aBIOTECH最新文献

{"title":"Harnessing artificial intelligence to decode the rhizosphere microbiome.","authors":"Juan Ma, Jiangfang Qiao, Yanyong Cao, Zeqiang Cheng","doi":"10.1016/j.abiote.2025.100005","DOIUrl":"10.1016/j.abiote.2025.100005","url":null,"abstract":"<p><p>The rhizosphere microbiome plays crucial roles in plant health by regulating nutrient cycling and enhancing stress resilience. However, due to its complexity, the rhizosphere microbiome is quite challenging to analyze using conventional approaches. Recent advances in artificial intelligence (AI) offer unprecedented opportunities to decipher intricate microbial interactions and leverage their potential for crop breeding. In this review, we assess AI methodologies derived from human microbiome studies that address foundational data challenges, including high dimensionality, compositionality, and sparsity. Next, we examine the uses of these methods for the functional prediction of microbial traits. We then shift our focus to the rhizosphere, exploring AI-driven approaches for predictive modeling of rhizosphere dynamics, integrating plant phenotypic and microbiome data, and designing synthetic microbial communities (SynComs). Finally, we discuss the major challenges and future prospects of using AI in rhizosphere microbiome research. Specifically, we propose an emerging AI paradigm that integrates complementary inside-out (hologenome-based genomic selection) and outside-in (SynCom design) strategies, powered by transformative technologies such as federated learning, large language models, digital twins, and autonomous AI agents. This review underscores the potential for AI to revolutionize microbiome science and crop improvement.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100005"},"PeriodicalIF":8.5,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624673","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":"Advances and applications in sequencing-based pathogen surveillance.","authors":"Hao Luo, Yao Wang, Huiyu Hou, Junbo Yang, Yong-Xin Liu","doi":"10.1016/j.abiote.2025.100004","DOIUrl":"10.1016/j.abiote.2025.100004","url":null,"abstract":"<p><p>The ongoing emergence of infectious diseases necessitates cutting-edge diagnostic methodologies. Traditional diagnostic methods are constrained by limited range, lengthy processing times, and inadequate sensitivity. High-throughput sequencing technologies, particularly multiplex polymerase chain reaction (PCR)-based targeted sequencing, have emerged as transformative tools for pathogen detection, offering enhanced sensitivity, specificity, and cost efficiency. However, challenges in primer design, such as dimerization and bias, limit the effectiveness of these approaches. This review explores advances in sequencing technologies, emphasizing the roles of culturomics, metagenomics, and metatranscriptomics in pathogen discovery. We spotlight innovative strategies for error-tolerant primer design that address existing limitations by balancing coverage and specificity, thereby optimizing the multiplex PCR process. Furthermore, integration of artificial intelligence enhances the precision and scalability of sequencing, enabling real-time diagnostics. Collectively, these advances offer promising pathways to bolster global health, food security, and ecological resilience through robust and sustainable pathogen-detection systems.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100004"},"PeriodicalIF":8.5,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624665","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":"NLRSeek: A reannotation-based pipeline for mining missing NLR genes in sequenced genomes.","authors":"Mengda Wang, Xiaowei Fu, Li Yin, Yi Zhao, Qingjie Yang, Xuteng Ye, Jun Cheng, Daolong Dou, Jinding Liu, Gan Ai","doi":"10.1016/j.abiote.2025.100001","DOIUrl":"10.1016/j.abiote.2025.100001","url":null,"abstract":"<p><p>Nucleotide-binding leucine-rich repeat (NLR) proteins function as receptors and signaling factors in plant immune systems. Identifying the genes encoding NLR proteins in genomic sequences provides crucial information for breeding disease-resistant crops. However, NLR proteins are frequently misannotated during automated proteome prediction and downstream identification tools that rely on proteomic data struggle to recover these missing NLRs. To address this problem, we developed NLRSeek (https://github.com/Wang-Mengda/NLRSeek), a genome reannotation-based pipeline for NLR identification. This workflow integrates <i>de novo</i> detection of NLR loci at the genome level with targeted genome reannotation, systematically reconciling these results with existing annotations to produce a comprehensive set of NLR predictions. Our pipeline identified a larger number of NLRs than other NLR annotation tools: even in the well-annotated model plant <i>Arabidopsis thaliana</i>, NLRSeek identified a previously unannotated NLR gene whose expression and translation were confirmed by transcriptome and ribosome-profiling data. The NLRSeek pipeline showed particularly strong performance for non-model species with incomplete annotations. For example, in the yam species <i>Dioscorea zingiberensis</i>, <i>Dioscorea tokoro</i>, and <i>Dioscorea dumetorum</i>, NLRSeek identified 33.8 ​%-127.5 ​% more NLR genes than conventional methods. Importantly, 45.1 ​% of the newly annotated NLRs exhibited detectable expression, suggesting that they are true genes that were previously overlooked. Analysis of the newly identified sequences revealed that NLRs have undergone expansion in <i>D. zingiberensis</i> through tandem duplication, an insight that was not attainable using previous NLR annotation tools. Our novel NLR identification pipeline may reveal untapped genetic resources for engineering disease-resistant crops.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100001"},"PeriodicalIF":8.5,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973398/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624729","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":"Detection technologies for RNA modifications and their applications in plants.","authors":"Jiayin Du, WingTing Cheung, Lixing Zhang, Pingxian Zhang, Guanqun Wang","doi":"10.1016/j.abiote.2025.100002","DOIUrl":"10.1016/j.abiote.2025.100002","url":null,"abstract":"<p><p>Chemical modifications of RNA molecules play diverse regulatory roles in gene expression by influencing RNA biogenesis, stability, and translation. Emerging evidence indicates that RNA modifications in plants have functional significance for enhancing crop performance, stress resistance, and agricultural productivity. Recent advances in quantitative mapping of RNA modifications at the single-base level have highlighted the critical roles of RNA modifications in regulating RNA metabolism and translation in mammals. However, our understanding of the regulatory roles of these chemical modifications at the single-base level remains limited in plants, hindering deeper insights into their biological significance. This gap can be attributed to the limited use of advanced base-resolution detection technologies in plant research. Here, we systematically review both conventional and base-resolution methods that have been used to detect RNA modifications in mammals and plants. We highlight the implications of RNA modifications at the single-base level, and discuss how modification levels could be manipulated during crop improvement and breeding to regulate RNA metabolism and translation without altering amino acid sequences.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100002"},"PeriodicalIF":8.5,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624675","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":"Synergistic function of RNA modifications in Arabidopsis and rice","authors":"Ancheng Ma,&nbsp;Shuaibin Wang,&nbsp;Xinxi He,&nbsp;Yongbo Qu,&nbsp;Shenglin Xie,&nbsp;Junping Gao,&nbsp;Yu Peng,&nbsp;Lisha Shen,&nbsp;Wenxuan Pu,&nbsp;Chongsheng He","doi":"10.1007/s42994-025-00248-x","DOIUrl":"10.1007/s42994-025-00248-x","url":null,"abstract":"<div><p>The epigenomic landscape regulates gene expression and chromatin dynamics, with histone and RNA modifications playing crucial roles. Although studies have elucidated the interactions among chromatin modifications, DNA methylation, and mRNA modifications, the relationships among RNA modifications and their collective influence on RNA metabolism remain poorly understood. Grasping these epigenetic mechanisms is essential for improving crop resilience and productivity. In this study, we explored the co-occurrence and functional interactions of three significant mRNA modifications in Arabidopsis (<i>Arabidopsis thaliana</i>) and rice (<i>Oryza sativa</i>): <i>N</i>^<i>4</i>-acetylcytidine (ac⁴C), <i>N</i>^<i>6</i>-methyladenosine (m⁶A), and 5-methylcytosine (m⁵C). Our results indicate that these modifications frequently coexist in the same transcripts, exhibiting distinct spatial distributions across species. Notably, the m⁶A modification enhances the ac⁴C-mediated destabilization of RNA secondary structures, especially when modifications are clustered, thereby promoting RNA stability. In Arabidopsis, the ac⁴C modification improved translational efficiency and the m⁶A modification amplified this effect in a distance-dependent manner; by contrast, in rice the influence of m⁶A is independent of distance. The m⁵C modification has minimal impact on RNA structure or stability but modulates m⁶A-associated transcript stability in a context-dependent manner. Our findings shed light on the dynamic regulatory code of combinatorial RNA modifications, highlighting species-specific mechanisms of post-transcriptional regulation. This research offers valuable insights into the intricate interplay of RNA modifications, with implications for advancing agricultural biotechnology through a deeper understanding of plant RNA functionality.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"803 - 815"},"PeriodicalIF":5.0,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00248-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595204","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":"A multi-omics cell atlas unlocks new frontiers in crop biotechnology","authors":"Xin Tian,&nbsp;Jian Xu","doi":"10.1007/s42994-025-00246-z","DOIUrl":"10.1007/s42994-025-00246-z","url":null,"abstract":"<div><p>Defining how plant cell types are specified and regulated has been a central challenge in biology. Previous single-cell studies in plants, relying on either RNA-seq or ATAC-seq, provided valuable insights but could not directly connect chromatin state to transcriptional programs. Writing in <i>Nature</i>, Wang et al. present the first multi-organ single-cell multi-omics atlas of rice. Profiling more than 116,000 nuclei across eight tissues, they delineate 56 distinct cell types with high resolution. Joint analysis of gene expression and chromatin accessibility reveals sharper cell-type boundaries, transient developmental states, and regulatory networks with unprecedented clarity. Importantly, the study links cell-specific regulatory programs to key agronomic traits, identifying candidate regulators of root architecture, photosynthesis, nitrogen metabolism, and yield. This atlas establishes both a foundational resource for comparative plant biology and crop biotechnology, providing a roadmap for precision breeding and resilient agriculture driven by cell-type insights.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"680 - 684"},"PeriodicalIF":5.0,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595205","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":"Targeted mutagenesis of FATTY ACID ELONGASE 1 entails near complete elimination of very long chain fatty acids in the seeds of camelina cultivar Ligena","authors":"Barno Ruzimurodovna Rezaeva,&nbsp;Amélie A. Kelly,&nbsp;Martin Fulda,&nbsp;Ingrid Otto,&nbsp;Iris Hoffie,&nbsp;Sindy Chamas,&nbsp;Ivo Feussner,&nbsp;Jochen Kumlehn","doi":"10.1007/s42994-025-00238-z","DOIUrl":"10.1007/s42994-025-00238-z","url":null,"abstract":"<div><p>Genome editing has the potential to enhance yield and quality traits of crops. However, standard genetic transformation methods are not always applicable to modern germplasm. To tackle this challenge in the widely cultivated variety Ligena of the oilseed crop camelina (<i>Camelina sativa</i> (L.) Crantz), an only recently established principle of adventitious shoot formation from immature zygotic embryos was employed to further improve its fatty acid profile. In this approach, the three subgenomic homeologs of the <i>FATTY ACID ELONGASE 1</i> (<i>FAE1</i>) gene were subjected to targeted mutagenesis. To pre-validate the Cas9-interacting, target motif-specific guide (g)RNAs, a robust protoplast-based DNA transfection method was established. This assay demonstrated that the preselected gRNAs were capable of eliciting mutations across all three camelina <i>FAE1</i> homeologs. Likewise, targeted mutagenesis was successful at the whole-plant level. Triple-homozygous <i>fae1</i> knockout mutants were identified amongst a segregating generation M₃ family. Gas chromatography of lipid extracts from M₄ seeds revealed a significant increase in all unsaturated C18 fatty acids including the particularly valuable α-linolenic acid. This was accompanied by a near elimination of the C20 and C22 very long-chain fatty acids including the nutritionally problematic erucic acid. Altogether, we have developed camelina elite lines with two significantly improved properties of high relevance for a health-promoting human nutrition.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"816 - 830"},"PeriodicalIF":5.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00238-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595148","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":"Robustness in jasmonate signaling: mechanisms of concerted regulation and implications for crop improvement","authors":"Ke Zhou,&nbsp;Tiantian Han,&nbsp;Bingqing Pan,&nbsp;Xiaomeng Hu,&nbsp;Xiaomei Chen,&nbsp;Xinyu Liu,&nbsp;Shihong Fei,&nbsp;Yating Yang,&nbsp;Wenhao Li,&nbsp;Minmin Du","doi":"10.1007/s42994-025-00244-1","DOIUrl":"10.1007/s42994-025-00244-1","url":null,"abstract":"<div><p>The jasmonate signaling pathway coordinates plant defenses and growth, thereby enhancing fitness in changing conditions. Jasmonate-mediated responses are triggered by the recognition of external signals via pattern recognition receptors (PRRs) located on the cell membrane. Following signal perception, cells rapidly activate jasmonic acid (JA) biosynthesis, resulting in the accumulation of the bioactive jasmonate, jasmonoyl-isoleucine (JA-Ile). In the nucleus, the coronatine insensitive 1–jasmonate-ZIM-domain (COI1–JAZ) complex recognizes JA-Ile and triggers JAZ ubiquitination and proteasomal degradation. Consequently, transcription factors (e.g., MYC2) bound by JAZ are released, enabling the activation and amplification of JA responses. In parallel to this activation, feedback regulation orchestrated by transcription factors terminates transcription, preventing overcommitment to JA signaling. In this review, we summarize recent advances in understanding JA signaling, emphasizing the connection between PRR activation and JA biosynthesis, and the feedback regulatory mechanisms that ensure precision and robustness of the JA signaling pathway. Finally, we discuss how these mechanistic insights can be leveraged to optimize JA signaling for crop genetic improvement.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"618 - 637"},"PeriodicalIF":5.0,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00244-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595210","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":"Targeted mutagenesis of SlGAD3 generates very high levels of GABA in commercial tomato cultivars","authors":"Lei Zhu,&nbsp;Shiyang Zhang,&nbsp;Qingfeng Niu,&nbsp;Yansha Li,&nbsp;Xiaomu Niu,&nbsp;Pengcheng Wang,&nbsp;Jian-Kang Zhu,&nbsp;Zhaobo Lang","doi":"10.1007/s42994-025-00249-w","DOIUrl":"10.1007/s42994-025-00249-w","url":null,"abstract":"<div><p>GABA, a non-proteinogenic amino acid with anti-hypertensive properties, holds health-beneficial potential when enriched in crops. Previous studies have established that targeted disruption of the calmodulin-binding domain (CaMBD) of the tomato glutamate decarboxylase 3 (SlGAD3) enhances GABA biosynthesis. In this study, we used CRISPR/Cas9-mediated gene editing to precisely modify the CaMBD coding sequence of <i>SlGAD3</i> in three elite tomato varieties (SFT1, SFT2, and SFT3). Under our experimental conditions, targeted editing of <i>SlGAD3</i> led to substantial accumulation of GABA in all three varieties without compromising key agronomic traits such as fruit size and number. Although flowering was delayed in <i>SFT2</i> and <i>SFT3</i> mutants, <i>SFT1</i> mutants had higher GABA levels but also maintained a wild-type flowering time. This result highlights the critical importance of selecting specific varieties, such as SFT1, to minimize pleiotropic effects. By identifying varieties that can accumulate high levels of GABA without major reductions in growth and yield potential, this work bridges a critical gap between plant metabolic-engineering research and practical applications in commercial crop-improvement programs.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"693 - 697"},"PeriodicalIF":5.0,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00249-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595211","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":"Nutrient storage and release in uninfected cells of soybean nodules support symbiotic nitrogen fixation in infected cells","authors":"Qian Liu,&nbsp;Qian Dong,&nbsp;Zhi-Chang Chen","doi":"10.1007/s42994-025-00247-y","DOIUrl":"10.1007/s42994-025-00247-y","url":null,"abstract":"<div><p>Symbiotic nitrogen fixation (SNF) between legumes and rhizobia contributes to sustainable agriculture. In root nodules, infected cells (ICs) are the primary sites of rhizobial colonization and nitrogen fixation. However, the function of the neighboring uninfected cells (UCs) has received little attention and is poorly understood. In this study, we employed a symplastic tracing approach to elucidate the role of UCs in nutrient storage and transport within root nodules. We uncovered an extensive network of plasmodesmata connecting ICs and UCs, while direct IC–IC connections were absent. By artificially inducing callose deposition at plasmodesmata, we demonstrate that plasmodesmata permeability between ICs and UCs regulates nutrient import into ICs, thereby influencing nutrient homeostasis and the SNF ability of nodules. Furthermore, high nitrogen levels triggered callose deposition at plasmodesmata, restricting nutrient transport, which may represent one mechanism by which excessive nitrogen inhibits SNF. These findings provide insights into the regulatory mechanisms of SNF and underscore the crucial role of UCs in optimizing nitrogen fixation efficiency.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"790 - 802"},"PeriodicalIF":5.0,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00247-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595154","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}