Plant Communications最新文献

{"title":"The origin, evolution and diversification of MADS-box transcription factors in green plants.","authors":"Jia-Peng Han, Jun-Nan Wan, Zhi-Lin Guan, Han Xu, Qing-Feng Wang, Tao Wan","doi":"10.1016/j.xplc.2025.101462","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101462","url":null,"abstract":"<p><p>MADS-box genes acted as one of the most important regulatory elements in eukaryotes and particularly diversified throughout the evolution of green plants (Viridiplantae). Although the evolution and function of MADS-box genes have been extensively studied, it remains incomplete regarding the picture of the origin and diversification of MADS-box genes in Viridiplantae. Here, we employed genomic data of 551 representative eukaryotes for systematical analyses on both sequences and protein structures, aiming to clarify the evolutionary footprint of MADS-box genes across green plant lineages. Our analyses suggested the polyphyletic origin of plant Type I genes, and the two subfamilies of plant Type II genes (i.e., MIKC^C and MIKC^∗ genes) have arisen from an ancient gene duplication in the stem group of streptophytes rather than in land plants. The sphere-like structures of MIKC^C proteins were uncovered in chlorophytes and charophytes, likely being an ancestral feature as physical constraint to tetramerization. The architectures of MIKC^C proteins largely evolved in land plants with significantly shortened C-termini where key domains fully exposed, offering a structural necessity for shaping tetramer. Meanwhile, we recovered the diversification of MIKC^C genes in ferns, implying a preacquisition of raw genetic basis for their explosive functional diversity in seed plants.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101462"},"PeriodicalIF":9.4,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676455","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 TaMYB44-TaMYB1 module regulates grain amylose biosynthesis and flour viscosity in wheat.","authors":"Sen Li, Guoyu Liu, Ziyan Wu, Dongxue Zhang, Chongyi Gan, Baoyun Li, Jie Liu, Zhongfu Ni, Qixin Sun, Rongqi Liang","doi":"10.1016/j.xplc.2025.101461","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101461","url":null,"abstract":"<p><p>Starch content and composition in wheat endosperm are the important factors determining wheat yield and quality. The amylose content is one of the key parameters to characterize the starch viscosity in wheat flour, which affects pasting time and peak viscosity (PV), and then affects the eating quality of flour-based food. However, the transcriptional regulatory mechanisms of amylose biosynthesis in wheat remain poorly understood. Here, we identified a MYB transcription factor, TaMYB44-4D that can bind to the TaWx-7A promoter through yeast one-hybrid screening. EMSA, Y1H and Transactivation assays demonstrated that TaMYB44-4D could bind to the TaWx-7A promoters and repress their transcription activity. Knock-out TaMYB44-A/B/D simultaneously increased the amylose content, total starch content, swelling power, and RVA parameters, whereas overexpression of TaMYB44-4D decreased these parameters. These results indicated that TaMYB44 functions as a transcriptional repressor of starch biosynthesis. We confirmed that TaMYB44 interacted with TaMYB1, and the similar phenotypes were observed in both the tamyb44-KO and tamyb1-KO lines, as well as in the TaMYB44-4D-OE and TaMYB1-6B-OE lines, suggesting that they acted as co-repressors. Finally, a single nucleotide polymorphism (SNP) T/C was found in the promoter of TaMYB44-D in different wheat varieties and had been confirmed to be associated with the expression levels of TaMYB44. Association analysis of phenotype and genotype in a wheat natural population revealed that varieties with the CC haplotype exhibited higher amylose content than those with the TT haplotype. In conclusion, our findings are of great significance for understanding the transcriptional regulation mechanism of wheat amylose synthesis and genetic improvement of wheat starch quality.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101461"},"PeriodicalIF":9.4,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676456","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 bHLH7-PDF2 module mediates transcriptional regulation to repress seed oil accumulation in Arabidopsis thaliana.","authors":"Zijin Liu, Yu Zhao, Lianying Mao, Dong Li, Bo Song, Minshan Jin, Jun Ma, Jianjun Wang, Shuangcheng He, Shixiang Wang, Huan Hu, Yuan Guo, Saiqi Yang, Mingxun Chen","doi":"10.1016/j.xplc.2025.101459","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101459","url":null,"abstract":"<p><p>Seed oil accumulation requires precise coordination of multiple factors, and transcription factors (TFs) play crucial roles in governing this process. However, the knowledge of how TFs and the crosstalk between different TF families coordinate the transcriptional network associated with seed oil accumulation is still lacking. Here, we report that both basic helix-loop-helix7 (bHLH7) and PROTODERMAL FACTOR2 (PDF2) TFs, highly expressed in the developing embryos, negatively control seed oil accumulation. bHLH7 and PDF2 physically interact and cooperatively inhibit the transcription of MYB96, PYRUVATE DEHYDROGENASE E1 BETA1 (PDH-E1β1), PDH-E1β2, and BIOTIN CARBOXYL CARRIER PROTEIN1 (BCCP1) by directly binding to their promoters. Further genetic findings demonstrated that bHLH7 and PDF2 act in an additive manner to repress seed oil accumulation, and this effect is partially dependent on PDH-E1β1 that significantly promotes seed oil deposition. Collectively, we provide insights into the mechanisms by which transcriptional regulation mediated by the bHLH7-PDF2 module controls oil accumulation in A. thaliana seeds.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101459"},"PeriodicalIF":9.4,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668995","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 bZIP transcription factor RISBZ1 balances grain filling and ER stress response in rice grains.","authors":"Qi Sun, Erchao Duan, Ruonan Jing, Yulong Ren, Huan Xu, Chuanwei Gu, Wenting Lv, Xiaokang Jiang, Rongbo Chen, Qingkai Wang, Yipeng Zhang, Rushuang Zhang, Hongyi Xu, Yunpeng Zhang, Jiajia Chi, Yunfei Fu, Yun Zhu, Yu Zhang, Binglei Zhang, Xuan Teng, Hui Dong, Xue Yang, Lei Zhou, Yunlu Tian, Xi Liu, Shijia Liu, Xiuping Guo, Cailin Lei, Ling Jiang, Yihua Wang, Jianmin Wan","doi":"10.1016/j.xplc.2025.101458","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101458","url":null,"abstract":"<p><p>In cereal crops, the endosperm is responsible for synthesizing large amounts of proteins, including storage proteins and functional factors essential for the accumulation of storage substances. The unfolded protein response (UPR) monitors the folding of nascent polypeptides in the endoplasmic reticulum (ER) to alleviate cellular stress. However, the molecular mechanisms linking UPR to endosperm development in plants remain poorly understood. In this study, we isolated and characterized a rice (Oryza sativa L) mutant with defective endosperm development, which we named floury endosperm27 (flo27). Molecular cloning revealed that FLO27 encodes RISBZ1/bZIP58, an endosperm-specific transcription factor that is co-expressed with seed storage protein (SSP) genes and starch biosynthesis-related genes in rice. We found that the flo27 mutant exhibits severe ER stress, accompanied by the upregulation of UPR-related genes. Notably, RISBZ1 interacts with bZIP50 and bZIP60 to antagonistically downregulate the expression of downstream UPR genes. These interactions simultaneously suppress the expression of SSP genes and starch biosynthesis-related genes, ultimately leading to reduced dry matter accumulation. In conclusion, our findings demonstrate that RISBZ1 acts as a \"brake signal\" to mitigate ER stress, thereby broadening our understanding of the delicate trade-off between grain-filling and adaptation to adverse environmental conditions in rice.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101458"},"PeriodicalIF":9.4,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668996","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 telomere-to-telomere genome assembly for greater yam (Dioscorea alata).","authors":"Yan-Mei Zhang, Zhi-Yan Wei, Cheng-Ao Yang, Xing-Yu Feng, Yue Wang, Sai-Xi Li, Xiao-Qin Sun, Zhu-Qing Shao, Jia-Yu Xue","doi":"10.1016/j.xplc.2025.101326","DOIUrl":"10.1016/j.xplc.2025.101326","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101326"},"PeriodicalIF":9.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781359","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":"Efficient haploid induction in Arabidopsis thaliana by fine-tuning CENH3 function.","authors":"Huan Yang, Ruihua Zhang, Siyu Wu, Shuai Yue, Jianlong Sun, Youfeng Yu, Keke Yi, Shouchuang Wang, Ze Wang, Jing Li","doi":"10.1016/j.xplc.2025.101349","DOIUrl":"10.1016/j.xplc.2025.101349","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101349"},"PeriodicalIF":9.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040421","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":"Smart agriculture in Asia.","authors":"Fahui Yuan, Ricardo Ospina, Anand Babu Perumal, Noboru Noguchi, Yong He, Yufei Liu","doi":"10.1016/j.xplc.2025.101377","DOIUrl":"10.1016/j.xplc.2025.101377","url":null,"abstract":"<p><p>Faced with a shortage of agricultural land and a changing climate, Asia urgently needs to focus on smart agriculture to meet the food demands of an increasing population. In recent years, advances in information technology and governmental support have promoted the rapid development of smart agriculture in Asia. This study provides a comprehensive review of the progress of smart agriculture in Asia. First, using bibliometrics, we conduct a comprehensive analysis of Asian smart-agriculture research in terms of countries, institutions, and keywords. Second, we investigate innovative technologies used in smart agriculture and provide a systematic summary of agricultural production in Asia, from breeding to harvest. In addition, we conduct qualitative and quantitative assessments of smart-agriculture policies across Asia and present cutting-edge solutions to key challenges such as climate change, labor shortage, and water scarcity. Currently, Asian smart-agriculture policies are insufficient in areas such as risk prevention and control, international cooperation, and standardization. Accordingly, future efforts may focus on enhancing data security and standardization to promote the global development and popularization of smart agriculture. Finally, we discuss trends and challenges that need to be considered and addressed in the future. This review aims to analyze the technical characteristics and application status of smart agriculture in Asia and to provide resources for researchers and policy makers.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101377"},"PeriodicalIF":9.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086921","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":"Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in rice roots.","authors":"Wenhui Li, Xinxin Zhu, Junjiao Yang, Xiangyu Zhou, Luchang Ming, Ling Yang, Jiacheng Li, Zengdong Tan, Chunjiao Xia, Dujun Wang, Xingbing Xu, Zhanxiang Zong, Hu Zhao, Meng Yang, Lizhong Xiong, Xingming Lian, Weibo Xie","doi":"10.1016/j.xplc.2025.101392","DOIUrl":"10.1016/j.xplc.2025.101392","url":null,"abstract":"<p><p>Nitrogen (N) is essential for rice growth; however, the transcriptional regulation of the primary nitrogen response (PNR), characterized by the rapid upregulation of N uptake and assimilation genes upon N resupply, remains poorly understood. This study investigated the dynamics of the PNR in the roots of two rice cultivars (Zhenshan 97 and Nipponbare) via time-series Assay for Transposase-Accessible Chromatin using sequencing and RNA sequencing analyses within 2 h of ammonium nitrate resupply. Regulatory regions responsive to N induction were precisely identified. Coordinated and cascading changes in chromatin accessibility and gene expression were observed, with chromatin state frequently preceding transcriptional changes. Integrative analysis of expression-chromatin accessibility associations revealed a redundant N-responsive regulatory network. OsLBD38 and OsLBD39, identified as early-response regulators, transcriptionally suppress nitrate reductases while enhancing nitrite reductases; they may function as metabolic safeguarders to prevent nitrite accumulation. OsbZIP23 was identified as a novel regulator directly binding to the promoters of N uptake and metabolism genes, regulating genes in patterns opposite to LBD-regulated genes, suggesting a complex regulatory interplay. Cross-species comparisons with Arabidopsis highlighted the conserved N-responsive regulatory roles of these hub regulators and their targets. Comparative analyses between cultivars revealed expression divergence and genetic differentiation in N-responsive genes, implying indica/japonica-specific adaptations. Furthermore, deep learning predictions of chromatin accessibility between cultivars indicated that expression variation in N uptake and metabolism genes is primarily influenced by trans-acting regulatory factors. These findings provide a comprehensive view of the dynamic regulatory landscape governing the PNR in rice.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101392"},"PeriodicalIF":9.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227594","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":"Dual roles of SOS1: Na⁺ extrusion and vacuolar compartmentation.","authors":"Yuting Qi, Quan-Sheng Qiu","doi":"10.1016/j.xplc.2025.101423","DOIUrl":"10.1016/j.xplc.2025.101423","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101423"},"PeriodicalIF":9.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340637","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":"Genetic and genomic insights into dichogamy in Zingiberaceae.","authors":"Shanshan Chen, Xiaochang Peng, Ziyan Xie, Mofan Zhang, Aodan Huang, Weibin Wang, Guisheng Xiang, Kaiquan Zhang, Ranran Gao, Baozhong Duan, Wei Sun, Yuanhong Fan, Shilin Chen, Zhichao Xu","doi":"10.1016/j.xplc.2025.101352","DOIUrl":"10.1016/j.xplc.2025.101352","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101352"},"PeriodicalIF":9.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057692","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}