aBIOTECH最新文献

{"title":"Identification of post-transcriptional regulation reveals complexity in peanut pod development by Direct RNA","authors":"Wei Wang,&nbsp;Haosong Guo,&nbsp;Jianxin Bian,&nbsp;Fa Cui,&nbsp;Xiaoqin Liu","doi":"10.1007/s42994-025-00224-5","DOIUrl":"10.1007/s42994-025-00224-5","url":null,"abstract":"<div><p>Peanut (<i>Arachis hypogaea</i>) is widely cultivated worldwide as an important source of edible vegetable oil and protein. Peanut seed pods develop below ground from a gynophore that forms above ground and then penetrates the soil surface to bury the developing pod. Numerous studies have explored transcriptional regulation during peanut pod development. Here, we explored post-transcriptional regulation, including polyadenylation, alternative splicing, and RNA adenosine methylation (m⁶A), in peanut pods across four developmental stages by performing direct RNA sequencing. This produced 70.43 million long reads with average lengths of 890–1,136 nucleotides (nt) from 12 samples across four developmental stages, yielding a total of 14,627 newly identified transcripts. We detected a negative relationship between poly(A) tail lengths and transcript abundance, with the shortest poly(A) tails at the subterranean peg and expanded pod 1 stages, and longest poly(A) tails at the aerial gynophore and expanded pod 2 stages. Moreover, throughout pod development, from the penetration of the gynophore into the soil to pod enlargement, the splicing machinery utilized more proximal than distal alternative polyadenylation sites in the transcripts. The date showed no correlation between m⁶A modification and gene expression in peanut, but found more transcripts with alternative first and last exon types of alternative splicing events. Transcripts that were differentially abundant across developmental stages were primarily enriched in the Gene Ontology terms photosynthesis, response to oxidative stress, response to auxin, plant-type cell wall organization, and lignin catabolism. This study lays a foundation for revealing the roles of epigenetics and post-transcriptional regulation in pod development in peanut. </p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"554 - 568"},"PeriodicalIF":5.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00224-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100600","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":"Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression","authors":"Lin Luo,&nbsp;Qi Qu,&nbsp;Mengxue Cao,&nbsp;Yihui Zhang,&nbsp;Yuanchang Sun,&nbsp;Fei Mao,&nbsp;Jiaming Chen,&nbsp;Yilin Zhu,&nbsp;Yaorou Yang,&nbsp; HuachengLiu,&nbsp;Chunxiao Li,&nbsp;Dongmei Lin,&nbsp;Guodong Lu,&nbsp;Zhanxi Lin,&nbsp;Fangjie Zhu,&nbsp;Jiajing Xiao","doi":"10.1007/s42994-025-00243-2","DOIUrl":"10.1007/s42994-025-00243-2","url":null,"abstract":"<div><p>Pearl millet (<i>Pennisetum glaucum</i>) is a major staple food in arid and semi-arid regions of sub-Saharan Africa, India, and South Asia. However, how epigenetic mechanisms regulate tissue-specific gene expression in this crop remains poorly understood. In this study, we profiled multiple epigenetic features in the young panicles and roots of pearl millet using RNA-seq, ATAC-seq, whole-genome bisulfite sequencing, and ChIP-seq (H3K4me3 and H3K36me3). We identified thousands of genes that were differentially expressed between these two tissues. Root-specific genes were enriched for plant hormone signaling, oxidative phosphorylation, and stress responses. Analysis of chromatin accessibility revealed that root-specific accessible chromatin regions (ACRs) were enriched in binding motifs for stress-responsive transcription factors (e.g., NAC, WRKY), whereas ACRs in young panicles were enriched in motifs for developmental regulators (e.g., AP2/ERF). DNA methylation profiling revealed 25,141 tissue-specific differentially methylated regions, with CHH methylation—rather than CG or CHG methylation—showing the strongest tissue specificity. Promoters of root-specific genes had higher levels of CHH methylation compared to those of young panicle–specific genes, suggesting that the roles of CHH methylation in regulating transcription might be tissue dependent. Notably, promoter-associated H3K4me3 marked panicle-specific genes, whereas root-specific expression was primarily linked to chromatin accessibility, suggesting a transcription factor–mediated regulatory mechanism. Together, our findings highlight the distinct epigenetic frameworks governing tissue-specific gene expression in pearl millet and provide valuable insights for advancing the genetic improvement of this crop.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"394 - 410"},"PeriodicalIF":5.0,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00243-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100765","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":"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":"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":"Epigenetic regulation of JASMONATE ZIM-DOMAIN genes contributes to heat tolerance in the heat-tolerant rice cultivar Nagina 22","authors":"Xiaoxuan Du,&nbsp;Yingnan Sun,&nbsp;Yonggang He,&nbsp;Haiya Cai,&nbsp;Xiangsong Chen","doi":"10.1007/s42994-025-00229-0","DOIUrl":"10.1007/s42994-025-00229-0","url":null,"abstract":"<div><p>Extreme hot weather severely limits rice (<i>Oryza sativa</i>) production. Rice cultivars from regions with hot weather are a valuable resource for breeding heat-tolerant rice, but the mechanisms mediating heat tolerance in these cultivars are not fully understood. Here, we investigated heat-tolerance mechanisms in rice using the well-known heat-tolerant cultivar Nagina 22 (N22) and comparing it with the less heat-tolerant cultivar 93–11. Following heat shock (HS) treatment (45 °C for 3 or 24 h), the expression of <i>JASMONATE ZIM-DOMAIN</i> (<i>JAZ</i>) genes spiked during the early stages of HS responses in N22 but not 93–11 and genes related to jasmonic acid (JA) signaling were repressed in N22. Promoting JA signaling in N22 via pretreatment with methyl JA (MeJA) impaired the heat tolerance of N22, measured as survival after HS treatment of 45 °C for 30 h, followed by a 7-d recovery. Furthermore, the N22-specific activation of <i>JAZ</i> genes was associated with increased histone acetylation and decreased DNA methylation. Comparing N22 to 93–11, we propose that the DNA demethylation process, rather than the hypomethylation status per se, is likely associated with <i>JAZ</i> activation. In summary, we revealed epigenetic mechanisms that may contribute to the heat tolerance of N22 via the JA signaling pathway; our findings have implications for improving heat tolerance in rice and other crops.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 3","pages":"441 - 451"},"PeriodicalIF":5.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00229-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100764","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}