Journal of Integrative Plant Biology最新文献

{"title":"Dissecting the genetic basis of climatic adaptation in wild relatives (Malus baccata) for climate-resilient apple breeding","authors":"Ying Su,&nbsp;Yani Hao,&nbsp;Xuejing Cao,&nbsp;Lin Wang,&nbsp;Zhiqi Xu,&nbsp;Fan Zhang,&nbsp;Zhiyao Ma,&nbsp;Xu Wang,&nbsp;Jiacui Li,&nbsp;Tianrong Fan,&nbsp;Ruoyan Zhao,&nbsp;Zhongqi Liu,&nbsp;Wenrui Wang,&nbsp;Yingchun Zhang,&nbsp;Xuanwen Yang,&nbsp;Sifan Yang,&nbsp;Dajiang Wang,&nbsp;Kun Wang,&nbsp;Simiao Sun,&nbsp;Zichen Li,&nbsp;Wen Tian,&nbsp;Yanming Sun,&nbsp;Zhao Liu,&nbsp;Yanshuai Xu,&nbsp;Hua Xiao,&nbsp;Yanling Peng,&nbsp;Xiaodong Xu,&nbsp;Ruirui Liu,&nbsp;Xinmin Tian,&nbsp;Yongfeng Zhou,&nbsp;Yuan Gao","doi":"10.1111/jipb.70194","DOIUrl":"10.1111/jipb.70194","url":null,"abstract":"<p>Climate change poses an increasing threat to global biodiversity and food security. As a wild relative of cultivated apples, <i>Malus baccata</i> exhibits broad environmental adaptability and robust stress tolerance. However, its effective utilization in breeding is constrained by the absence of a complete reference genome and insufficient population-level genomic characterization. In this study, we assembled a haplotype-resolved, telomere-to-telomere genome for <i>M. baccata</i>, providing unprecedented resolution for a wild apple reference genome. Population genomic analyses revealed four distinct genetic clusters. Among these, the Hebei Group 2 harbors the highest genetic diversity and heterozygosity, alongside the lowest runs of homozygosity, suggesting a complex history of genetic admixture in this population. By integrating population genomics with genotype-environment association analyses, we identified a series of climate-associated single-nucleotide polymorphisms and structural variants. A substantial proportion of these adaptive variants is localized within the coding and regulatory regions of candidate genes, providing a genomic basis for their roles in environmental adaptation. Notably, <i>DREB1A/D</i> and <i>NAC6</i> are associated with temperature seasonality and annual precipitation, respectively. Furthermore, future climate projections indicate that the Northeastern (NE) clusters face the highest risk of maladaptation, especially under high-emission scenarios. Collectively, these findings provide critical insights into the genetic basis of climatic adaptation in wild apples, establishing a solid foundation for the conservation of crop wild relatives and the breeding of climate-resilient cultivars.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 10","pages":"3705-3726"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.70194","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147300476","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":"Uncovering the role of the PPR protein PHOTOSYSTEM ONE BIOGENESIS FACTOR6 in splicing chloroplast group II introns.","authors":"Mengyu Li, Mengwei Sun, Jinlian Lv, Mingming Song, Siyu Lu, Aihong Zhang, Congming Lu","doi":"10.1111/jipb.70289","DOIUrl":"10.1111/jipb.70289","url":null,"abstract":"<p><p>Nucleus-encoded proteins are involved in intron splicing in plant chloroplasts. Although many splicing factors were discovered, the mechanisms for chloroplast intron splicing remain unknown. Here, we identified a P-class pentatricopeptide repeat (PPR) protein, PHOTOSYSTEM ONE BIOGENESIS FACTOR6 (PBF6), that is essential for the accumulation of photosystem I complex. PBF6 bound to ycf3 intron 1 and clpP1 intron 2, and the introns of petB, ndhA, and ndhB transcripts, and was required for their splicing. Truncated PBF6 containing the 10 N-terminal PPR motifs bound to specific sequences to ycf3 intron 1, clpP1 intron 2, and to the introns of petB, ndhA, and ndhB. PBF6 formed two multi-subunit splicing complexes with other known splicing factors from the CRM, peptidyl-tRNA hydrolase, RNase III, PORR, APO, DEAD-box RNA helicase, and mTERF families. PBF6-containing complex I was about 600 kDa, comprising nine known splicing factors: CAF1, CAF2, CRS2, CFM3a, RNC1, WTF1, APO2, RH3, and mTERF2. PBF6-containing complex II was about 300 kDa and contained three known splicing factors: CAF1, CAF2, and CFM2. Furthermore, two known PPR-type splicing factors, PBF2 and ECD2, both of which are required for splicing the ycf3 intron 1, also formed two multi-subunit splicing complexes with other known splicing factors. Importantly, these three PPR-type splicing factors formed their splicing complexes independently. Our data suggest that a PPR-type splicing factor forms splicing complexes with other known splicing factors under transient expression conditions to facilitate intron splicing and that several PPR-type splicing factors work together to promote the splicing of the same intron through forming respective splicing complexes.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":"3809-3829"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13629276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939759","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.70394","DOIUrl":"https://doi.org/10.1111/jipb.70394","url":null,"abstract":"","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 10","pages":"3525-3527"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.70394","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149099614","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":"A cytochrome P450 gene, GmSUR2a, confers submergence tolerance and improves yield in soybean by modulating auxin homeostasis","authors":"Yangyang Chen,&nbsp;Pingzhang Feng,&nbsp;Mengwei Zheng,&nbsp;Lipei Zhao,&nbsp;Yi Li,&nbsp;Yali Jing,&nbsp;Yisa Wang,&nbsp;Bo Zhang,&nbsp;Changzhong Liu,&nbsp;Chengyu Wei,&nbsp;Jijun Yan,&nbsp;Jinfang Chu,&nbsp;Shanshan Chu,&nbsp;Erhui Xiong,&nbsp;Yongqing Jiao","doi":"10.1111/jipb.70299","DOIUrl":"10.1111/jipb.70299","url":null,"abstract":"<p>Flooding is one of the most devastating abiotic stresses in agriculture, and enhancing flood tolerance is critical for sustainable crop production. Soybean (<i>Glycine max</i>) is highly susceptible to flooding stress. However, the molecular mechanism underlying soybean response to flooding stress remains largely unknown, and the genes available for improving soybean flood tolerance are relatively limited. In this study, we characterized the function of the predicted cytochrome P450 gene, <i>GmSUR2^a</i>, in regulating submergence tolerance in both soybean and <i>Arabidopsis</i>. The <i>Arabidopsis SUR2</i> gene played a positive role in regulating submergence tolerance. The <i>GmSUR2</i>^<i>a</i>, which localizes to a previously identified quantitative trait locus (QTL) for waterlogging tolerance on soybean chromosome 03, shared conserved functions with <i>AtSUR2</i> in regulating submergence tolerance. Transgenic soybean plants overexpressing <i>GmSUR2</i>^<i>a</i> displayed enhanced submergence tolerance accompanied by reduced auxin levels. Further experiments revealed that auxin negatively regulates submergence tolerance: Exogenous auxin application decreased survival rates, and auxin signaling mutants exhibited improved tolerance. We also identified that <i>GmAGL15</i> transcription factor directly repressed <i>GmSUR2</i>^<i>a</i> expression. Importantly, field trials confirmed that <i>GmSUR2</i>^<i>a</i> overexpression not only improved submergence tolerance but also increased the yield of transgenic soybean plants. Our findings provide new insights into the molecular mechanisms of submergence tolerance and establish <i>GmSUR2</i>^<i>a</i> as a promising target for breeding flood-resistant soybean varieties.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"68 10","pages":"3628-3643"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.70299","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012664","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":"The transcription factor CsbHLH60 relieves high-temperature inhibition of chlorophyll degradation in citrus.","authors":"Zhehui Zhang, Yongjun Hu, Ming Wang, Ziyi Lei, Shengcai Liao, Liping Li, Xiongjie Zheng, Kaijie Zhu, Lijun Chai, Junli Ye, Xiuxin Deng","doi":"10.1111/jipb.70297","DOIUrl":"10.1111/jipb.70297","url":null,"abstract":"<p><p>Rising global temperature threatens fruit quality. As one of the most economically valuable fruits worldwide, citrus suffers from high-temperature-induced chlorophyll retention during ripening, significantly reducing commercial value. Comparative physiological analyses revealed that citrus fruit stored at 30°C exhibited markedly impaired chlorophyll degradation and failed to undergo normal degreening, in stark contrast to those maintained at 20°C. This temperature-dependent suppression of degreening was closely associated with a significant downregulation of key chlorophyll catabolic genes (CCGs). By integrating weighted gene co-expression network analysis (WGCNA) of a stay-green mutant, we identified the transcription factor CsbHLH60, a nuclear-localized transcriptional activator, from a chlorophyll-associated module. CsbHLH60 directly binds E-box motifs in the promoters of CsSGR and CsRCCR to drive their expression, a finding validated by ChIP-qPCR and EMSA assays. Transient overexpression of CsbHLH60 in citrus peel accelerated chlorophyll degradation and, importantly, overcame high-temperature-induced repression to restore degreening, whereas RNAi-mediated silencing at 20°C significantly impeded normal degreening of the peel. Mechanistically, high temperature imposes a dual \"double-lock\" suppression on CsbHLH60, concurrently repressing its transcription and promoting its protein degradation, thereby depleting functional activator levels. Collectively, our findings establish CsbHLH60 as a pivotal temperature-responsive regulator that directly couples temperature signaling to chlorophyll catabolism and is capable of overriding the high-temperature-induced suppression of chlorophyll degradation, thereby highlighting its potential as a molecular target for mitigating climate-driven declines in citrus fruit appearance quality.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":"3790-3808"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012607","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":"Natural promoter variation in OsDSF7 contributes to drought and salt tolerance in rice.","authors":"Huanyu Wang, Run Li, Liang Zhang, Xiaosong Ma, Sheng Zhao, Aipeng Li, Liang Xu, Yuanyuan Tan, Pengcheng Wei, Qingyao Shu, Shiyong Song","doi":"10.1111/jipb.70413","DOIUrl":"https://doi.org/10.1111/jipb.70413","url":null,"abstract":"<p><p>The tetratricopeptide repeat protein gene OsDSF7 gene helps rice withstand drought and salt stresses. Naturally occurring differences in its regulatory region alter gene activity and stress tolerance. A favorable version improves field performance, particularly under salt conditions, offering a resource for breeding resilient rice.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101765","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":"Disabling a conserved module confers broad-spectrum resistance","authors":"Zhen Zeng,&nbsp;Yachun Su,&nbsp;Hui Ling,&nbsp;Youxiong Que","doi":"10.1111/jipb.70286","DOIUrl":"10.1111/jipb.70286","url":null,"abstract":"<p>This commentary reviews the discovery by Yuan et al. of a conserved susceptibility module where fungal Gas2 stabilizes host SnRK1β1A to suppress nuclear immunity in rice. It discusses the mechanism for broad-spectrum resistance via genome editing and considers the essential balance between enhanced defense and associated agronomic trade-offs.\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 10","pages":"3537-3539"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.70286","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147831479","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":"OmicsCanvas: A multi-omics platform for integration and visualization of epigenetic regulation","authors":"Zeyu Zhang,&nbsp;Zuoling Ma,&nbsp;Tian Hua,&nbsp;Xuqing Liu,&nbsp;Shengcai Xiang,&nbsp;Lianfeng Gu","doi":"10.1111/jipb.70258","DOIUrl":"10.1111/jipb.70258","url":null,"abstract":"<p>OmicsCanvas integrates diverse epigenomic and transcriptomic data into a unified framework, enabling users to visualize complex multi-omics patterns, generate publication-ready figures, and uncover regulatory relationships. This tool makes multi-omics analysis accessible to biologists without bioinformatics expertise.\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 10","pages":"3546-3548"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.70258","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147669394","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":"Rewiring the SPX-mediated signaling for climate-resilient and nutrient-efficient crops","authors":"Xuge Lou,&nbsp;Keke Yi","doi":"10.1111/jipb.70255","DOIUrl":"10.1111/jipb.70255","url":null,"abstract":"<p>This Commentary summarizes the original work by Liao et al. on the role of NITROGEN LIMITATION ADAPTATION (NLA) in cold tolerance, places it within the broader context of climate change and nutrient constraints, and discusses the engineered <i>NLA^Δ12</i> allele and its implications for overcoming the trade-off between cold tolerance and phosphorus use efficiency.\u0000\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 10","pages":"3535-3536"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.70255","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147589076","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":"The ZmRACK1-ZmCDPK7-ZmAPX1 module regulates plant antiviral immunity.","authors":"Yuyang Zhang, Niannian Li, Qiongqiong Wang, Yingchao Sun, Yajuan Shi, Lianwei Yu, Xiaoyu Han, Xiaoxi Feng, Zaifeng Fan, Linlin Chen, Honglian Li, Xue Yang, Hongxia Yuan, Yan Shi","doi":"10.1111/jipb.70285","DOIUrl":"10.1111/jipb.70285","url":null,"abstract":"<p><p>Calcium-dependent protein kinases (CDPKs) in plants play crucial roles in mediating responses to both biotic and abiotic stresses. However, the molecular mechanism through which CDPKs regulate antiviral immunity in plants remains largely elusive. In this study, we identified ZmCDPK7 as a key player in response to various stimuli. Lines overexpressing ZmCDPK7 exhibited enhanced resistance to maize chlorotic mottle virus (MCMV) infection, while ZmCDPK7 knock-out lines demonstrated increased sensitivity, indicating that ZmCDPK7 positively regulates maize immunity against MCMV. Furthermore, ZmCDPK7 interacts with ZmAPX1 and enhances its enzymatic activity by phosphorylating ZmAPX1 at Thr164, thereby reducing reactive oxygen species (ROS) production. The scaffold protein ZmRACK1 interacts with both ZmCDPK7 and ZmAPX1, facilitating the formation of a ternary complex that enhances ZmCDPK7-mediated ZmAPX1 enzymatic activity. Lines overexpressing ZmAPX1 also showed increased resistance to MCMV infection, while ZmAPX1 mutant lines (Zmapx1 MU1 and Zmapx1 MU2) exhibited increased sensitivity. Additionally, CRISPR/Cas9-mediated genome editing of ZmRACK1 in maize resulted in increased susceptibility to MCMV. To counteract plant defense, the MCMV protein P31 interacts with ZmCDPK7 and ZmRACK1, disrupting the interaction between ZmRACK1-ZmCDPK7 and ZmCDPK7-ZmAPX1, thereby blocking the ternary complex formation. Moreover, ZmCDPK7 is also implicated in defense against drought stress and corn stalk rot. Overall, our findings provide valuable insights into the molecular mechanisms by which the ZmRACK1-ZmCDPK7-ZmAPX1 module regulates plant immunity, identifying the potential new targets for the genetic control of maize viral diseases.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":"3830-3845"},"PeriodicalIF":12.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13629256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147866034","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}