农学最新文献

{"title":"Untargeted metabolomic genome-wide association study reveals genetic and biochemical insights into polyphenols of apple fruit.","authors":"Jun Song, Beatrice Amyotte, Leslie Campbell Palmer, Melinda Vinqvist-Tymchuk, Kyra Dougherty, Letitia Da Ros","doi":"10.1093/hr/uhaf159","DOIUrl":"https://doi.org/10.1093/hr/uhaf159","url":null,"abstract":"<p><p>Apple (<i>Malus × domestica</i>) is one of the most popular fruits grown and consumed worldwide, contributing to human health with significant amounts of polyphenols and other bioactive compounds, and providing positive impacts to the economy and society. Understanding the diversity and inheritance of health-active compounds in apple can provide novel selection criteria for future breeding and cultivar development, as consumers increasingly prioritize the health benefits of their food choices. We therefore conducted an untargeted metabolomic analysis using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS) to investigate thousands of semipolar chemicals, mainly phenolic compounds, in 439 diverse apple accessions, and quantified 2066 features in positive ion mode. To identify key areas of genetic control for apple metabolite abundance, we performed a metabolomic genome-wide association study (mGWAS) on the quantified mass features using ~280 000 single nucleotide polymorphisms (SNPs). The mGWAS revealed >630 significant loci with hotspots for various groups of known and unknown phenolic compounds including flavonols on Chromosome 1, dihydrochalcones on Chromosome 5, and flavanols on Chromosomes 15 and 16. The most significant hotspot on Chromosome 16 included bHLH and C2H2 transcription factors that may play a role in controlling the abundance and complexity of phenolic compounds through regulation of the flavonoid biosynthesis pathway. Our analysis links the apple metabolome with candidate genes and biosynthetic mechanisms and establishes a foundation for marker-assisted breeding and gene editing to improve and modify phenolic compounds in apple for marketability and the benefit of human health.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"12 9","pages":"uhaf159"},"PeriodicalIF":8.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12377893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Progress on small non-coding RNAs in male reproductive development and intergenerational inheritance.","authors":"Yu-Qian Shi, Jian-Feng Ma, Si-Yu Chen, Li-Xin Zhou, Jia Xue, Lin-Yuan Shen, Li Zhu, Mai-Lin Gan","doi":"10.16288/j.yczz.24-335","DOIUrl":"10.16288/j.yczz.24-335","url":null,"abstract":"<p><p>Small non-coding RNAs (sncRNAs) are crucial in epigenetics, playing a significant regulatory role in the normal development and intergenerational inheritance of male reproduction. Research has shown that highly expressed sncRNAs, including miRNAs, piRNAs, and tsRNAs, are vital in maintaining male germ cell development and spermatogenesis. sncRNAs regulate gene expression, influence protein translation, and modify sperm epigenetics, contributing to male reproductive development at various stages. Abnormal expression of sncRNAs is closely linked to male infertility. Furthermore, growing evidence suggests that environmental exposures affect sperm epigenetic modifications, often leading to phenotypic changes in future generations. In this review, we summarize the types and functions of sncRNAs in male germ cells and examine their role in intergenerational inheritance due to environmental factors. It aims to provide new insights into male reproductive health and potential targets for preventing and treating male infertility and related diseases.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 8","pages":"861-875"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875602","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":"Mass spectrometry-based analysis of RNA and its modifications.","authors":"Ying Feng, Xiao-Li He, Yu Liu, Jin Wang","doi":"10.16288/j.yczz.25-052","DOIUrl":"10.16288/j.yczz.25-052","url":null,"abstract":"<p><p>Ribonucleic acids (RNAs) are key biomolecules responsible for the transmission of genetic information, the synthesis of proteins and its regulation, and modulation of many biochemical processes. They are also the key components of many viruses. Chemically modified synthetic RNAs or oligoribonucleotides are becoming more widely used as therapeutics and vaccines. Demands for technologies to detect, sequence, identify, and quantify RNA and its modifications far exceed requirements found in the DNA realm. Currently, mass spectrometry (MS) has become the primary technology for identifying, sequencing, and quantifying RNA and its modifications. This paper mainly reviews latest advances in mass spectrometry for the research of RNA and its modifications, and discusses the strengths and weaknesses of this technology, aiming to provide readers with a comprehensive perspective from technical fundamentals to application prospects, promote the broader application of mass spectrometry in RNA research, and provide important references for method developers and biological researchers in the field.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 8","pages":"885-902"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875599","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 basis of microRNA stability and degradation in plants.","authors":"Meng-Wei Guo, You-Hong Fan, Guo-Dong Ren","doi":"10.16288/j.yczz.25-030","DOIUrl":"10.16288/j.yczz.25-030","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs with 20 to 24 nucleotides in length. They primarily regulate gene expression at the post-transcriptional level and influence numerous biological processes, including reproduction, development, and responses to environmental stimuli in both plants and animals. The spatiotemporal expression of miRNAs across organs, tissues, and cells is tightly regulated at multiple levels, encompassing transcription, processing, stability control, and targeted degradation. The biochemical pathway of miRNA biogenesis, including transcription and processing, has been established, and its regulatory mechanisms have also been extensively studied. In this review, we systematically summarize current advances in post-biogenesis regulation of miRNA stability, turnover, and targeted degradation in plants, with comparative analyses of similarities and differences in animal systems. By integrating these advances, this review seeks to provide a framework for further elucidating the molecular mechanisms controlling intracellular miRNA abundance.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 8","pages":"944-957"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875600","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":"Application and prospects of current computational methods in m⁶A research: a comprehensive review.","authors":"Ding-Wei Lei, Rui-Chu Gu, Xiao-Xue Xie, Shi-Zhi Ding, Han Wen","doi":"10.16288/j.yczz.24-373","DOIUrl":"10.16288/j.yczz.24-373","url":null,"abstract":"<p><p><i>N</i>⁶-methyladenosine (m⁶A) is the most prevalent modification in eukaryotic mRNA, playing a pivotal role in regulating various aspects of mRNA metabolism, including splicing, processing, degradation, and translation. This review provides a comprehensive overview of computational strategies employed in m⁶A research, with an emphasis on data-driven methodologies for the prediction of m⁶A sites and molecular dynamics simulations for deciphering m⁶A-associated biological mechanisms. The article first discusses the evolution of m⁶A detection technologies, outlines the corresponding data processing methods, and summarizes publicly available datasets that serve as essential resources for constructing computational models. Subsequently, we highlight research advancements in machine learning and deep learning models for m⁶A site prediction. Finally, we demonstrate the contributions of molecular dynamics simulations in unravelling m⁶A-related molecular mechanisms, illustrating how computational methods facilitate the understanding of this complex epigenetic regulation. By systematically synthesizing relevant content, this review further discusses the latest research progress and application values of computational methods in m⁶A modification, offering new perspectives and insights for in-depth investigations.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 8","pages":"903-927"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875596","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":"Biogenesis, action, function of plant small RNAs and their potential application in agriculture.","authors":"Huai-Hao Yang, Bing-Lian Zheng","doi":"10.16288/j.yczz.25-163","DOIUrl":"10.16288/j.yczz.25-163","url":null,"abstract":"<p><p>Plant small RNAs (sRNAs) are essential regulators of gene expression and genome stability in plants. Based on their biogenesis and mechanisms of action, they are primarily classified into two major categories: microRNAs (miRNAs) and small interfering RNAs (siRNAs). These sRNAs rely on distinct processing proteins for their production and effector proteins to execute their functions, playing pivotal roles in diverse developmental processes and environmental responses. Recent advances in next-generation sequencing have identified numerous novel sRNAs across multiple plant species, while studies in <i>Arabidopsis thaliana</i> and various crops have significantly enhanced our understanding of their biogenesis, regulatory networks, and biological functions. In this review, we systematically summarize the research progress on different classes of plant sRNAs, focusing on their biosynthetic pathways, molecular mechanisms, and biological function. Furthermore, we discuss the potential applications of plant sRNAs in agriculture, including their prospects as next-generation RNA pesticides, supported by current technological developments. This review aims to provide a theoretical foundation for further research on plant sRNAs and their agricultural applications.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 8","pages":"928-943"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875597","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":"Progress on nucleos(t)idyl lipid-based nanoparticles for nucleic acid drugs delivery.","authors":"Jia-Mei Hong, Hong-Yi Liu, Hua Guo, Jing Yu, Qi Zhang, Zhu Guan, Zhen-Jun Yang","doi":"10.16288/j.yczz.24-378","DOIUrl":"10.16288/j.yczz.24-378","url":null,"abstract":"<p><p>Nucleic acid drugs can function at the gene level, and have the advantages of simple synthesis, easy modification and high specificity. However, there are many obstacles in transfection and <i>in vivo</i> delivery due to their negative charge, high molecular weight, and hydrophilicity. Lipid nanoparticles (LNPs) can encapsulate siRNA or mRNA through electrostatic interactions and five related drugs have been approved as of April 2025. However, due to the inevitable immunogenicity and hepatosplenic toxicity, most LNP-encapsulated nucleic acid drugs were terminated in the early clinical stage. Nucleos(t)idyl lipids are a class of amphiphilic molecules composed of nucleobases or nucleos(t)idyl heads, linkers and lipid tail chains, which can bind with the bases of nucleic acid drugs through hydrogen bonding and π-π stacking and self-assemble to form nanoparticles or micelles with broad application prospects. In this review, we summarize the research progress in delivery systems of nucleic acid drugs based on nucleos(t)idyl lipids and peptidyl lipids, and discuss their differences with LNP-encapsulated nucleic acid drugs, including structural characterization, molecular dynamics simulation, <i>in vivo</i> distribution, as well as efficacy and safety, so as to provide new ideas for improving the targeting delivery of nucleic acid drugs.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 8","pages":"823-841"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875601","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":"CRISPR/Cas system targeting RNA and its derivative technology.","authors":"Xun Zhou, Shi-Jie Zhou, Jie Liu, Yu-Xiang Wang","doi":"10.16288/j.yczz.24-311","DOIUrl":"10.16288/j.yczz.24-311","url":null,"abstract":"<p><p>RNA editing is one of the important research directions in the field of epigenetics. With further research, scientists have discovered that the CRISPR/Cas system can target not only DNA but also RNA, thereby achieving precise gene editing at the transcriptional level. Moreover, using the CRISPR/Cas system for RNA editing can also avoid damage to genome. At present, a variety of derivative technologies based on RNA-targeting CRISPR systems have been developed, including RNA knockdown and editing, nucleic acid detection and imaging, and RNA tracking. The emergence of these derivative technologies provides powerful tools for deciphering biological genetic mechanisms and disease treatment. In this review, we summarize the structure, function, mechanisms, and derived technologies of RNA-targeting CRISPR/Cas systems, aiming to enrich people's understanding of CRISPR/Cas-mediated RNA editing.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 8","pages":"842-860"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875598","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":"RNAi-based antiviral immunity.","authors":"De-Yu Xu, Xi Zhou, Yu-Jie Ren","doi":"10.16288/j.yczz.25-077","DOIUrl":"10.16288/j.yczz.25-077","url":null,"abstract":"<p><p>RNA interference (RNAi) is a gene silencing mechanism mediated by small RNAs derived from double-stranded RNA (dsRNA), capable of silencing specific genes. Following viral invasion, the dsRNA produced during viral replication is cleaved by the host cell's Dicer protein, generating virus-derived small interfering RNAs (virus-derived small interference RNAs, vsiRNA). These vsiRNAs then guide the cleavage and degradation of viral RNA <i>via</i> the RNAi pathway, exerting an antiviral effect. Therefore, RNAi is also recognized as an efficient antiviral immune pathway during viral infection. However, through long-term evolution, viruses have developed various strategies to counteract RNAi. For instance, they encode specific viral suppressors of RNAi (VSRs) that target and antagonize key molecules in this pathway. Research indicates that designing drugs to specifically target VSRs can \"unlock\" the antiviral function of RNAi within host cells, demonstrating highly potent and relatively broad-spectrum antiviral activity. Furthermore, viral infection can also be regulated by host- or virus-derived microRNAs (miRNAs). The role of miRNAs in viral infection provides new targets for antiviral therapy. In this review, we summarize the mechanism of RNAi in antiviral immunity, recent research advances, and its application prospects in antiviral therapy, aiming to provide theoretical support for antiviral immunity research and treatment.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 8","pages":"876-884"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875603","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":"Correction to: Discovery of bifunctional diterpene cyclases/synthases in bacteria supports a bacterial origin for the plant terpene synthase gene family.","authors":"","doi":"10.1093/hr/uhaf170","DOIUrl":"10.1093/hr/uhaf170","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/hr/uhaf139.].</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"12 8","pages":"uhaf170"},"PeriodicalIF":8.5,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}