Journal of Integrative Plant Biology最新文献

{"title":"Correction to \"Recognition of a salivary effector by the TNL protein RCSP promotes effector-triggered immunity and systemic resistance in Nicotiana benthamiana\".","authors":"","doi":"10.1111/jipb.70390","DOIUrl":"https://doi.org/10.1111/jipb.70390","url":null,"abstract":"","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148962811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant cis-regulatory grammar: Decoding the multidimensional code of transcriptional regulation for programmable crop engineering.","authors":"Libin Zhang, Maoteng Li","doi":"10.1111/jipb.70386","DOIUrl":"https://doi.org/10.1111/jipb.70386","url":null,"abstract":"<p><p>Cis-regulatory elements (CREs) orchestrate the spatiotemporal precision of gene expression that underlies plant development, adaptation, and domestication. Decoding the cis-regulatory grammar of plant genomes remains a central challenge in modern biology, with profound implications for programmable crop engineering. Here, recent conceptual and technological advances are synthesized to reshape our understanding of plant CREs. This review first argues that CRE function is not only an intrinsic property of DNA sequence alone but also emerges from a multidimensional context, including chromatin accessibility, histone modifications, three-dimensional genome topology, and cell type-specific regulatory landscapes. Furthermore, the convergence of single-cell epigenomics, high-throughput functional assays, and CRISPR-based dissection has begun to unravel this contextual grammar, revealing the computational principles governing transcriptional regulation. Critically, we propose that artificial intelligence (AI) platforms are catalyzing an ongoing transition from descriptive discovery to predictive engineering, wherein these platforms outperform natural evolution in designing synthetic CREs. Finally, a roadmap is outlined toward a plant regulatory grammar foundation model, which will enable truly predictive engineering of gene expression when fine-tuned for specific tasks. Collectively, the integration of single-cell resolution maps, precise genome editing, AI-driven design, and regulatory-compliant delivery systems promises to transform our ability to reprogram plant gene regulation for next-generation agriculture, bridging the gap between foundational regulatory biology and tangible crop improvement.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in research on plant CNGCs, the Ca²⁺-permeable channels.","authors":"Yan-Qiu Tan, Yang Yang, Yong-Fei Wang","doi":"10.1111/jipb.70385","DOIUrl":"https://doi.org/10.1111/jipb.70385","url":null,"abstract":"<p><p>Cyclic nucleotide-gated channels (CNGCs) in plants are the orthologs of cyclic nucleotide-gated (CNG) channels, which function as non-selective cation channels in olfactory and visual signal transduction in animals. In land plants, CNGCs form a large Ca²⁺-permeable cation channel family, and function in diverse biological processes, mainly including the uptake of cationic nutrients and toxic heavy metals from the soil, the transport, distribution, and homeostasis of these cations, and Ca²⁺ signaling in plants. Significant advances have been made in recent years, with new findings that have greatly expanded our understanding of plant CNGCs. This review summarizes the major progress over the past 5 years and discusses the open scientific questions that remain to be addressed.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148899916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TaHDA1-mediated histone and non-histone deacetylation orchestrates drought tolerance in wheat.","authors":"Jinpeng Li, Danyang Zhao, Xiao Peng, Xinran Wu, Chenji Zhang, Huitao An, Wei Chu, Jingchen Lin, Zehui Liu, Qun Yang, Debiao Liu, Xiaoyu Liu, Wanghongan Jia, Yi Pei, Mingming Xin, Yingyin Yao, Weilong Guo, Huiru Peng, Zhongfu Ni, Qixin Sun, Xingbei Liu, Zhaorong Hu","doi":"10.1111/jipb.70384","DOIUrl":"https://doi.org/10.1111/jipb.70384","url":null,"abstract":"<p><p>Drought stress severely constrains wheat (Triticum aestivum L.) growth and productivity. Here, we identify the histone deacetylase TaHDA1 as a negative regulator of drought tolerance in wheat. We demonstrate that TaHDA1 interacts with and deacetylates the L-glutamate decarboxylase TaGAD1 at lysine 493, promoting its ubiquitination-dependent degradation and thereby suppressing γ-aminobutyric acid (GABA) accumulation. Loss of TaHDA1 function enhances TaGAD1 stability, increases GABA levels, and confers markedly improved drought tolerance, along with elevated grain GABA content. Integrated multi-omics analyses further reveal that TaHDA1 globally modulates H3K9 acetylation to orchestrate drought-responsive transcriptional programs. Notably, tahda1-ko mutants show a slight reduction in grain size under normal conditions, but maintain stable yield under drought stress. Our findings uncover a dual mechanism by which TaHDA1 integrates non-histone and histone deacetylation to balance growth and stress adaptation, providing a promising target for breeding drought-resilient and nutritionally enhanced wheat varieties.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148899955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Base editing in rice using nuclease-deactivated CRISPR/Cas-SF01","authors":"Meng Jia,&nbsp;Yangqing Xie,&nbsp;Chuang Wei,&nbsp;Hongzhi Wang,&nbsp;Li Xue,&nbsp;Chunyu Zou,&nbsp;Jian-Kang Zhu,&nbsp;Mugui Wang","doi":"10.1111/jipb.70265","DOIUrl":"10.1111/jipb.70265","url":null,"abstract":"<p>Adenine and cytosine base editing using dCas-SF01 and the 35S-CmYLCV-U6 composite promoter successfully introduced targeted base substitutions at multiple loci in rice, with average editing efficiency of 33.3%. Using the protospacer adjacent motif (PAM)-relaxed SF01-IKRR variant enabled base editing using 5'-NTN PAMs in rice.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 9","pages":"3181-3183"},"PeriodicalIF":12.5,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13545825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147687439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing CRISPR-Cas12a base editing in plants with LbCas12a variants and introns","authors":"Yanhao Cheng,&nbsp;Gen Li,&nbsp;Man Zhou,&nbsp;Rushil Mandlik,&nbsp;Doris Wang,&nbsp;Yiping Qi","doi":"10.1111/jipb.70249","DOIUrl":"10.1111/jipb.70249","url":null,"abstract":"<p>Cytosine base editors (CBEs) and adenine base editors (ABEs) are powerful tools for precise genome editing in plants. Conventionally, such base editors are built upon the CRISPR-Cas9 systems where Cas9 nickases are used. To expand the base editing scope and minimize off-target effects, base editors derived from the CRISPR-Cas12a systems are desired. However, the use of deactivated Cas12a (dCas12a) in such base editors constrains the editing activity, preventing the wide use of Cas12a base editors for plant research and trait development. In this study, we demonstrate the use of an ABE based on the efficient LbCas12a-RRV variant to introduce herbicide-resistant mutations in <i>OsACCase</i> in rice. To improve Cas12a CBEs and ABEs, we inserted introns into the coding sequence of dLbCas12a-RRV. This intron-containing Cas12a-CBE shows substantial improvement in editing efficiency in rice, compared to the intron-less counterparts. By contrast, the improvement of ABE with the intron-containing dLbCas12a-RRV is very limited, partly due to the already high baseline editing efficiency of the intron-less dLbCas12a-RRV ABE. Testing of these base editors in poplar shows elevated C-to-T base editing by dLbCas12a-RRV–intron-CBE. For A-to-G editing, ABEs built upon dLbCas12a-RV and dLbCas12a-RRV variants showed significant improvement over ABEs derived from wild-type LbCas12a and the ttLbCas12a variant. The addition of introns to dLbCas12a-RRV does not further improve the base editing efficiency. With whole genome sequencing in rice, we evaluated genome editing specificities with these improved Cas12a base editors. Our analyses show that both intron-containing Cas12a CBE and ABE barely introduce guide RNA-dependent off-target mutations. However, they can generate guide RNA-independent off-target mutations, which are likely attributed to the high enzymatic activities of the deaminases. Collectively, our study demonstrates the successful use of a Cas12a base editor for trait development and reports improved Cas12a CBEs and ABEs for precise base editing in plants.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 9","pages":"3243-3259"},"PeriodicalIF":12.5,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13545857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147607705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced Cas12i3 system enables precise OsAUX3 editing for rice grain improvement","authors":"Rui Zhang,&nbsp;Xu Tang,&nbsp;Xinruolan Yang,&nbsp;Yong Zhang","doi":"10.1111/jipb.70337","DOIUrl":"10.1111/jipb.70337","url":null,"abstract":"<p>An optimized Cas12i3 genome-editing system enables highly efficient and predictable editing of regulatory sequences in rice. Precise promoter engineering fine-tunes gene expression, improves grain size, and enhances production potential, demonstrating a powerful new approach for crop improvement through targeted regulation rather than gene disruption.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 9","pages":"3187-3189"},"PeriodicalIF":12.5,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13545849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148343598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient CRISPR/Cas-SF01 genome editing tools with high editing efficiency in allotetraploid oilseed rape","authors":"Mengyu Hao,&nbsp;Meili Zhou,&nbsp;Fei Pan,&nbsp;Tiantian Liu,&nbsp;Yilin Li,&nbsp;Nan Su,&nbsp;Ayub Ashfaq,&nbsp;Miaoying Song,&nbsp;Hui Wang,&nbsp;Wenxiang Wang,&nbsp;Jia Liu,&nbsp;Chao Li,&nbsp;Li Fu,&nbsp;Ping He,&nbsp;Qiong Hu,&nbsp;Desheng Mei,&nbsp;Hongtao Cheng","doi":"10.1111/jipb.70221","DOIUrl":"10.1111/jipb.70221","url":null,"abstract":"<div>\u0000 \u0000 <p>CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 has been widely utilized for plant genome editing, but the protospacer adjacent motif (PAM) requirement limits its editing scope. CRISPR/Cas12i3 belongs to the type-VI Cas system that has gained extensive attention due to its smaller size and less restricted canonical TTN PAM sequence. In this study, we explored the newly developed Cas-SF01 system (Cas12i3 variant) for genome editing in oilseed rape. We established an efficient protoplast transformation system in oilseed rape to compare editing efficiency between Cas-SF01 and Cas9. Cas-SF01 shows cleavage activities at the tested 5′-TTN-3′ PAM sites with editing outcomes sharing considerable similarities with the CRISPR-Cas9 system in protoplast. Cas-SF01 also induces high efficiency mutagenesis for multiple target sites in stable transformed oilseed rape lines, generating mutants with multilocular silique and male sterile phenotypes. Furthermore, Cas-SF01-derived cytosine base editors (CBEs) were developed to produce targeted C-to-T base edits. Compared to SpCas9, Cas-SF01 has an expanded PAM range and effectively recognizes TTN PAMs, which has substantially broadened the scope of editable sites within the rapeseed genome. No mutations were identified at the putative off-target sites among the edited plants. This study developed a robust, first-of-its-kind Cas12 system in the allotetraploid <i>Brassica napus</i>, expanding the scope of editing and enriching genome-editing toolkits for biological research and genetic improvement.</p></div>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 9","pages":"3220-3230"},"PeriodicalIF":12.5,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147388816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking the power and potential of the Cas12 family members and their ancestors for crop genome editing","authors":"Lanqin Xia,&nbsp;Jinsheng Lai,&nbsp;Jian-Kang Zhu","doi":"10.1111/jipb.70361","DOIUrl":"10.1111/jipb.70361","url":null,"abstract":"&lt;p&gt;Genome editing technologies have revolutionized plant research and offer great potential for crop improvement. Among them, CRISPR/Cas, as a versatile, simple, and inexpensive system for genetic manipulation, has dominated the genome editing field over the past decade. The applications of CRISPR/Cas in both plant biological sciences and crop improvement are particularly important in the context of global climate change, as well as in addressing current agricultural, environmental, and ecological challenges. Members of the Cas12 family, including Cas12a, Cas12b, Cas12i1, Cas12i2, Cas12i3, Cas12j, and Casδ, which belong to the Class II Type V CRISPR system, as well as their ancestors Fanzors and TnpBs, have received extensive attention in recent years due to their relatively smaller protein size, and alternative protospacer adjacent motifs (PAMs) or target adjacent motifs (TAMs), compared to the widely used SpCas9, representing promising alternative genome editing tools for crop improvement. This special section compiles a set of 19 articles, including 7 research papers and 12 brief communications, covering the latest advances in unlocking the potential of Cas12a and novel Cas12 family members as well as their ancestors for crop genome editing.&lt;/p&gt;&lt;p&gt;TnpBs, as the RNA-guided endonucleases ancestral to the CRISPR-Cas12 family, are components of the insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. TnpBs belong to the obligate mobile element-guided activity (OMEGA) system and can specifically cleave double-stranded DNA by coordinating with their cognate obligate mobile element-guided activity RNAs (ωRNAs) or the so-called right-end element RNAs (reRNAs). TnpBs are promising alternatives to the larger CRISPR-Cas systems, due to their smaller sizes and hypercompact nature, which are advantageous for viral delivery in crop genome editing. So far, a number of TnpB family members have been exploited. However, most of them showed relatively lower editing efficiencies and generally produced a higher proportion of chimerism in the T&lt;sub&gt;0&lt;/sub&gt; generation, complicating the recovery of stable edited lines for crop improvement. In this issue, to overcome these limitations, on the basis of a previously reported ISDra2-based TnpBmax, &lt;span&gt;Li et al. (2026)&lt;/span&gt; developed an efficient ISDra2-based TnpBmax system for crop genome editing by integrating ωRNA truncation, T5 exonuclease fusion, and a surrogate selection strategy. This engineered ISDra2-based TnpBmax system significantly improved the editing efficiencies by up to 81.5% and 34.9% in rice and tomato, respectively. Furthermore, it drastically reduced chimerism from 68.6% to 21% and from 83.3% to 38.6% in rice and tomato, respectively, facilitating the recovery of transgene-free stable edited homozygous lines in the progeny for either functional genomics or crop improvement.&lt;/p&gt;&lt;p&gt;Fanzors (Fz), as the eukaryotic orthologs of prokaryotic TnpBs, are the programmable RNA-guided DN","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 9","pages":"3157-3159"},"PeriodicalIF":12.5,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13545841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148662963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Issue information page","authors":"","doi":"10.1111/jipb.70381","DOIUrl":"https://doi.org/10.1111/jipb.70381","url":null,"abstract":"","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 9","pages":"3153-3156"},"PeriodicalIF":12.5,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.70381","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148903751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}