The Plant Journal最新文献

{"title":"A Jasmonate ZIM-domain subfamily protein regulates drought tolerance via modulating the stomatal density in rice.","authors":"Xiaoche Wang, Zhiwen Yu, Hao Chen, Jiahao Lu, Xiang Li, Binxu Wang, Fengcheng Li, Hai Xu, Wenfu Chen, Quan Xu","doi":"10.1111/tpj.70539","DOIUrl":"https://doi.org/10.1111/tpj.70539","url":null,"abstract":"<p><p>Stomata, which serve as vital interfaces between plants and the atmosphere, are closely associated with drought adaptation via changes in stomatal density. In this study, we identified DROUGHT TOLERANCE 3 (DT3) as a key gene that regulates drought tolerance in rice by controlling stomatal density. DT3 belongs to the JAZ (Jasmonate ZIM-domain) subfamily of the TIFY gene family in rice. DT3 interacts with the basic helix-loop-helix (bHLH) transcription factor bHLH048 and disrupts its suppression of the abscisic acid (ABA) biosynthesis gene 9-CIS-EPOXYCAROTENOID DIOXYGENASE 2 (NCED2). As a result, elevated expression of NCED2 increases endogenous ABA levels, which reduces stomatal density and enhances drought tolerance in rice. Moreover, the natural variation in the promoter region of DT3 contributed to the various expression levels of DT3. Therefore, manipulating the DT3-bHLH048-NCED2-ABA pathway represents a promising climate-adaptive strategy to improve drought tolerance in rice.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 2","pages":"e70539"},"PeriodicalIF":5.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353220","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":"An elegant co-transformation strategy for recalcitrant wheat using morphogenic regulators.","authors":"Guanghui Guo, Dihu Sun, Junrong Li, Chongjia Zhong, Can Li, Hui Liang, Tiantian He, Ranzhe Li, Zhen Zhang, Kai Wang, Hao Li, Yun Zhou, Chun-Peng Song","doi":"10.1111/tpj.70541","DOIUrl":"https://doi.org/10.1111/tpj.70541","url":null,"abstract":"<p><p>Common wheat (Triticum aestivum L.) is a vital global crop, but many elite cultivars remain recalcitrant to genetic transformation, hindering functional genomics and crop improvement. Here, we developed an efficient co-transformation strategy for recalcitrant wheat varieties (e.g., Aikang58 and Xinong979) using the morphogenic gene mTaGRF4-TaGIF1. This approach entails mixing Agrobacterium tumefaciens cultures carrying two separate vectors: a standard gene-of-interest (GOI) vector (containing a selectable marker) and a gene-of-co-transformation vector (GOC, expressing mTaGRF4-TaGIF1 without a selectable marker). Co-transformation enhanced regeneration efficiency to ~37.38% in AK58, a marked improvement over conventional methods, enabling consistent recovery of transgenic plants. Among regenerants, ~63.25% carried both GOI and GOC (GOI&GOC), while ~11.92% contained only the GOI. Only-GOI plants could also be obtained through progeny segregation from GOI&GOC lines. We successfully generated GUS- and RUBY-expressing transgenic lines, as well as CRISPR-Cas9-edited mutants targeting Q and Ph1 genes, confirming the method's efficacy for both gain-of-function and genome editing application. Furthermore, the strategy was successfully extended to another recalcitrant variety Xinong979, demonstrating its potential for broad applicability. Unlike existing methods dependent on complex excision systems or tissue-specific promoters, our co-transformation methodology significantly simplifies both vector design and procedural workflow while maintaining high efficiency. Collectively, these findings establish a technically advanced yet operationally simplified transformation platform that addresses the long-standing challenge of genetic transformation in recalcitrant wheat varieties, providing researchers with a powerful tool for functional genomics studies and accelerating precision breeding programs in elite wheat cultivars.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 2","pages":"e70541"},"PeriodicalIF":5.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342404","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":"A six-repeat PPR protein WPR directly binds target RNAs and coordinates chloroplast RNA processing via dual recruitment of MORF1, MORF8b, and CAF2 proteins in rice.","authors":"Bo Zhao, Guojuan Xu, Yajun Zhu, Hui Zhang, Yuanbo Zhang, Chunxue Wei, Xi Chen, Zhichao Wu, Ruifang Liu, Kai Chen, Congcong Shen, Ling Ding, Xu Wang, Wenhui Jiang, Wangang An, Lei Ren, Zhan Xu, Jianlong Xu, Yong Xiang","doi":"10.1111/tpj.70526","DOIUrl":"https://doi.org/10.1111/tpj.70526","url":null,"abstract":"<p><p>Pentatricopeptide repeat (PPR) proteins are key regulators of organelle RNA metabolism in plants, yet their precise mechanisms in chloroplast RNA processing remain unclear. Here, we identify WPR, a unique P-type PPR protein in rice (Oryza sativa L.), as a critical factor in chloroplast RNA splicing and editing. A ~112-kb chromosomal inversion upstream of WPR causes an albino panicle rachis phenotype (wpr mutant), while complete loss of WPR function leads to seedling lethality. WPR deficiency disrupts the splicing of multiple group II introns (atpF, ndhA, ndhB, petB, rpl2, and rps12) and impairs RNA editing in transcripts such as ndhA, ndhB, ndhG, rps14, and ycf3. Electrophoretic mobility shift assay (EMSA) data confirm that WPR directly binds to precursor mRNAs of atpF, ndhA, petB, rpl2, and rps12. Strikingly, WPR interacts with both RNA editing factors (MORF1, MORF8b) and the splicing factor CAF2, but not with other PPR proteins targeting the same transcripts. Unlike most PPR proteins, WPR contains only six PPR repeats, which is the fewest among all functionally characterized rice PPR proteins. With few informative repeats, WPR likely possesses a broad, low-specificity RNA-binding activity. Moreover, WPR may act on chloroplast RNA maturation by recruiting MORFs and CAF2 rather than other PPR proteins, highlighting a novel regulatory mode in which P-type PPR protein may act as an RNA-binding scaffold to integrate diverse RNA-processing machineries. This study advances the understanding of PPR protein diversity and provides new insights into the molecular mechanisms of chloroplast RNA processing in rice.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 2","pages":"e70526"},"PeriodicalIF":5.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353201","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":"The MIR169:NF-YA module enhances biomass and yield via ARGOS in Arabidopsis and tomato.","authors":"Apoorva Gupta, Sombir Rao, Sarita Jha, Debasish Ghosh, Richa Virmani, Monika Shrivastava, Adesh Kumar, Laxmipriaya Sahoo, Jaishri Rubina Das, Martin Crespi, Saloni Mathur","doi":"10.1111/tpj.70538","DOIUrl":"https://doi.org/10.1111/tpj.70538","url":null,"abstract":"<p><p>Molecular links between miRNA: target modules regulating downstream genes for crop maturation/yield are poorly understood. Here, we report that elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle. In agreement, increased NF-YA2 levels in (1) NF-YA2-OE (overexpression) lines, (2) miR169d-target-mimicry lines (in which miR169d is chelated), and (3) miR169d-non-cleavable NF-YA2 resistant target lines show the opposite phenotype. Further, we find increased auxin levels in MIR169d-OE and nf-ya2 mutant lines, supporting the enrichment of 'auxin terms' in MIR169-OE transcriptome data. We show that ARGOS (auxin-regulated gene involved in organ size) is upregulated in MIR169d-OE due to reduced NF-YA2 repressor levels and that NF-YA2 directly binds the ARGOS promoter. Genetic screens of this module show that neither overexpressing miR169d in an argos mutant background nor the nf-ya2:argos double mutants rescue the argos mutant phenotype, suggesting a parallel pathway of ARGOS regulation via the MIR169:NF-YA2 node, independent of auxin. To assess the translational potential of this module in a crop, we show that Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants. In contrast, Sly-STTM169 plants inhibited for Sly-miR169 action and having increased levels of Sly-NF-YA10 have a longer life cycle with reduced biomass, decreased fruit set, and an overall reduction in yield. Thus, our findings show a conserved MIR169:NF-YA:ARGOS module which can be applied to crops for addressing future food demands.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 2","pages":"e70538"},"PeriodicalIF":5.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342475","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":"Correction.","authors":"","doi":"10.1111/tpj.70508","DOIUrl":"https://doi.org/10.1111/tpj.70508","url":null,"abstract":"","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 2","pages":"e70508"},"PeriodicalIF":5.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342445","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":"Discovery and enzymatic engineering of two non-canonical flavonoid C3-hydroxylases from Camptotheca acuminata Decne.","authors":"Jin-Wei He, Yu-Ke Liu, Zhi-Hui Ai, Xiao-Xue He, Shi-Yuan Tong, Xin-Yue Dai, Qi-Qi Wu, Jia-Yu Hu, Han-Guang Wang, Wei Wang, Qian-Ming Huang, Li Zhang, Wei Wu, Xiang Pu","doi":"10.1111/tpj.70536","DOIUrl":"https://doi.org/10.1111/tpj.70536","url":null,"abstract":"<p><p>Hydroxylation significantly enhances the structural diversity and biological activities of flavonoids. While most characterized CYP450-type hydroxylases catalyze hydroxylation at the C2, C6, C8, C2', C3', or C5' positions of flavonoids, the canonical flavonoid C3 hydroxylase (F3H) is a 2-oxoglutarate-dependent dioxygenase. This study biochemically characterizes two non-canonical CaF3Hs, CYP71AU223 and CYP71AU224, identified from the medicinal plant Camptotheca acuminata Decne through multi-omics analysis. Quantitative expression analysis shows that CYP71AU223 is predominantly expressed in leaves and roots, whereas CYP71AU224 is primarily expressed in roots. Both CaF3Hs localize to the endoplasmic reticulum. Among them, CYP71AU223 demonstrates a higher affinity for naringenin and superior catalytic performance compared to CYP71AU224. Cross-species collinearity analysis identifies two syntenic homologs, CsCYP71A and GmCYP71A in Camellia sinensis and Glycine max, respectively, which also exhibit F3H activity. These findings indicate that non-canonical CYP450-type F3Hs are not exclusive to C. acuminata but are distributed across other flavanone-producing plants. All these newly observed CYP450-type F3Hs originate from a shared ancestral gene. Molecular docking and site-directed mutagenesis of CYP71AU223 and CYP71AU224 reveal critical residues involved in naringenin binding, including SER-131 and ASP-329 in CYP71AU223 and ARG-101 and THR-501 in CYP71AU224, which stabilize substrate orientation. Enzymatic engineering further enhances the catalytic efficiency and expands the catalytic repertoire of both enzymes. This study reports the first identification of non-canonical F3Hs across three plant species, providing molecular insights into their functions, evolutionary origins, and roles in CYP450-mediated flavonoid hydroxylation.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 2","pages":"e70536"},"PeriodicalIF":5.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342502","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":"Too hot to defend: elevated temperature compromises systemic acquired resistance","authors":"Martin Balcerowicz","doi":"10.1111/tpj.70492","DOIUrl":"10.1111/tpj.70492","url":null,"abstract":"&lt;p&gt;When exposed to pathogens, plants activate immune responses at the infection site to fend off the invader; these include both broad-spectrum pattern-triggered immunity (PTI) and more specialized effector-triggered immunity (ETI). Local immune responses also generate long-distance signals that prepare distal, uninfected tissues for secondary pathogen attack in a process called systemic acquired resistance (SAR). SAR depends on major signaling molecules that act through partially parallel pathways, including the central defense phytohormone salicylic acid (SA) and &lt;i&gt;N&lt;/i&gt;-hydroxypipecolic acid (NHP), a major constituent of the SAR signal (Gao et al., &lt;span&gt;2021&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;Pathogen attack typically slows plant growth, while conditions favoring rapid growth—such as shade or elevated temperature—increase susceptibility to disease. This balance, commonly referred to as the “growth-defense trade-off,” is usually attributed to the reallocation of resources from one process to the other (He et al., &lt;span&gt;2022&lt;/span&gt;). Elevated temperature reduces the level and activity of multiple immunity-promoting factors (Hua &amp; Dong, &lt;span&gt;2022&lt;/span&gt;), and the transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) links the promotion of growth under high temperature with the suppression of immunity (Gangappa et al., &lt;span&gt;2017&lt;/span&gt;). But while the effects of elevated temperature on local immunity signaling and response have been well-documented, its impact on SAR remained unexplored.&lt;/p&gt;&lt;p&gt;Christian Danve Castroverde and his team at Wilfrid Laurier University study how temperature affects plant immunity and disease resistance, aiming to better understand the “plant–pathogen–environment” disease triangle and to leverage this knowledge for improving plant resilience in a warming climate. In the highlighted study, MSc student Alyssa Shields tackled a key question in this context: does elevated temperature influence immunity only locally or also systemically? To address this, she infected lower leaves of &lt;i&gt;Arabidopsis thaliana&lt;/i&gt; plants with the model pathogen &lt;i&gt;Pseudomonas syringae&lt;/i&gt; pv &lt;i&gt;tomato&lt;/i&gt; (&lt;i&gt;Pst&lt;/i&gt;), which causes bacterial speck disease; upper, previously uninfected (systemic) leaves were then challenged with &lt;i&gt;Pst&lt;/i&gt; 2 days later. At 23°C, bacterial growth in the systemic leaves was strongly suppressed, indicating effective SAR; at 28°C, however, this protection was lost, suggesting that SAR is impaired at elevated temperatures.&lt;/p&gt;&lt;p&gt;Lingya Yao, an assistant research fellow under the supervision of Xiu-Fang Xin at the CAS Center for Excellence in Molecular Plant Science at the time, joined the project to help uncover the underlying mechanisms. Integrating a SAR transcriptome (Hartmann et al., &lt;span&gt;2018&lt;/span&gt;) with the group's own temperature-regulated transcriptome (Kim et al., &lt;span&gt;2022&lt;/span&gt;), they found more than 1100 SAR-induced genes that are downregulated at elevated temperature, many of them involved in the PTI, ETI, ","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70492","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190496","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 CRISPR/Cas9 mutant resource for OsSm RNA-binding genes in rice","authors":"Xiongxia Jin,&nbsp;Chao Ouyang,&nbsp;Tong Sun,&nbsp;Cong Li,&nbsp;Jinbao Gu,&nbsp;Baoguang An,&nbsp;Zhenyu Wang","doi":"10.1111/tpj.70475","DOIUrl":"10.1111/tpj.70475","url":null,"abstract":"<div>\u0000 \u0000 <p>Pre-mRNA, produced by eukaryotic DNA transcription, undergoes splicing by the spliceosome, which removes introns and joins exons to form mRNA. The spliceosome is a large and highly dynamic molecular machine. Its core components include five small nuclear ribonucleoproteins (snRNPs) and the various spliceosome-related proteins. The conserved Smith (Sm) complex and the Sm-like proteins (LSm) serve as primary components of the snRNPs. Sm proteins are involved in processes such as pre-mRNA splicing and mRNA degradation, which can regulate gene expression, thereby influencing plant growth, development, and stress responses. While 25 Sm proteins have been identified in rice, their specific roles in regulating rice growth and development remain unclear. In this study, we employed the CRISPR/Cas9 system to edit 15 <i>OsSm</i> genes, and 13 mutants were obtained, with mutation rates ranging from 20.83 to 83.87%. In comparison to the wild type (WT), the mutants exhibited dwarfism, reduced tiller numbers, lower seed-setting rates or sterility, and increased susceptibility to diseases. One Sm mutant, <i>ossmf-2</i>, exhibited dwarfism, delayed flowering, and small grains. Through transcriptome analysis, three target genes, <i>OsMRG702</i>, <i>OsRGG2</i>, and <i>OsLA1</i>, were identified. Mutations of the OsSmF protein may lead to the abnormal splicing of these genes and finally lead to the inhibition of growth and development. Our study first edited the <i>OsSm</i> genes and generated a mutant library in rice. Most of the mutants exhibited abnormal growth and development, underscoring the essential roles of OsSm proteins in rice physiology. Furthermore, this work addresses a critical gap in the functional characterization of Sm proteins in rice. The resulting mutant collection offers valuable germplasm resources and lays a theoretical foundation for elucidating the molecular regulatory networks involving spliceosomal components and their target genes in the control of crop growth, development, and reproduction.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190531","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":"DNA methylation controls the expression of tanshinone synthesis genes and the tanshinone accumulation in Salvia miltiorrhiza and Salvia bowleyana","authors":"Li-Wei Liu,&nbsp;Xin-Ru Du,&nbsp;Rui Chu,&nbsp;Xin-Yu He,&nbsp;Yi-Wen Chen,&nbsp;Hua-Qian You,&nbsp;Itezaz Younas,&nbsp;Yi-Hong Li,&nbsp;Wei Li,&nbsp;Rui Zhang,&nbsp;Ye-Long Sheng,&nbsp;Ming Zhou,&nbsp;Qi Cui,&nbsp;Zong-Suo Liang,&nbsp;Dong-Feng Yang","doi":"10.1111/tpj.70494","DOIUrl":"10.1111/tpj.70494","url":null,"abstract":"<div>\u0000 \u0000 <p>DNA methylation plays pivotal roles in regulating gene expression and the secondary metabolism in plants. <i>Salvia miltiorrhiza</i> and <i>Salvia bowleyana</i> are traditional Chinese medicinal plants with roots enriched with tanshinone components. However, the regulatory mechanism of DNA methylation on tanshinone production remains elusive. Here, we analyzed 30-day-old hairy roots of <i>S. miltiorrhiza</i> and <i>S. bowleyana</i> using targeted high-performance liquid chromatography analysis and found significantly higher tanshinone content in <i>S. miltiorrhiza</i>. Whole-genome bisulfite sequencing revealed elevated DNA methylation levels in <i>S. miltiorrhiza</i>, potentially due to the upregulation of methylation-related genes, including <i>DOMAINS REARRANGED METHYLTRANSFERASE 1</i> (<i>DRM1</i>), <i>DECREASE IN DNA METHYLATION 1</i> (<i>DDM1</i>), <i>CHROMOMETHYLASE 2</i> (<i>CMT1</i>), and <i>CHROMOMETHYLASE 3</i> (<i>CMT3</i>), alongside the low expression of the demethylase gene REPRESSOR OF SILENCING 1 (<i>ROS1</i>) in <i>S. miltiorrhiza</i>. Additionally, four genes that are involved in tanshinone biosynthesis, including <i>1-DEOXY-<span>D</span>-XYLULOSE-5-PHOSPHATE REDUCTASE</i> (<i>DXS1</i>), <i>GERANYLGERANYL DIPHOSPHATE SYNTHASE</i> (<i>GGPPS2</i>), <i>4-HYDROXY-3-METHYLBUT-2-ENYL PYROPHOSPHATE REDUCTASE</i> (<i>HDR2</i>), and <i>COPALYL PYROPHOSPHATE SYNTHASE</i> (<i>CPS3</i>), showed lower methylation levels in the promoters of <i>DXS1</i>, <i>GGPPS2</i>, and <i>CPS3</i> and a higher DNA methylation level in the gene body of <i>HDR2</i> in <i>S. miltiorrhiza</i>, which may lead to their high expression and the accumulation of tanshinones. Consistently, overexpression of the <i>SmCMT3</i> in <i>S. miltiorrhiza</i> significantly reduced the contents of cryptotanshinone, tanshinone I, and tanshinone IIA. Transcriptomic and methylome analyses confirmed that the expression levels of the tanshinone biosynthesis-related genes, including <i>SmMK</i>, <i>SmCPS1</i>, <i>SmDXS2,</i> and <i>SmAACT1</i>, were correlated with their promoter or gene body DNA methylation levels. Our findings reveal that DNA methylation critically regulates tanshinone biosynthesis in <i>S. miltiorrhiza</i> and <i>S. bowleyana</i>, offering valuable insights for breeding.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184402","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":"Subgenomic divergence and functional innovation following whole-genome duplication in Maleae species of Rosaceae","authors":"Yangxin Zhang,&nbsp;Kecheng Qian,&nbsp;Qiaoming Yu,&nbsp;Xiangxiang Chen,&nbsp;Jiakai Liang,&nbsp;Zhiguang Liu,&nbsp;Zhuoxuan Dong,&nbsp;Yunxiao Liu,&nbsp;Yaqiang Sun,&nbsp;Zhenhua Guo,&nbsp;Fengwang Ma,&nbsp;Tao Zhao","doi":"10.1111/tpj.70499","DOIUrl":"10.1111/tpj.70499","url":null,"abstract":"<div>\u0000 \u0000 <p>Whole-genome duplication (WGD) drives plant evolution by inducing karyotype rearrangements and gene loss through subgenome fractionation. In this study, we investigate post-WGD evolutionary dynamics in Rosaceae, focusing on Maleae species, which uniquely experienced an additional WGD. Using phylogenetic and synteny analyses, we reveal that chromosomal breakpoints act as hotspots for localized fractionation, contributing to blurred homoeologous origins and influencing gene retention patterns. Here, we reconstruct karyotype evolution across Rosaceae subfamilies, highlighting chromosome reductions and lineage-specific rearrangements in Dryadoideae, Rosoideae, and Amygdaloideae. We also identify a bias for retaining transcription factors and hormone-related genes from older WGDs in subsequent polyploidy events. Transcriptome analysis classifies WGD-derived genes in Maleae species, such as apple and loquat, into three expression groups, with hormone-enriched genes playing roles in lignification and fruit-related innovations. These findings demonstrate the interplay between chromosomal breakpoints, biased retention, and functional divergence, revealing their contributions to genomic and phenotypic evolution in Maleae and their adaptive success within Rosaceae.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184349","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}