Plant Communications最新文献

{"title":"Branching angles in the modulation of plant architecture: Molecular mechanisms, dynamic regulation, and evolution.","authors":"Chen Yun, Wanzhuang Ma, Jun Feng, Lanxin Li","doi":"10.1016/j.xplc.2025.101292","DOIUrl":"10.1016/j.xplc.2025.101292","url":null,"abstract":"<p><p>Plants develop branches to expand areas for assimilation and reproduction. Branching angles coordinate with branching types, creating diverse plant shapes that are adapted to various environments. Two types of branching angle-the angle between shoots and the angle in relation to gravity or the gravitropic set-point angle (GSA) along shoots-determine the spacing between shoots and the shape of the aboveground plant parts. However, it remains unclear how these branching angles are modulated throughout shoot development and how they interact with other factors that contribute to plant architecture. In this review, we systematically focus on the molecular mechanisms that regulate branching angles across various species, including gravitropism, anti-gravitropic offset, phototropism, and other regulatory factors, which collectively highlight comprehensive mechanisms centered on auxin. We also discuss the dynamics of branching angles during development and their relationships with branching number, stress resistance, and crop yield. Finally, we provide an evolutionary perspective on the conserved role of auxin in the regulation of branching angles.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101292"},"PeriodicalIF":9.4,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143505942","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":"Conditional knockdown of gene expression in plants via 3' UTR editing.","authors":"Tianzhen Liu, Jiaqi Shen, Dating Zhong, Kelin Wang, Jiarui Yan, Qi Yao, Lu Ye, Kai Li, Qi Deng, Yuming Lu","doi":"10.1016/j.xplc.2025.101291","DOIUrl":"10.1016/j.xplc.2025.101291","url":null,"abstract":"<p><p>The spatiotemporal knockdown of genes through genome editing heralds a new frontier in molecular breeding, yet it remains largely unexplored. Recognizing the intricate regulatory networks of endogenous microRNAs (miRNAs), we posited that integration of specific miRNA target sequences into the 3' untranslated region (UTR) of a gene could construct artificial miRNA-dependent regulatory circuits, facilitating precise spatiotemporal gene suppression. To test this hypothesis, we selected three endogenous miRNAs with unique expression profiles by analyzing rice miRNA expression profiles. Results from both transient assays and stably-edited rice plants confirmed that in-locus incorporation of miRNA targets into the 3' UTR of target genes can substantially reduce their expression in a spatiotemporal manner. Using GID1 as a target gene, we found that knockin of the miR156a target led to a remarkable 97% constitutive reduction; knockin of the tissue-specifically expressed miR396c target significantly reduced its expression in shoots alone; and knock-in of the long-day-induced miR528 target triggered a dramatic and temporal decrease of 95% specifically under such light exposure. These findings underscore the viability of miRNA-mediated, in-locus knockdown (MiRKD) as a convenient approach for crop breeding, leveraging miRNA expression traits and genome editing for conditional gene suppression.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101291"},"PeriodicalIF":9.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484684","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":"WP-MOD: A multi-omics and taxonomy database for woody plants.","authors":"Qi Wang, Shaoxuan Luo, Yixiang Yang, Yawen Bai, Junrong Wei, Ke-Wang Xu, Yong Yang, Meng Li, Xiaozeng Yang, Yifan Duan, Zhonglong Guo","doi":"10.1016/j.xplc.2025.101290","DOIUrl":"10.1016/j.xplc.2025.101290","url":null,"abstract":"<p><p>Woody plants, including trees, shrubs, and woody vines, are vital components of terrestrial ecosystems and are critical for maintaining biodiversity, regulating climate, and supporting human livelihoods. Over the past decade, the accumulation of high-throughput sequencing data, multi-omics data, and taxonomic information on woody plants has increased significantly, highlighting the need for an integrative database. Here, we present the Woody Plant Multi-Omics Database (WP-MOD, https://www.woodyplant.com), a comprehensive and user-friendly platform designed to meet the growing need for specialized resources in woody plant research. The WP-MOD integrates extensive taxonomic information and multi-omics data from 373 species across 35 orders and provides a centralized resource for the analysis and exploration of woody plant biology. The database includes high-quality reference genomes and reanalyzed data from RNA sequencing, small RNA sequencing, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin sequencing, and bisulfite sequencing, along with 17 tools for sequence and omics analysis. The WP-MOD supports both genetic and molecular research and contributes to the conservation and sustainable management of woody plants. We believe that the WP-MOD will be an essential tool for plant science researchers.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101290"},"PeriodicalIF":9.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484690","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":"GWAS-based population genetic analysis identifies bZIP29 as a heterotic gene in maize.","authors":"Jie Zhang, Riliang Gu, Xinxin Miao, Renate H Schmidt, Zhenxiang Xu, Jiawen Lu, Yuting Ma, Tao Yang, Pingxi Wang, Yangyang Liu, Xiaoli Wang, Xuemei Du, Nannan Zheng, Sihan Zhen, Chengyong Liang, Yuxin Xie, Yongrui Wu, Lin Li, Jochen C Reif, Yong Jiang, Jianhua Wang, Junjie Fu, Hongwei Zhang","doi":"10.1016/j.xplc.2025.101289","DOIUrl":"10.1016/j.xplc.2025.101289","url":null,"abstract":"<p><p>Understanding the role of heterotic genes in contributing to heterosis is essential for advancing hybrid breeding. We analyzed plant height (PH), ear height (EH), and transcriptomic data from a maize hybrid population. Genome-wide association studies (GWASs) revealed that dominance effects of quantitative trait loci (QTLs) play a significant role in hybrid traits and mid-parent heterosis. By integrating GWAS, expression GWAS (eGWAS), and module eGWAS analysis, we prioritized six candidate heterotic genes underlying six QTLs, including one QTL that spans the bZIP29 gene. In the hybrid population, bZIP29 exhibits additive expression and dominance effects for both hybrid traits and mid-parent heterosis, with its favorable allele correlating positively with PH and EH. bZIP29 demonstrates dominance or over-dominance patterns in hybrids derived from crosses between transgenic and wild-type lines, contingent upon its expression. A tsCUT&Tag assay revealed that bZIP29 protein binds directly to a gene regulated by its associated expression QTL (eQTL) and six genes within expression modules governed by its associated module-eQTLs (meQTLs). Regulatory networks involving bZIP29 are more extensive in hybrid subpopulations than in the parental population. This study offers insights into key heterotic genes and networks that underpin the robust growth of hybrid maize.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101289"},"PeriodicalIF":9.4,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477250","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":"Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism.","authors":"Bhagwat Nawade, Su-Hyeon Shim, Sang-Ho Chu, Weiguo Zhao, Sang-Kyu Lee, Aueangporn Somsri, Thant Zin Maung, Kwon Kyoo Kang, Jae Yoon Kim, Chang-Yong Lee, Min-Seok Kim, Moo-Yeol Baik, Jong-Seong Jeon, Yong-Jin Park","doi":"10.1016/j.xplc.2025.101287","DOIUrl":"10.1016/j.xplc.2025.101287","url":null,"abstract":"<p><p>Rice eating and cooking quality (ECQ) is significantly influenced by the physicochemical properties of rice starch. This study integrates whole-genome resequencing, transcriptomic data, and phenotypic analysis to identify the genetic factors that regulate transcript expression levels and contribute to phenotypic variation in rice ECQ traits. A TWAS (transcriptome-wide association study) identified 285 transcripts linked to 6 ECQ traits. Genome-wide mapping of these transcripts revealed 21 747 local eQTLs (expression quantitative trait loci) and 45 158 distal eQTLs. TWAS and eQTL analysis detected several known and novel genes, including starch synthesis-related genes, heat shock proteins, transcription factors, genes related to ATP accumulation, and UDP-glucosyltransferases, showcasing the complex genetic regulation of rice ECQ. WGCNA (weighted gene co-expression network analysis) uncovered key co-expression networks, including a module that links alpha-globulin1 (GLB1) to starch and sucrose metabolism. Genetic diversity analysis of the GLB1 gene across a Korean rice collection identified 26 haplotypes, with indica and aus forming 7 and 3 haplotypes, respectively, which showed significant phenotypic effects on ECQ traits. CRISPR-Cas9-created knockout lines validated these findings, demonstrating that loss of GLB1 function caused significant changes in seed storage proteins, reduced amylose content, altered starch granules, and modified pasting properties without affecting plant phenotypes. By integrating TWAS, eQTL mapping, haplotype analysis, gene expression networks, and CRISPR validation, this study establishes GLB1 as a regulator of ECQ, linking starch biosynthesis and protein accumulation pathways. This transcriptogenomic convergence approach provides novel insights into the genetic regulation of ECQ in rice, demonstrating its effectiveness for characterizing complex traits and enabling precision breeding.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101287"},"PeriodicalIF":9.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469880","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":"AtKC1 inhibits AKT1 activation via its amino-terminal inhibitory domain.","authors":"Zijie Zheng, Yannan Qu, Jiexin Chen, Yuyue Tang, Dongliang Liu, Zhuo Huang, Huaizong Shen","doi":"10.1016/j.xplc.2025.101288","DOIUrl":"10.1016/j.xplc.2025.101288","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101288"},"PeriodicalIF":9.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469948","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":"Three cytochrome P450 enzymes consecutively catalyze the biosynthesis of furanoclerodane precursors in Salvia species.","authors":"Ruoxi Lin, Haixiu Li, Yiren Xiao, Zhuo Wang, Licheng Liu, Gerhard Saalbach, Carlo Martins, Matthew Furry, Christopher D Vanderwal, Cathie Martin, Evangelos C Tatsis","doi":"10.1016/j.xplc.2025.101286","DOIUrl":"10.1016/j.xplc.2025.101286","url":null,"abstract":"<p><p>Salvia species native to the Americas are rich in valuable bioactive furanoclerodanes like the psychoactive salvinorin A found in Salvia divinorum, which is used in the treatment of opioid addiction. However, relatively little is known about their biosynthesis. To address this, we investigated the biosynthesis of salviarin, the most abundant furanoclerodane structure in the ornamental sage Salvia splendens. Using a self-organizing map and mutual rank analysis of RNA-seq co-expression data, we identified three cytochrome P450 enzymes responsible for the consecutive conversion of kolavenol into the salviarin precursors: annonene, hardwickiic acid, and hautriwaic acid. Annonene and hardwickiic acid have been proposed as intermediates in the biosynthesis of salvinorin A, and we therefore tested for a common evolutionary origin of the furanoclerodane pathway in these Salvia species by searching for homologous genes in available data for S. divinorum. The enzymes encoded by orthologous genes from S. divinorum displayed kolavenol synthase, annonene synthase, and hardwickiic acid synthase activity, respectively, supporting the view that these are intermediate steps in the biosynthesis of salvinorin A. We further investigated the origin of annonene synthase and the role of gene duplication in the evolution of this specific activity. Our work shows how S. splendens can serve as a model species for the study of furanoclerodane biosynthesis in Salvia species, contributes to understanding the evolution of specialized metabolism in plants, and provides new tools for the production of salvinorin A in biotechnological chassis.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101286"},"PeriodicalIF":9.4,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460594","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 core morning clock component CCA1 enhances UPR target gene expression to facilitate ER stress recovery.","authors":"Gyeongik Ahn, In Jung Jung, Gyeong-Im Shin, Song Yi Jeong, Myung Geun Ji, Jin-Sung Huh, Ji-Won Hwang, Jeongsik Kim, Joon-Yung Cha, Sang Yeol Lee, Min Gab Kim, Woe-Yeon Kim","doi":"10.1016/j.xplc.2025.101284","DOIUrl":"10.1016/j.xplc.2025.101284","url":null,"abstract":"<p><p>The endoplasmic reticulum (ER) is a cellular organelle responsible for protein synthesis and folding. When its protein folding capacity is exceeded, unfolded or misfolded proteins accumulate, causing ER stress and triggering the unfolded protein response (UPR) to restore ER proteostasis. Although UPR gene expression in plants follows a diel cycle, the mechanisms by which the circadian clock regulates these genes remain unclear. Here, we demonstrate that sensitivity to ER stress in root growth exhibits time-of-day phases and that the circadian clock regulates UPR target gene expression during ER stress. Notably, mutations in the core morning clock component CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) impair ER stress recovery. CCA1 forms a complex with the UPR modulator basic leucine zipper 28 (bZIP28) and acts as an upstream regulator of ER stress recovery. Upon ER stress, CCA1 is stabilized and associates with bZIP28 at the ER stress response element within the BiP3 promoter, enhancing the ER stress response. Thus, CCA1 and bZIP28 coordinate a time-dependent adaptive response to ER stress to maintain ER proteostasis. Our results suggest that the circadian clock primes the timing and levels of ER chaperone expression to enhance ER stress tolerance.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101284"},"PeriodicalIF":9.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426596","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":"Two duplicated GhMML3 genes coordinately control development of lint and fuzz fibers in cotton.","authors":"Rui Chen, Jun Zhang, Jun Li, Jinwen Chen, Fan Dai, Yue Tian, Yan Hu, Qian-Hao Zhu, Tianzhen Zhang","doi":"10.1016/j.xplc.2025.101281","DOIUrl":"10.1016/j.xplc.2025.101281","url":null,"abstract":"<p><p>Cotton produces two types of fibers: fuzz and lint. Cotton yield is determined by the number of epidermal cells that develop into lint fibers. Despite numerous studies, the genetic and molecular mechanisms that control lint and fuzz fiber development remain unclear. Here, using the recessive naked-seed or fuzzless-linted mutant (n₂NSM) in combination with gene editing and complementation, we found that the recessive fuzzless gene n₂ encodes the MYBMIXTA-like (MML) transcription factor GhMML3_D12. Overexpression of GhMML3_D12 in n₂NSM restored fuzz fiber development, whereas CRISPR-Cas9 knockout of GhMML3_D12 in wild-type cotton (J668) resulted in a fuzzless-linted phenotype. Interestingly, simultaneous edits to GhMML3_D12 and its duplicate GhMML3_A12 resulted in plants with a fiberless (fuzzless-lintless) phenotype. Detailed investigation of the seed fiber phenotypes of segregating progeny derived from a cross between J668 and a fiberless gene-edited mutant of GhMML3 (#mml3s) not only identified progeny that mimicked natural fuzzless and fiberless mutants but also revealed that the duplicated GhMML3_A12 and GhMML3_D12 regulate the development of fuzz and lint fibers in a dose-dependent manner. Comparative transcriptome analysis and single-cell RNA sequencing identified GhMML3 as the central hub of the gene network that regulates fiber initiation and early-stage elongation. The gene regulatory network revealed potential candidate genes and key regulators that may contribute to fiber initiation and development, and a model for the control of lint and fuzz fiber development by GhMML3 was proposed. We also found that the GhMML3_D12 protein can bind directly to the promoters of GhHD-1 and GhMYB25, two key genes involved in fiber initiation, thereby activating their expression. This study provides new insights into the fundamental mechanisms that underlie cotton fiber development.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101281"},"PeriodicalIF":9.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411488","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 aleurone layer of cereal grains: Development, genetic regulation, and breeding applications.","authors":"Huawei Liang, Jian Zhou, Chen Chen","doi":"10.1016/j.xplc.2025.101283","DOIUrl":"10.1016/j.xplc.2025.101283","url":null,"abstract":"<p><p>Cereal aleurone cells are differentiated from triploid endosperm cells and exhibit distinct cytological, physiological, and biochemical characteristics that distinguish them from the starchy endosperm cells of cereals. Aleurone cells maintain viability throughout seed development, whereas starchy endosperm cells undergo programmed cell death during maturation. Despite variations in aleurone-related traits among cereal species, the aleurone layer plays a crucial role in regulating many aspects of seed development, including the accumulation of storage reserves, the acquisition of dormancy, and germination. Given that many nutrients-such as lipids, dietary fibers, vitamins, and minerals like iron and zinc-are predominantly accumulated in the aleurone cells of cereal grains, this layer has attracted considerable attention aimed at improving the nutritional value of cereals. This review provides a comprehensive overview of the developmental, genetic, and molecular basis of aleurone cell differentiation and proliferation. It focuses on the improvement of aleurone-related traits informed by knowledge of the molecular networks governing aleurone development and presents a detailed discussion on the challenges and potential solutions associated with cereal improvement through the manipulation of aleurone-related traits.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101283"},"PeriodicalIF":9.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416119","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}