Functional & Integrative Genomics最新文献

{"title":"Transforming tomatoes into GABA-rich functional foods through genome editing: A modern biotechnological approach","authors":"Kausalya Sakthivel,&nbsp;Rajagopal Balasubramanian,&nbsp;Vellaikumar Sampathrajan,&nbsp;Ravichandran Veerasamy,&nbsp;Sathiyamurthy V. Appachi,&nbsp;Kumar K.K","doi":"10.1007/s10142-025-01538-9","DOIUrl":"10.1007/s10142-025-01538-9","url":null,"abstract":"<div><p>Gamma-aminobutyric acid (GABA) functions as an inhibitory neurotransmitter which blocks the impulses between nerve cells in the brain. Due to the increasing awareness about the health promoting benefits associated with GABA, it is also artificially synthesized and consumed as a nutritional supplement by people in some regions of the world. Though among the fresh vegetables, tomato fruits do contain a comparatively higher amount of GABA (0.07 to 2.01 mg g⁻¹ FW), it needs to be further enhanced to fully impart its potential health benefits. Achieving this feat through classical breeding approaches is time and resource consuming, and is also associated with linkage drag. On the other hand, precise targeting of specific sites in the genome with less off- target effects is mediated by CRISPR/Cas9 genome editing tool and is widely used to overcome the barriers associated with traditional breeding approaches. Combining genome editing with speed breeding techniques can enable the rapid development of GABA-rich tomato cultivars, paving a way to unlock a new era of functional foods, where every bite contributes to cognitive well-being and holistic health. This review highlights the significance of GABA boosted functional foods and explores the potential of CRISPR/Cas9 technology for developing GABA enriched tomatoes.\u0000</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051227","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":"Mitochondria and its epigenetic dynamics: Insight into synaptic regulation and synaptopathies","authors":"Shiwangi Gupta,&nbsp;Abhinoy Kishore,&nbsp;Vikas Rishi,&nbsp;Aanchal Aggarwal","doi":"10.1007/s10142-025-01530-3","DOIUrl":"10.1007/s10142-025-01530-3","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Mitochondria, the cellular powerhouses, are pivotal to neuronal function and health, particularly through their role in regulating synaptic structure and function. Spine reprogramming, which underlies synapse development, depends heavily on mitochondrial dynamics-such as biogenesis, fission, fusion, and mitophagy as well as functions including ATP production, calcium (Ca&lt;sup&gt;2+&lt;/sup&gt;) regulation, and retrograde signaling. Mitochondria supply the energy necessary for assisting synapse development and plasticity, while also regulating intracellular Ca&lt;sup&gt;2+&lt;/sup&gt; homeostasis to prevent excitotoxicity and support synaptic neurotransmission. Additionally, the dynamic processes of mitochondria ensure mitochondrial quality and adaptability, which are essential for maintaining effective synaptic activity. Emerging evidence highlights the significant role of epigenetic modifications in regulating mitochondrial dynamics and function. Epigenetic changes influence gene expression, which in turn affects mitochondrial activity, ensuring coordinated responses necessary for synapse development. Furthermore, metabolic changes within mitochondria can impact the epigenetic machinery, thereby modulating gene expression patterns that support synaptic integrity. Altered epigenetic regulation affecting mitochondrial dynamics and functions is linked to several neurological disorders, including Amyotrophic Lateral Sclerosis, Huntington’s, Alzheimer’s, and Parkinson’s diseases, emphasizing its crucial function. The review delves into the molecular machinery involved in mitochondrial dynamics, ATP and Ca&lt;sup&gt;2+&lt;/sup&gt; regulation, highlighting the role of key proteins that facilitate the processes. Additionally, it also shed light on the emerging epigenetic factors influencing these regulations. It provides a thorough summary on the current understanding of the role of mitochondria in synapse development and emphasizes the importance of both molecular and epigenetic mechanisms in maintaining synaptic integrity.&lt;/p&gt;&lt;h3&gt;Graphical abstract &lt;/h3&gt;&lt;p&gt;&lt;b&gt;Effect of epigenetic regulation on mitochondrial processes that assist synapse development:&lt;/b&gt; This figure illustrates the intricate interplay between mitochondrial dynamics, bioenergetics, and epigenetic regulation, all of which are essential for synaptic function. A) Mitochondrial fission, driven by dynamin-related protein 1 (Drp1) and K-Ras, and C) Fusion, mediated by mitochondrial fusion protein 1 and 2 (Mfn1, Mfn2) and optic nerve atrophy 1 (Opa1), work together to maintain mitochondrial integrity and function. B) Biogenesis, regulated by peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), mechanistic target of rapamycin (mTOR), and transcription factors, alongside mitophagy involving PARKIN, PTEN-induced kinase 1 (PINK1), and BCL2-interacting protein 3 (BNIP3), ensures mitochondrial quality control and adaptation. D) The tricarboxylic acid (TCA) cycle drives the production of electron don","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027662","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":"The interactive role of microRNA and other non-coding RNA in hepatitis B (HBV) associated fibrogenesis","authors":"Kurt Sartorius,&nbsp;Yanglong Wang,&nbsp;Benn Sartorius,&nbsp;Samuel O. Antwi,&nbsp;Xiaodong Li,&nbsp;Anil Chuturgoon,&nbsp;Chongyuan Yu,&nbsp;Yunjie Lu,&nbsp;Yu Wang","doi":"10.1007/s10142-024-01519-4","DOIUrl":"10.1007/s10142-024-01519-4","url":null,"abstract":"<div><p>One of the outstanding features of chronic hepatitis B infection (CHB) is its strong association with liver fibrosis. CHB induced inflammation and injury trigger multiple biochemical and physical changes that include the promotion of a wide range of cytokines, chemokines and growth factors that activate hepatic stellate cells (HSCs) CHB induced activation of hepatic stellate cells (HSCs) is regarded as a central event in fibrogenesis to directly promote the synthesis of myofibroblasts and the expression of a range of materials to repair injured liver tissue. Fibrogenesis is modulated by the mainstream epigenetic machinery, as well as by non-coding RNA (ncRNA) that are often referred to as an ancillary epigenetic response to fine tune gene expression. Although extensive research has explained the regulatory role of ncRNA in liver fibrogenesis, most of this research relates to non-CHB etiologies. This review paper outlines the complex interactive regulatory role of microRNA (miRNA) and their interaction with long non-coding RNA (lncRNA), circular RNA (circRNA) and the mainstream epigenetic machinery in CHB induced liver fibrosis. The paper also illustrates some of the difficulties involved in translating candidate ncRNA into approved drugs or diagnostic tools. In conclusion, the important regulatory role of ncRNA in CHB induced liver fibrosis warrants further investigation to exploit their undoubted potential as diagnostic and therapeutic agents.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021485","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":"Heterogeneity analysis and prognostic model construction of HPV negative oral squamous cell carcinoma T cells using ScRNA-seq and bulk-RNA analysis","authors":"Chunyan Li,&nbsp;Zengbo Lv,&nbsp;Chongxin Li,&nbsp;Shixuan Yang,&nbsp;Feineng Liu,&nbsp;Tengfei Zhang,&nbsp;Lin Wang,&nbsp;Wen Zhang,&nbsp;Ruoyu Deng,&nbsp;Guoyu Xu,&nbsp;Huan Luo,&nbsp;Yinhong Zhao,&nbsp;Jialing Lv,&nbsp;Chao Zhang","doi":"10.1007/s10142-024-01525-6","DOIUrl":"10.1007/s10142-024-01525-6","url":null,"abstract":"<div><h3>Background</h3><p>T cells are involved in every stage of tumor development and significantly influence the tumor microenvironment (TME). Our objective was to assess T-cell marker gene expression profiles, develop a predictive risk model for human papilloma virus (HPV)-negative oral squamous cell carcinoma (OSCC) utilizing these genes, and examine the correlation between the risk score and the immunotherapy response.</p><h3>Methods</h3><p>We acquired scRNA-seq data for HPV-negative OSCC from the GEO datasets. We performed cell‒cell communication, trajectory, and pathway enrichment analyses of T-cell-associated genes. In addition, we constructed and validated a T-cell-associated gene prognostic model for HPV-negative OSCC patients using TCGA and GEO data and assessed the immune infiltration status of HPV-negative OSCC patients .qRT-PCR was used to detect the expression level of prognosis-related genes in different risk groups.</p><h3>Results</h3><p>ScRNA-seq was conducted on 28,000 cells derived from 14 HPV-negative OSCC samples and 6 normal samples. We identified 4,635 T cells from these cells and identified 774 differentially expressed genes(DEGs) associated with T cells across five distinct T-cell subtypes. Through the integration of bulk-RNAseq data, we established a prognostic model based on DEGs related to T cells. By separating patients into high-risk and low-risk groups according to these prognostic related genes, we can accurately predict their survival rates and the immune infiltration status of the TME.qRT-PCR results showed that compared with the patients of low risk group, the expression of PMEPA1, SH2D2A, SMS and PRDX4 were significantly up-regulated in high risk group.</p><h3>Conclusion</h3><p>This study provides a resource for understanding the heterogeneity of T cells in HPV-negative OSCC patients and associated prognostic risk models. It provides new insights for predicting survival and level of immune infiltration in patients with HPV-negative OSCC.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027649","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":"The role of nanoparticles in transforming plant genetic engineering: advancements, challenges and future prospects","authors":"Neelam Rani,&nbsp;Kusum Kumari,&nbsp;Vinita Hooda","doi":"10.1007/s10142-025-01528-x","DOIUrl":"10.1007/s10142-025-01528-x","url":null,"abstract":"<div><p>Despite years of progress in biotechnology, altering the genetic makeup of many plant species, especially their plastids, remains challenging. The existence of a cell wall poses a significant obstacle to the effectual transportation of biomolecules. Developing efficient methods to introduce genes into plant cells and organelles without causing harm is an ongoing area of research. Traditional approaches like <i>Agrobacterium-</i>mediated transformation, biolistic particle delivery, electroporation and polyethylene glycol (PEG) transformation have shown some success but come with limitations like laborious, time-consuming and causing tissue damage. For instance, the <i>Agrobacterium</i> method can be applied only to the restricted host range, while PEG transformation and biolistic particle delivery are not very efficient. In contrast, nanotechnology made an appearance in the field of genetic engineering. Nanoparticles act as delivery vehicles for many cargos in animals. However, in plants, the application of nanocarriers for the delivery of biomolecules is still in its infant stage. Nonetheless, it holds immense potential for the future of plant biotechnology and genome editing.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995643","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":"High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine","authors":"Dipali Barku Dongare,&nbsp;Shaik Shireen Nishad,&nbsp;Sakshi Y. Mastoli,&nbsp;Shubhini A. Saraf,&nbsp;Nidhi Srivastava,&nbsp;Abhishek Dey","doi":"10.1007/s10142-025-01529-w","DOIUrl":"10.1007/s10142-025-01529-w","url":null,"abstract":"<div><p>High-resolution insights into the nucleotide arrangement within an organism’s genome are pivotal for deciphering its genetic composition, function, and evolutionary trajectory. Over the years, nucleic acid sequencing has been instrumental in driving significant advancements in genomics and molecular biology. The advent of high-throughput or next-generation sequencing (NGS) technologies has revolutionized whole genome sequencing, revealing novel and intriguing features of genomes, such as single nucleotide polymorphisms and lethal mutations in both coding and non-coding regions. These platforms provide a practical approach to comprehensively identifying and analyzing whole genomes with remarkable throughput, accuracy, and scalability within a short time frame. The resulting data holds immense potential for enhancing healthcare systems, developing novel and personalized therapies, and preparing for future pandemics and outbreaks. Given the wide array of available high-throughput sequencing platforms, selecting the appropriate technology based on specific needs is crucial. However, there is limited information regarding sample preparation, sequencing principles, and output data to facilitate a comparative evaluation of these platforms. This review details various NGS technologies and approaches, examining their advantages, limitations, and future potential. Despite being in their early stages and facing challenges, ongoing advancements in NGS are expected to yield significant future benefits. </p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995642","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":"Comparison of the rhizospheric soil bacteriomes of Oryza sativa and Solanum melongena crop cultivars reveals key genes and pathways involved in biosynthesis of ectoine, lysine, and catechol meta-cleavage","authors":"Manisha Mandal,&nbsp;Biswajit Ghosh,&nbsp;Shyamapada Mandal","doi":"10.1007/s10142-025-01536-x","DOIUrl":"10.1007/s10142-025-01536-x","url":null,"abstract":"<div><p>Rice (<i>Oryza sativa</i> L.), <i>Poaceae</i> family, forms staple diet of half of world’s population, and brinjal (<i>Solanum melongena</i> L.), an important solanaceous crop, are consumed worldwide. Rhizosphere research is gaining importance towards application of knowledge for improving productivity, sustainable agricultural practice, and rhizoremediation for nature restoration. While there are reports on rhizobacteriome of rice, studies comparing structural, functional and metabolomic traits of microbial communities in rhizospheres of rice and brinjal are not yet available. We demonstrated, in <i>Oryza sativa</i> (1144-Hybrid, Dhiren, Local Saran cultivars) and <i>Solanum melongena</i> (Jhiloria, Chandtara, Jotshna cultivars) rhizospheres from Malda, India, using integrated approach of 16 S ribosomal sequencing, shotgun metagenomics, and microbial metabolomics to decipher microbial diversity, association with soil physicochemical characteristics, key genes and pathways. Ectoine biosynthesis was significantly expressed in brinjal (Jhiloria), but not in rice rhizosphere. The dominant brinjal rhizobacteriome-specific bacteria comprised <i>Thermus</i> sp., <i>Petrobacter succinatimandens</i>, <i>Thermoanaerobacter</i> sp., and <i>Diaphorobacter</i> sp., that were involved in house-keeping functions including pentose phosphate pathway, biosynthesis of amino acids, lipopolysaccharide, and photosynthesis. The dominant bacteria unique to rice rhizobacteriome (Local Saran) consisted of <i>Aeromonas</i> sp., associated with catechol meta-cleavage, while <i>Clostridium</i> sp., <i>Faecalibacterium prausnitzii</i>, and <i>Roseburia</i> sp. were involved with lysine biosysnthesis in rice (1144-Hybrid). Our results imply novel information for improved breeding of brinjal specific cultivar with enhanced ectoine production associated with osmotic stress tolerance, rice specific cultivars with enhanced lysine production significant to human nutrition and catechol removal for the maintenance of environmental quality.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995697","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":"SUMMER: an integrated nanopore sequencing pipeline for variants detection and clinical annotation on the human genome","authors":"Renqiuguo Li,&nbsp;Hongyuan Chu,&nbsp;Kai Gao,&nbsp;Huaxia Luo,&nbsp;Yuwu Jiang","doi":"10.1007/s10142-025-01534-z","DOIUrl":"10.1007/s10142-025-01534-z","url":null,"abstract":"<div><p>Long-read sequencing has emerged as a transformative technology in recent years, offering significant potential for the molecular diagnosis of unresolved genetic disorders. Despite its promise, the comprehensive detection and clinical annotation of genomic variants remain intricate and technically demanding. We present SUMMER, an integrated and structured workflow specifically designed to process raw Nanopore sequencing reads. SUMMER facilitates an in-depth analysis of multiple variant types, including SNV, SV, short tandem repeat and mobile element insertion. For clinical applications, SUMMER employs SvAnna to prioritize SV candidates based on phenotype relevance and utilizes Straglr to provide reference distributions of non-pathogenic unit counts for 55 known pathogenic short tandem repeats. By addressing critical challenges in variant detection and annotation, SUMMER seeks to advance the clinical utility of long-read sequencing in diagnostic genomics. SUMMER is available on the web at https://github.com/carolhuaxia/summer.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01534-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995757","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":"Prioritization of candidate genes regulating the dwarfness in rice by integration of whole-genome and transcriptome analyses","authors":"Gunasekaran Ariharasutharsan,&nbsp;Adhimoolam Karthikeyan,&nbsp;Seshadri Geetha,&nbsp;Muthurajan Raveendran,&nbsp;Ravi Lalitha,&nbsp;Latha Ananda-Lekshmi,&nbsp;Manoharan Akilan,&nbsp;Dhanalakshmi Veeraraj Sushmitharaj,&nbsp;Manickam Dhasarathan,&nbsp;Ramasamy Saraswathi,&nbsp;Paramasivam Arunachalam","doi":"10.1007/s10142-025-01532-1","DOIUrl":"10.1007/s10142-025-01532-1","url":null,"abstract":"<div><p>Dwarfism is a major trait for developing lodging-resistant rice cultivars. Gamma irradiation-induced mutagenesis has proven to be an effective method for generating dwarf rice mutants. In this research, we isolated a dwarf mutant from Anna R (4) in the M₂ generation and subsequently stabilized the trait through successive selfing of progeny across the M₃-M₇ generations. We then employed whole-genome re-sequencing (WGRS) and RNA sequencing (RNA-seq) analyses of Anna R (4) and the mutant (designated as ACM-20001) to elucidate the underlying mechanisms and identify candidate genes associated with dwarfness. Numerous genetic variations were identified between Anna (R) 4 and ACM-20001 through WGRS. In total, 2049 genetic variants, including 343 InDels and 1706 nonsynonymous SNPs, were identified across 697 genes. Additionally, RNA-seq analysis revealed 2,881 differentially expressed genes between the wild-type Anna (R) 4 and the mutant ACM-20001, with 1,451 genes up-regulated and 1,430 genes down-regulated in ACM-20001 compared to Anna (R) 4. By integrating WGRS and RNA-seq data with functional annotation analysis, we identified the most likely candidate genes (i.e., <i>Os02g0506400</i>, <i>Os05g0515200</i>, <i>Os06g0154200</i> and <i>Os08g0250900</i>) related to dwarfness. Quantitative real-time PCR analysis verified the expression of these genes. Collectively, our study provides valuable insights in to the genes and mechanisms underlying dwarfness in rice. Further studies are required to elucidate the roles of these candidate genes in dwarfness, which contribute to advancements rice breeding programs.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995084","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":"Genomics-assisted stacking of waxy1, opaque2, and crtRB1 genes for enhancing amylopectin in biofortified maize for industrial utilization and nutritional security","authors":"Subhra J. Mishra,&nbsp;Firoz Hossain,&nbsp;Rajkumar U. Zunjare,&nbsp;Rashmi Chhabra,&nbsp;Ashvinkumar Katral,&nbsp;Ikkurti Gopinath,&nbsp;Vinay Bhatt,&nbsp;Govinda Rai Sarma,&nbsp;Zahirul A. Talukder,&nbsp;Ravindra K. Kasana,&nbsp;Elangbam L. Devi,&nbsp;Konsam Sarika,&nbsp;Brijesh K. Mehta,&nbsp;Satish K. Guleria,&nbsp;Jitender Kumar,&nbsp;Vignesh Muthusamy","doi":"10.1007/s10142-024-01523-8","DOIUrl":"10.1007/s10142-024-01523-8","url":null,"abstract":"<div><p>Waxy maize is highly preferred diet in developing countries due to its high amylopectin content. Enriching amylopectin in biofortified maize meets food security and fulfils the demand of rising industrial applications, especially bioethanol. The mutant <i>waxy1</i> (<i>wx1</i>) gene is responsible for increased amylopectin in maize starch, with a wide range of food and industrial applications. Conventional maize has a modest amount of amylopectin (70–75% of starch), but waxy maize, with favourable <i>wx1</i> allele, has ~ 95–100% amylopectin. In this study, the <i>wx1</i> allele was introgressed into the multi-nutrient-rich maize parental inbreds (PMI-PV9 and PMI-PV5) of APQH8, a multi-nutrient rich maize hybrid having high lysine, tryptophan, and provitamin-A nutritionally superior over the traditional hybrids. Gene-specific markers specific for <i>o2</i> and <i>crtRB1</i> were employed to select desirable gene segregants from BC₁F₁, BC₂F₁, and BC₂F₂. Background selection was employed with &gt; 90 SSR markers. Selected backcross progenies showed high recovery of recurrent parent genomes (RPG: 94.8–96.8%). The reconstituted waxy hybrids exhibited an increase in amylopectin (mean: 98.4%) compared to the original hybrid (mean: 72.7%). The reconstituted hybrids also recorded enhanced lysine (mean: 0.382%), tryptophan (mean: 0.092%), and provitamin-A (mean: 10.36 ppm), respectively, than normal maize, however similar to the original hybrid with high lysine: 0.330%, tryptophan: 0.079% and provitamin-A: 10.42 ppm. Furthermore, MAS-derived genotypes showed similar agro-morphological traits and grain yield. These biofortified waxy maize hybrids, rich in provitamin-A, lysine, and tryptophan with enhanced amylopectin hold great potential in diverse industrial applications and nutritional security.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142994919","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}