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Metabolic engineering in Nicotiana benthamiana 本菌烟草的代谢工程
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-09-10 DOI: 10.1007/s42994-025-00234-3
Karim Farmanpour Kalalagh, Nicolas Papon, Vincent Courdavault, Sander van der Krol, Iris F. Kappers, Arman Beyraghdar Kashkooli
{"title":"Metabolic engineering in Nicotiana benthamiana","authors":"Karim Farmanpour Kalalagh,&nbsp;Nicolas Papon,&nbsp;Vincent Courdavault,&nbsp;Sander van der Krol,&nbsp;Iris F. Kappers,&nbsp;Arman Beyraghdar Kashkooli","doi":"10.1007/s42994-025-00234-3","DOIUrl":"10.1007/s42994-025-00234-3","url":null,"abstract":"<div><p>Plants can produce compounds with extraordinary chemical structures and a wide range of applications in the treatment of human diseases. The biosynthesis of such compounds in plants is often complex and limited to specific tissues and specialized cells, resulting in low yields. Unlike many medicinal plants, <i>Nicotiana benthamiana</i> is easy to grow and is amenable to genetic manipulation. Indeed, many metabolic pathways for valuable medicinal compounds have been elucidated and reconstructed in <i>N. benthamiana</i> through <i>Agrobacterium tumefaciens</i>-mediated transient expression of the relevant metabolic genes. Here, we review different aspects to consider when characterizing candidate metabolic genes and their products, as well as reconstructing their biosynthetic pathways in <i>N. benthamiana</i>. We discuss how high yields from ectopically expressed pathways may benefit from boosting precursor levels, as well as from eliminating competing enzymatic activities and various detoxification reactions. Finally, we discuss innovative approaches to studying the export of compounds through the plasma membrane and cell wall and explain how these approaches may influence the industrial-scale production of valuable compounds in <i>N. benthamiana</i>.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"638 - 662"},"PeriodicalIF":5.0,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00234-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595241","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}
引用次数: 0
Identification of post-transcriptional regulation reveals complexity in peanut pod development by Direct RNA 转录后调控的鉴定揭示了直接RNA在花生豆荚发育中的复杂性
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-09-08 DOI: 10.1007/s42994-025-00224-5
Wei Wang, Haosong Guo, Jianxin Bian, Fa Cui, Xiaoqin Liu
{"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 (m<sup>6</sup>A), 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 m<sup>6</sup>A 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}
引用次数: 0
FHBDSR-Net: automated measurement of diseased spikelet rate of Fusarium Head Blight on wheat spikes FHBDSR-Net:小麦穗上赤霉病病穗率的自动测定
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-09-02 DOI: 10.1007/s42994-025-00245-0
Ze Wu, Haowei Zhao, Zeyu Chen, Yongqiang Suo, Seena Joseph, Xiaohui Yuan, Caixia Lan, Weizhen Liu
{"title":"FHBDSR-Net: automated measurement of diseased spikelet rate of Fusarium Head Blight on wheat spikes","authors":"Ze Wu,&nbsp;Haowei Zhao,&nbsp;Zeyu Chen,&nbsp;Yongqiang Suo,&nbsp;Seena Joseph,&nbsp;Xiaohui Yuan,&nbsp;Caixia Lan,&nbsp;Weizhen Liu","doi":"10.1007/s42994-025-00245-0","DOIUrl":"10.1007/s42994-025-00245-0","url":null,"abstract":"<div><p>Fusarium Head Blight (FHB), a fungal wheat (<i>Triticum aestivum</i>) disease that threatens global food security, requires precise quantification of diseased spikelet rate (DSR) as a phenotypic indicator for resistance breeding. Most techniques for measuring DSR rely on manual spikelet-by-spikelet observation and counting, which is inefficient and destructive. Although deep learning offers great promise for automated DSR measurement, existing intelligent detection algorithms are hampered by the lack of spikelet-level annotated data, insufficient feature representation for diseased spikelets, and weak spatial encoding of densely arranged spikelets. To address these challenges, we constructed a dataset of 620 high-resolution RGB images of wheat spikes with 5,222 spikelet-level annotations to systematically analyze spikelet size distributions to fill small-object detection data gaps in this field. We designed FHBDSR-Net, a light framework for automated DSR measurement centered on diseased spikelet detection, which features (1) multi-scale feature enhancement architecture that dynamically combines lesion textures, morphological features, and lesion-awn contrast through adaptive multi-scale kernels to suppress background noise; (2) the Inner-EfficiCIoU loss function to reduce small-target localization errors in dense contexts; and (3) a scale-aware attention module using dilated convolutions and self-attention to encode multi-scale pathological patterns and spatial distributions to enhance dense spikelet resolution. FHBDSR-Net detected diseased spikelets with an average precision of 93.8% with a lightweight design of 7.2 M parameters. The results were strongly correlated with expert evaluations, with a Pearson correlation coefficient of 0.901. Our method is suitable for deployment on resource-constrained mobile devices, facilitating portable plant phenotyping and smart breeding.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"726 - 743"},"PeriodicalIF":5.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00245-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595240","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}
引用次数: 0
Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression 珍珠粟的表观遗传图谱揭示了CHH甲基化在调节组织特异性基因表达中的重要作用
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-08-26 DOI: 10.1007/s42994-025-00243-2
Lin Luo, Qi Qu, Mengxue Cao, Yihui Zhang, Yuanchang Sun, Fei Mao, Jiaming Chen, Yilin Zhu, Yaorou Yang,  HuachengLiu, Chunxiao Li, Dongmei Lin, Guodong Lu, Zhanxi Lin, Fangjie Zhu, Jiajing Xiao
{"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}
引用次数: 0
DU-Net-L: an effective and lightweight segmentation model for alfalfa images that integrates the strengths of DeepLabV3+ and U-Net DU-Net-L:一种有效且轻量级的苜蓿图像分割模型,它融合了DeepLabV3+和U-Net的优点
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-08-22 DOI: 10.1007/s42994-025-00235-2
Wei Tian, Kang Chong, Jingyu Zhang
{"title":"DU-Net-L: an effective and lightweight segmentation model for alfalfa images that integrates the strengths of DeepLabV3+ and U-Net","authors":"Wei Tian,&nbsp;Kang Chong,&nbsp;Jingyu Zhang","doi":"10.1007/s42994-025-00235-2","DOIUrl":"10.1007/s42994-025-00235-2","url":null,"abstract":"<div><p>Alfalfa (<i>Medicago sativa</i>), a globally important crop known for its high yields, wide adaptability, and high protein content, provides an excellent feed source for livestock. Smart breeding, an emerging technology that integrates genomics and phenomics, holds considerable promise for accelerating the development of elite varieties of alfalfa. Nevertheless, there are few phenotypic analysis tools available for alfalfa. Here, we present DU-Net-L, an effective and lightweight model for segmenting alfalfa images that enables preliminary analysis of branch phenotypes based on digital images. In our study, the DeepLabV3+ model struggled to handle petioles, while U-Net performed poorly with images captured under high light. To address these issues, we have created a new model utilizing ResNet34 as its feature extraction module and retaining the architectures of both DeepLabV3+ and U-Net. An analysis based on test data indicated that the new model overcame the shortcomings of using either of the two base models individually. Subsequently, we lightened the fused model by reducing output channels in each block, while maintaining its predictive capability. We have named the lightened model DU-Net-L. Ultimately, we adopted an exponential decay strategy for the learning rate and increased the number of training epochs to select an optimal parameter combination. This approach achieved 99.83% accuracy and a mean intersection over union of 0.9411, with a size of 25.42 MB. In summary, we have provided a lightweight model that effectively segments stems and leaves in alfalfa images, fulfilling the requirements for the preliminary analysis of branch phenotypes.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"763 - 773"},"PeriodicalIF":5.0,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00235-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595147","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}
引用次数: 0
Dissecting the genetic basis of agronomic traits by multi-trait GWAS and genetic networks in maize (Zea mays L.) 利用多性状GWAS和遗传网络剖析玉米农艺性状的遗传基础
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-08-14 DOI: 10.1007/s42994-025-00241-4
Ying Zhou, Yanfang Heng, Shoukun Chen, Jinglu Wang, Kunhui He, Jiahui Geng, Kaijian Fan, Yonggui Xiao, Changling Huang, Jiankang Wang, Enying Zhang, Liang Li, Huihui Li
{"title":"Dissecting the genetic basis of agronomic traits by multi-trait GWAS and genetic networks in maize (Zea mays L.)","authors":"Ying Zhou,&nbsp;Yanfang Heng,&nbsp;Shoukun Chen,&nbsp;Jinglu Wang,&nbsp;Kunhui He,&nbsp;Jiahui Geng,&nbsp;Kaijian Fan,&nbsp;Yonggui Xiao,&nbsp;Changling Huang,&nbsp;Jiankang Wang,&nbsp;Enying Zhang,&nbsp;Liang Li,&nbsp;Huihui Li","doi":"10.1007/s42994-025-00241-4","DOIUrl":"10.1007/s42994-025-00241-4","url":null,"abstract":"<div><p>Agronomic traits in maize (<i>Zea mays</i> L.) are complex and modulated by pleiotropic loci and interconnected genetic networks. However, the traditional single-trait genome-wide association study (GWAS) method often misses genetic associations among traits, overlooks pleiotropic effects, and underestimates shared regulatory mechanisms. In the current study, we employed multi-trait analysis of GWAS (MTAG) and constructed a genetic network to dissect the genetic architecture of 18 agronomic traits across a genetically diverse panel of 2,448 maize inbred lines. Incorporating MTAG significantly improved the detection of pleiotropic loci that had not been detected by single-trait GWAS. Using a genetic network, we uncovered numerous previously unrecognized connections among traits related to plant architecture, yield, and flowering time. The 49 detected hub nodes, including Zm00001d028840 and Zm00001d033859 (<i>knotted1</i>), influence multiple traits. Co-expression analysis of candidate genes across two developmental stages validated their distinct yet complementary roles, with Zm00001d028840 linked to early cell wall remodeling and Zm00001d033849 involved in chromatin remodeling during tasseling. Moreover, we integrated results from GWAS, MTAG, and genetic network analyses to prioritize pleiotropic loci and hub genes that regulate multiple agronomic traits. This integrative approach offers a practical framework for selecting stable, multi-trait-associated targets, thereby supporting more precise and efficient crop improvement strategies.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"707 - 725"},"PeriodicalIF":5.0,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00241-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595208","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}
引用次数: 0
RNA modifications unlock the hidden code of synonymous mutations in crop domestication RNA修饰解开了作物驯化过程中同义突变的隐藏密码
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-08-14 DOI: 10.1007/s42994-025-00242-3
Bin Zhang, Yan Li, Hao Yu
{"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 m<sup>6</sup>A RNA methylation. The authors identify a synonymous 1287C &gt; T mutation in the <i>ACS2</i> gene that reduces m<sup>6</sup>A methylation at the adjacent A<sup>1286</sup> 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><sup><i>1287C</i></sup> is exclusively found in wild cucumber populations, suggesting that <i>ACS2</i><sup><i>1287T</i></sup> has been favored during domestication for its agronomic benefits. Notably, the study also uncovers a genotype-dependent interaction between <i>ACS2</i> and the m<sup>6</sup>A 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}
引用次数: 0
Cis-regulatory elements: systematic identification and horticultural applications 顺式调控要素:系统识别和园艺应用
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-08-08 DOI: 10.1007/s42994-025-00237-0
Tian Li, Wen Zeng, Fangjie Zhu, Peitao Lü
{"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}
引用次数: 0
Epigenetically poised chromatin states regulate PRR and NLR genes in soybean 表观遗传平衡的染色质状态调控大豆的PRR和NLR基因
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-08-08 DOI: 10.1007/s42994-025-00233-4
Linzhe Jin, Yihan Zhang, Jiayuan Guo, Xuexia Liu, Yanling Lai, Xinfang Huang, Yuhan Zou, Shichuang Yan, Xianzhe Dai, Zhenhui Zhong
{"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}
引用次数: 0
Regulatory roles of RNA modifications in plant development and fruit ripening RNA修饰在植物发育和果实成熟中的调控作用
IF 5 4区 农林科学
aBIOTECH Pub Date : 2025-08-08 DOI: 10.1007/s42994-025-00240-5
Tianxiang Li, Junmei Huang, Guanqun Wang, Haoxuan Li, Peitao Lü
{"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 N<sup>6</sup>-methyladenosine (m<sup>6</sup>A)-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 m<sup>6</sup>A, 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}
引用次数: 0
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