农学最新文献

{"title":"RNA modifications unlock the hidden code of synonymous mutations in crop domestication","authors":"Bin Zhang,&nbsp;Yan Li,&nbsp;Hao Yu","doi":"10.1007/s42994-025-00242-3","DOIUrl":"10.1007/s42994-025-00242-3","url":null,"abstract":"<div><p>Synonymous mutations have traditionally been regarded as functionally neutral because they do not alter protein sequences. However, growing evidence suggests these variants can affect gene expression, RNA structure, and protein function, ultimately influencing phenotypes. A recent study by Xin et al. (2025) provides strong evidence that synonymous mutations can exert regulatory effects through epitranscriptomic mechanisms, particularly m⁶A RNA methylation. The authors identify a synonymous 1287C &gt; T mutation in the <i>ACS2</i> gene that reduces m⁶A methylation at the adjacent A¹²⁸⁶ site. This reduction alters RNA secondary structure, creating a more compact conformation that impairs translation efficiency, leading to decreased ACS2 protein levels and promoting fruit elongation in cultivated cucumbers. The mutation lies within a domestication sweep region and <i>ACS2</i>^<i>1287C</i> is exclusively found in wild cucumber populations, suggesting that <i>ACS2</i>^<i>1287T</i> has been favored during domestication for its agronomic benefits. Notably, the study also uncovers a genotype-dependent interaction between <i>ACS2</i> and the m⁶A reader protein YTH1, which binds only to methylated transcripts, further illustrating how genetic background modulates epitranscriptomic regulation. These findings challenge the long-standing assumption that synonymous variants are biologically irrelevant and introduce RNA methylation as a key, dynamic regulatory layer in crop domestication and breeding, offering new opportunities for RNA-based precision breeding.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"389 - 393"},"PeriodicalIF":5.0,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"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":"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":"Cis-regulatory elements: systematic identification and horticultural applications","authors":"Tian Li,&nbsp;Wen Zeng,&nbsp;Fangjie Zhu,&nbsp;Peitao Lü","doi":"10.1007/s42994-025-00237-0","DOIUrl":"10.1007/s42994-025-00237-0","url":null,"abstract":"<div><p><i>Cis</i>-regulatory elements (CREs) are the genetic DNA fragments bound by transcription factors (TFs). CREs function as molecular switches that precisely modulate the dosage and spatiotemporal patterns of gene expression. The systematic identification of CREs not only facilitates the annotation of the functional non-coding genome but also provides essential insights into the architecture of gene regulatory networks and sheds light on an accurate selection of the target sites for genetic engineering of crops. In this review, we summarize the current high-throughput methodologies used for identifying CREs, illustrate the associations between CREs and agronomic traits in horticultural crops, and discuss how CREs can be exploited to facilitate crop breeding.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"510 - 527"},"PeriodicalIF":5.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00237-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetically poised chromatin states regulate PRR and NLR genes in soybean","authors":"Linzhe Jin,&nbsp;Yihan Zhang,&nbsp;Jiayuan Guo,&nbsp;Xuexia Liu,&nbsp;Yanling Lai,&nbsp;Xinfang Huang,&nbsp;Yuhan Zou,&nbsp;Shichuang Yan,&nbsp;Xianzhe Dai,&nbsp;Zhenhui Zhong","doi":"10.1007/s42994-025-00233-4","DOIUrl":"10.1007/s42994-025-00233-4","url":null,"abstract":"<div><p>In the plant innate immune system, pattern recognition receptor (PRR) and nucleotide-binding domain leucine-rich repeat (NLR) proteins recognize pathogens and activate defenses. To prevent excessive immune responses that could affect growth, plants regulate PRRs and NLRs at the transcriptional and post-transcriptional levels. Poised or bivalent chromatin states, marked by the simultaneous presence of active and repressive epigenetic modifications, maintain genes in a transcriptionally primed state, keeping their expression low while enabling their rapid activation in response to stress. Here, we investigated how poised chromatin states regulate PRR and NLR genes in soybean (<i>Glycine max</i>). Our integrative epigenomic and transcriptomic analysis revealed that although NLR and PRR genes both harbor abundant active and repressive histone modifications and exhibit high chromatin accessibility, their basal expression levels remain relatively low. Moreover, clustered NLR and PRR genes residing within the same topologically associating domains shared similar chromatin states and expression dynamics, suggesting coordinated control. These gene families had distinct epigenetic features: NLR genes displayed narrow H3K27me3 peaks together with strong pausing of RNA Polymerase II at their 5′ ends, whereas PRR genes were characterized by broader H3K27me3 peaks. Together, our results shed light on the role of poised chromatin states in coordinating growth and defense responses in soybean.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"411 - 423"},"PeriodicalIF":5.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00233-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulatory roles of RNA modifications in plant development and fruit ripening","authors":"Tianxiang Li,&nbsp;Junmei Huang,&nbsp;Guanqun Wang,&nbsp;Haoxuan Li,&nbsp;Peitao Lü","doi":"10.1007/s42994-025-00240-5","DOIUrl":"10.1007/s42994-025-00240-5","url":null,"abstract":"<div><p>The emerging field of epitranscriptomics has revolutionized our understanding of post-transcriptional regulation in plant systems. This review focuses on cutting-edge discoveries in the area of RNA modification, with a particular emphasis on the N⁶-methyladenosine (m⁶A)-mediated regulatory networks that govern plant development and fruit maturation. We systematically summarize the spatiotemporal patterns of RNA modifications and their integration into phytohormone signaling cascades and responses to environmental stimuli. Advanced epitranscriptome sequencing platforms have identified evolutionarily conserved modification signatures across angiosperm species, while simultaneously revealing species-specific regulatory architectures. Despite substantial progress, our understanding of the molecular mechanisms that underlie RNA modifications, especially those other than m⁶A, remains limited. We propose an innovative roadmap that combines CRISPR-based writer/eraser manipulation, single-cell spatial epitranscriptomics, and synthetic biology approaches to harness RNA modification networks for precision agriculture. We also underscore the importance of interdisciplinary collaboration that integrates findings from biology, chemistry, physics, and computer science to decode the plant epitranscriptome. To enable precise control of postharvest physiology, future priorities should include the development of biosensors for specific modification types, the engineering of RNA modification–dependent translation control systems, and the development of RNA epigenetic editing tools.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"472 - 488"},"PeriodicalIF":5.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00240-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GmMYB93 increases aroma formation in soybean by inhibiting the expression of a betaine aldehyde dehydrogenase gene","authors":"Jingnan Xu,&nbsp;Faming Lin,&nbsp;Chenhao Zhao,&nbsp;Shaolong Yang,&nbsp;Yu Zhang,&nbsp;Yongchun Shi,&nbsp;Xiaoran Wang,&nbsp;Ran Wang","doi":"10.1007/s42994-025-00236-1","DOIUrl":"10.1007/s42994-025-00236-1","url":null,"abstract":"<div><p>Soybean (<i>Glycine max</i>), an exceptionally nutritious crop rich in high-quality proteins and oils, is extensively used in various food products. Aromatic varieties of soybeans are in particular demand. Characterized by its distinctive popcorn-like aroma, 2-acetyl-1-pyrroline (2-AP) is an important volatile compound present in soybeans and other plants. The enzyme betaine aldehyde dehydrogenase (BADH) is closely associated with 2-AP production. However, the transcriptional regulatory network that governs <i>BADH</i> gene expression in soybean remains undefined. In this study, we determined that the transcript levels of the <i>BADH</i> gene, <i>GmBADH2</i>, vary significantly across different soybean organs and differ markedly from those of <i>GmBADH1</i>. We showed that GmMYB93 is a transcriptional repressor that directly regulates the expression of <i>GmBADH2</i> by binding to the CAGTTA elements in its promoter. Furthermore, the silencing of <i>GmMYB93</i> significantly reduced 2-AP accumulation in soybeans. Our findings shed light on the genetic mechanisms underlying soybean aroma formation and lay a foundation for developing novel aromatic soybean varieties.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"569 - 579"},"PeriodicalIF":5.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00236-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Soyasaponin β-glucosidase confers soybean resistance to pod borer (Leguminivora glycinivorella)","authors":"Chengyong Feng,&nbsp;Xindan Xu,&nbsp;Jia Yuan,&nbsp;Mingyu Yang,&nbsp;Fanli Meng,&nbsp;Guodong Wang","doi":"10.1007/s42994-025-00219-2","DOIUrl":"10.1007/s42994-025-00219-2","url":null,"abstract":"","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"580 - 585"},"PeriodicalIF":5.0,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00219-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanisms and crop improvement potential of RNA N6-methyladenosine in plants","authors":"Diyi Fu,&nbsp;Huiyuan Wang,&nbsp;Bochen Jiang","doi":"10.1007/s42994-025-00228-1","DOIUrl":"10.1007/s42994-025-00228-1","url":null,"abstract":"<div><p>N⁶-methyladenosine (m⁶A) is the most prevalent internal modification in eukaryotic mRNAs and contributes to the post-transcriptional regulation of gene expression. In plants, m⁶A modulates RNA splicing, stability, and translation, thereby influencing developmental processes and responses to environmental stimuli. This review systematically examines current advances in the understanding of m⁶A regulation in plants. We begin with an overview of the m⁶A modification and its associated regulatory machinery, including the writers (methyltransferases), erasers (demethylases), and readers (m⁶A-binding proteins) components, and discuss their roles in orchestrating RNA metabolism and determining plant phenotypes. Subsequent sections focus on the functional implications of m⁶A in economically important crops, with evidence drawn from model systems such as <i>Arabidopsis thaliana</i> and key species including rice (<i>Oryza sativa</i>), tomato (<i>Solanum lycopersicum</i>), and strawberry (<i>Fragaria vesca</i>), where m⁶A modifications have been linked to traits such as yield, maturation, and aroma. Finally, we explore emerging biotechnological strategies that harness m⁶A-mediated regulatory pathways to enhance crop quality, such as overexpression of human <i>FTO</i> encoding an m⁶A demethylase, quantitative m⁶A profiling at single-base resolution, CRISPR/Cas13-targeted m⁶A regulation, the application of small-molecule inhibitors, and m⁶A-driven multi-omics integration. These strategies provide a comprehensive framework for understanding the multifaceted roles of m⁶A in plant biology and underscore the potential of this modification as a target for next-generation crop improvement.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"489 - 509"},"PeriodicalIF":5.0,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00228-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","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}