological functions. We anticipate that this study will help to enhance the systems-level analysis of <i>D. melanogaster</i> as a model organism.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143446604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of phenylalanine ammonia-lyase protein family from algae to angiosperm","authors":"Chao Zhang,&nbsp;Huan Guo,&nbsp;Zhongling Li,&nbsp;Shuning Yue","doi":"10.1007/s10142-025-01548-7","DOIUrl":"10.1007/s10142-025-01548-7","url":null,"abstract":"<div><p>Phenylpropanes, the precursors of various phenolic compounds in plants, are widely distributed. Phenylalanine ammonia-lyase (PAL) is the main enzyme that catalyzes the early step of the phenylpropanoid pathway to generate trans-cinnamic acid, which is the common precursor for the lignin and flavonoid biosynthetic pathways. Therefore, in this study, we focused on PAL evolution. A total of 584 PAL-like protein sequences were obtained, and only two PAL-like genes were found in algae, primary. Three main groups are separated by their different evolutionary stages. Group I mainly cluster ancient plants, and groups II and III are formed by angiosperms, which separate monocots (group II) and eudicots (group III). According to the sequence alignment, five main differences in amino acids may correlate with this separation, which involve the change of amino acid phosphorylation. The prediction analysis of GO and KEGG annotation information of each PAL protein showed that the proteins were clustered in cytoplasm and correlated with phenylalanine ammonia-lyase activity. Our results suggested that the PAL enzyme family expanded alongside the development of vascular tissues and underwent duplication events that facilitated gene cluster expansion and phenotypic diversity. Analysis of a reassembled and publicly available gene database confirmed that only two PAL genes were present in algae, whereas land plants possess a significantly greater number of PAL-like genes. This expansion is closely of PAL genes in land plants is closely associated with gene duplication events occurring at various evolutionary stages after algae plants. Futhermore, investigation into miRNAs revealed limited specificity across the plant evolution spectrum, with their primary role being the regulation and modulation of gene function. Additionally, analysis of PAL proteins across the plant kingdom ultimately elucidates that the evolution of their functions is intricately linked to the widespread distribution of cis-acting elements. This evolutionary trajectory reflected the natural selection processes that plants had undergone over time to enhance their eadaptability to diverse environments. These findings provide a valuable reference for future research into the functional evolution of PAL genes and their role in .plant adaptation and phenotypic diversity. </p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling key genes and pathways involved in Verticillium wilt resistance by integrative GWAS and transcriptomic approaches in Upland cotton","authors":"Majid Khan,&nbsp;Daowu Hu,&nbsp;Shuai Dai,&nbsp;Hongge Li,&nbsp;Zhen Peng,&nbsp;Shoupu He,&nbsp;Muhammad Awais,&nbsp;Xiongming Du,&nbsp;Xiaoli Geng","doi":"10.1007/s10142-025-01539-8","DOIUrl":"10.1007/s10142-025-01539-8","url":null,"abstract":"<div><p><i>Verticillium dahliae</i> Kleb, the cause of Verticillium wilt, is a particularly destructive soil-borne vascular disease that affects cotton, resulting in serious decline in fiber quality and causing significant losses in cotton production worldwide. However, the progress in identification of wilt-resistance loci or genes in cotton has been limited, most probably due to the highly complex genetic nature of the trait. Nevertheless, the molecular mechanism behind the Verticillium wilt resistance remains poorly understood. In the present study, we investigated the phenotypic variations in Verticillium tolerance and conducted a genome wide association study (GWAS) among a natural population containing 383 accessions of upland cotton germplasm and performed transcriptomic analysis of cotton genotypes with differential responses to Verticillium wilt. GWAS detected 70 significant SNPs and 116 genes associated with resistance loci in two peak signals on D02 and D11 in E1. The transcriptome analysis identified a total of 2689 and 13289 differentially expressed genes (DEGs) among the Verticillium wilt-tolerant (J46) and wilt-susceptible (J11) genotypes, respectively. The DEGs were predominantly enriched in metabolism, plant hormone signal transduction, phenylpropanoid pathway, MAPK cascade pathway and plant-pathogen interaction pathway in GO and KEGG analyses. The identified DEGs were found to comprise several transcription factor (TF) gene families, primarily including AP2/ERF, ZF, WRKY, NAC and MYB, in addition to pentatricopeptide repeat (PPR) proteins and Resistance (R) genes. Finally, by integrating the two results, 34 candidate genes were found to overlap between GWAS and RNA-seq analyses, associated with Verticillium-wilt resistance, including <i>WRKY, MYB, CYP</i> and <i>RGA.</i> This work contributes to our knowledge of the molecular processes underlying cotton responses to Verticillium wilt<i>,</i> offering crucial insights for additional research into the genes and pathways implicated in these responses and paving the way for developing Verticillium wilt-resistant cotton varieties through accelerated breeding by providing a plethora of candidate genes.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NSUN7 promotes cervical cancer progression through activation of ErbB signaling pathway","authors":"Yuxia Li,&nbsp;Ruijiao Lu,&nbsp;Xieyidai Abuduhailili,&nbsp;Yangchun Feng","doi":"10.1007/s10142-025-01546-9","DOIUrl":"10.1007/s10142-025-01546-9","url":null,"abstract":"<div><p>We aimed to investigate the role of NSUN7 in the progression of Cervical Cancer through a combination of bioinformatics analysis and cell and animal culture experiments. We comprehensively assessed the expression levels of NSUN7 in the TCGA and CCLE databases, and explored its correlations with clinicopathological features, immune cell infiltration, DNA damage repair gene function, drug sensitivity, and methylation status. The NSUN7 gene was disrupted through lentiviral infection, and the effects on cell proliferation, invasion, and apoptosis were evaluated using CCK-8 assay, Transwell migration assay, and flow cytometry analysis. Gene enrichment analysis wasidentify the biological pathways associated with NSUN7 and cervical cancer development. Additionally, a xenograft model of cervical cancer was established to assess the in vivo inhibitory effect of NSUN7 and its impact on pathway molecules. The results of both in vitro and in vivo experiments confirmed that silencing the NSUN7 gene significantly inhibited the growth, spread, and metastasis of cervical cancer cells, while promoting apoptosis. TUNEL assay and HE staining further verified the apoptotic effect of NSUN7 on tumor tissues, and KEGG enrichment analysis revealed a significant enrichment of NSUN7 in the ErbB pathway. Silencing of NSUN7 resulted in a significant down-regulation of key ErbB pathway proteins (HER2, STAT5, PI3K/p-PI3K) as demonstrated by quantitative real-time PCR and Western blot. These findings suggest that NSUN7 may affect the biological behavior of cervical cancer cells and promote tumor development by activating the ErbB signaling pathway.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TFAP2A-regulated CRNDE enhances colon cancer progression and chemoresistance via RIPK3 interaction","authors":"Xin Gao,&nbsp;Yanming Huang,&nbsp;Tonghui Wei,&nbsp;Jingmin Xue,&nbsp;Filippov Iurii,&nbsp;Laishou Yang,&nbsp;Liying Wang,&nbsp;Hao Li,&nbsp;Genshen Mo,&nbsp;Yuze Huang,&nbsp;Haonan Xie,&nbsp;Hang Wang,&nbsp;Shenghan Lou,&nbsp;Peng Han","doi":"10.1007/s10142-025-01545-w","DOIUrl":"10.1007/s10142-025-01545-w","url":null,"abstract":"<div><p>Colon cancer (CC) is a common malignancy with rising incidence worldwide. Despite advances in treatment strategies, many patients still face a poor prognosis due to the development of drug resistance. Long non-coding RNAs (lncRNAs) have emerged as important regulators of various biological processes and have been implicated in cancer progression. Among them, colorectal neoplasia differentially expressed (CRNDE) has drawn attention for its potential roles in different cancers. However, its specific functions in CC remain unclear. In this study, we identified CRNDE as highly expressed in CC, contributing to tumor progression and drug resistance. Mechanically, CRNDE is regulated by the transcription factor TFAP2A. Additionally, CRNDE inhibits pyroptosis, a form of programmed cell death, by promoting the ubiquitin-mediated degradation of RIPK3, thereby reducing the sensitivity of CC cells to 5-fluorouracil (5-FU). Our findings suggest that the TFAP2A/CRNDE/RIPK3 axis plays critical roles in colon cancer progression and chemoresistance, highlighting potential therapeutic targets for improving treatment outcomes.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01545-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering nutrient stress in plants: integrative insight from metabolomics and proteomics","authors":"Abiodun Yusuff Moshood,&nbsp;Mukhtar Iderawumi Abdulraheem,&nbsp;Linze Li,&nbsp;Yanyan Zhang,&nbsp;Vijaya Raghavan,&nbsp;Jiandong Hu","doi":"10.1007/s10142-025-01551-y","DOIUrl":"10.1007/s10142-025-01551-y","url":null,"abstract":"<div><p>To comprehend the responses and resilience of plants under unfavorable environmental conditions, it is crucial to study the metabolomics and proteomic insights into nutrient stress. Nutrient stress substantially challenges agriculture, impacting plant growth, development, and productivity due to a lack or imbalance of essential nutrients, which can happen due to poor soil quality, limited nutrient availability, or unfavorable climatic conditions. Although there has been significant progress in the study of plant nutrient stress using metabolomics and proteomics, several challenges and research gaps still need to be addressed, such as the standardized experimental protocols, data integration strategies, and bioinformatic tools are necessary for comparative analysis and interpretation of omics data. Hence, this review explores the theoretical frameworks of metabolomics and proteomics as powerful tools to decode plant responses to nutrient stress, addressing critical knowledge gaps in the field. This review highlights the advantages of integrative analyses, combining metabolomics, proteomics, and transcriptomics, to uncover the molecular networks governing nutrient stress resilience. Key findings underscore the potential of these techniques to enhance breeding strategies and genetic engineering efforts aimed at developing nutrient-efficient crops. Through metabolomics and proteomic analyses, novel molecular components and regulatory networks have been revealed as responsive to nutrient stress, and this breakthrough has the potential to bolster plant resilience and optimize nutrient utilization. Understanding the synergistic roles of metabolites and proteins in nutrient stress resilience has profound implications for crop improvement and agricultural sustainability. Future research should focus on refining integrative methodologies and exploring their applications across diverse plant species and environmental conditions, paving the way for innovative solutions to nutrient stress challenges. </p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of 4-coumarate CoA ligase (4CL) gene family and functional study of Sm4CL2/3/7/9 in Salvia miltiorrhiza","authors":"Fan Fu,&nbsp;Huiting Qin,&nbsp;Yujie Xin,&nbsp;Qianmo Li,&nbsp;Heng Kang,&nbsp;Limin Han,&nbsp;Wenping Hua,&nbsp;Xiaoyan Cao","doi":"10.1007/s10142-025-01541-0","DOIUrl":"10.1007/s10142-025-01541-0","url":null,"abstract":"<div><p>The 4-coumarate CoA ligase (4CL, EC6.2.1.12) enzyme is pivotal for the final step of three shared stages in the general phenylpropane metabolic pathway, which plays a critical role in the biosynthesis of a diverse array of metabolites (e.g., phenolic acids, flavonoids, lignin, anthocyanins, and coumarins). Ten <i>4CL</i> genes have been identified in the genome of <i>Salvia miltiorrhiza</i> (a model medicinal plant), the majority of these genes have not yet been characterized. In this study, the expression profiles of the <i>Sm4CLs</i> gene family were analyzed by qRT-PCR. Among the ten members, <i>Sm4CL7</i> had the highest expression across various tissues, while <i>Sm4CL5</i> showed the lowest transcription levels. Notably, <i>Sm4CL2/3/4/6/7/9/10</i> were significantly responsive to methyl jasmonate (MeJA) treatments. Ten <i>4CLs</i> were divided into four groups via phylogenetic analysis, while <i>Sm4CL2/3/7/9</i> that represented each group were selected for further investigation. The GUS staining results of <i>proSm4CL2/3/7/9::GUS</i> transgenic <i>Arabidopsis thaliana</i> were strongly consistent with the qRT-PCR results, and all four <i>Sm4CLs</i> were located in the cytoplasm. Compared with the control, transgenic <i>S. miltiorrhiza</i> plants that overexpressed <i>Sm4CL2/3/7/9</i> possessed reduced contents of p-coumaric acid and caffeic acid, albeit higher levels of rosmarinic acid and salvianolic acid. In conclusion, this research expands our understanding of the <i>Sm4CL</i> gene family and offers insights into enhancing the quality of <i>S. miltiorrhiza</i> and the production of secondary metabolites through the targeted manipulation of 4CL enzymes.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143373271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive insights and In silico analysis into the emerging role of LincRNAs in lung diseases pathogenesis; a step toward ncRNA precision","authors":"Nadia M. Hamdy,&nbsp;Mohamed Bakr Zaki,&nbsp;Nourhan M. Abdelmaksoud,&nbsp;Shereen Saeid Elshaer,&nbsp;Mai A. Abd-Elmawla,&nbsp;Nehal I. Rizk,&nbsp;Doaa Fathi,&nbsp;Ahmed S. Doghish,&nbsp;Ahmed I. Abulsoud","doi":"10.1007/s10142-025-01540-1","DOIUrl":"10.1007/s10142-025-01540-1","url":null,"abstract":"<div><p>Long non-coding RNAs (lncRNAs) have emerged as essential regulators of gene expression, significantly influencing various biological processes. Approximately half of all lncRNAs are classified as long intergenic non-coding RNAs (lincRNAs), which are situated among coding genes. Recent studies have documented the role of lincRNAs in the pathogenesis of lung diseases, including lung cancer, pulmonary fibrosis, and pulmonary arterial hypertension. These lincRNAs can modulate gene expression through various mechanisms, including epigenetic modifications, transcriptional regulation, and post-transcriptional regulation. By functioning as competing endogenous RNAs (ceRNAs), lincRNAs can affect the activity of microRNAs (miRNAs) and their corresponding target genes. This review delves into the intricate mechanisms by which lincRNAs contribute to the development and progression of various lung diseases. Furthermore, it discusses the potential of lincRNAs as therapeutic targets.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01540-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miRNAs and their multifaceted role in cutaneous wound healing","authors":"Reda M. Mansour,&nbsp;Sherif S. Abdel Mageed,&nbsp;Farah A. Awad,&nbsp;Mohamed M. Sadek,&nbsp;Shehab Ahmed Adel,&nbsp;Alaa Ashraf,&nbsp;Khaled M. Alam-Eldein,&nbsp;Nada E. Ahmed,&nbsp;Rana Y. Abdelaziz,&nbsp;Esraa Farid Tolba,&nbsp;Hend H. Mohamed,&nbsp;Nehal I. Rizk,&nbsp;Mohamed O. Mohamed,&nbsp;Osama A. Mohammed,&nbsp;Ahmed S. Doghish","doi":"10.1007/s10142-025-01535-y","DOIUrl":"10.1007/s10142-025-01535-y","url":null,"abstract":"<div><p>The dynamic, complex process of cutaneous wound healing is required to restore skin integrity following an injury. This intricate process consists of four sequential and overlapping phases: hemostasis, inflammation, proliferation, and remodeling. Hemostasis immediately begins to function in response to vascular injury, forming a clot that stops the bleeding. To fight infection and remove debris, immune cells are enlisted during the inflammatory phase. Angiogenesis, re-epithelialization, and the creation of new tissue are all components of proliferation, whereas tissue maturation and scarring are the outcomes of remodeling. Chronic wounds, like those found in diabetic ulcers, frequently stay in a state of chronic inflammation because they are unable to go through these stages in a coordinated manner. The important regulatory roles that microRNAs (miRNAs) play in both normal and pathological wound healing have been highlighted by recent investigations. The miRNAs, small non-coding RNAs, modulate gene expression post-transcriptionally, profoundly impacting cellular functions. During the inflammatory phase, miRNAs control pro- and anti-inflammatory cytokines, as well as the activity of immune cells such as neutrophils and macrophages. Additionally, miRNAs are essential components of signaling networks related to inflammation, such as the toll-like receptor (TLR), nuclear factor kappa B (NF-kB), and Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathways. Some miRNAs have been discovered to either increase or alleviate inflammatory reactions, indicating their potential as therapeutic targets. Other miRNAs aid in angiogenesis by promoting the development of new blood vessels, which are essential for providing oxygen and nutrients to the healing tissue. They also affect keratinocyte migration and proliferation during the re-epithelialization phase, which involves growing new epithelial cells over the lesion. Another function of miRNAs is that they control the deposition of extracellular matrix (ECM) and the creation of scars during the remodeling phase. The abnormal expression of miRNAs in chronic wounds has led to the exploration of miRNA-based treatments. With a focus on resistant instances such as diabetic wounds, these therapeutic techniques seek to improve wound healing results by correcting the dysregulated miRNA expression.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143108052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancing vegetable genetics with gene editing: a pathway to food security and nutritional resilience in climate-shifted environments","authors":"Rajib Roychowdhury,&nbsp;Soumya Prakash Das,&nbsp;Siddhartha Das,&nbsp;Sabarni Biswas,&nbsp;Manish Kumar Patel,&nbsp;Ajay Kumar,&nbsp;Umakanta Sarker,&nbsp;Sikander Pal Choudhary,&nbsp;Ranjan Das,&nbsp;Kalenahalli Yogendra,&nbsp;Sunil S Gangurde","doi":"10.1007/s10142-025-01533-0","DOIUrl":"10.1007/s10142-025-01533-0","url":null,"abstract":"<div><p>As global populations grow and climate change increasingly disrupts agricultural systems, ensuring food security and nutritional resilience has become a critical challenge. In addition to grains and legumes, vegetables are very important for both human and animals because they contain vitamins, minerals, and fibre. Enhancing the ability of vegetables to withstand climate change threats is essential; however, traditional breeding methods face challenges due to the complexity of the genomic clonal multiplication process. In the postgenomic era, gene editing (GE) has emerged as a powerful tool for improving vegetables. GE can help to increase traits such as abiotic stress tolerance, herbicide tolerance, and disease resistance; improve agricultural productivity; and improve nutritional content and shelf-life by fine-tuning key genes. GE technologies such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR-Cas9) have revolutionized vegetable breeding by enabling specific gene modifications in the genome. This review highlights recent advances in CRISPR-mediated editing across various vegetable species, highlighting successful modifications that increase their resilience to climatic stressors. Additionally, it explores the potential of GE to address malnutrition by increasing the nutrient content of vegetable crops, thereby contributing to public health and food system sustainability. Additionally, it addresses the implementation of GE-guided breeding strategies in agriculture, considering regulatory, ethical, and public acceptance issues. Enhancing vegetable genetics via GE may provide a reliable and nutritious food supply for an expanding global population under more unpredictable environmental circumstances.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}