Plant Molecular Biology最新文献_第6页

How it all begins: molecular players of the early graviresponse in the non-elongating part of flax stem. 这一切是如何开始的：在亚麻茎的非伸长部分的早期重力反应的分子玩家。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-04-26 DOI: 10.1007/s11103-025-01588-4

Tatyana Gorshkova, Oleg Gorshkov, Natalia Mokshina

{"title":"How it all begins: molecular players of the early graviresponse in the non-elongating part of flax stem.","authors":"Tatyana Gorshkova, Oleg Gorshkov, Natalia Mokshina","doi":"10.1007/s11103-025-01588-4","DOIUrl":"10.1007/s11103-025-01588-4","url":null,"abstract":"Plants have developed two major strategies to adjust their position in response to gravity: differential cell growth on opposing sides of elongating regions and complex processes in non-elongating stem parts, such as the development of reaction wood. Gravistimulation of flax plants induces gravitropic curvature in non-elongating stem parts, largely associated with modifications in phloem and xylem fibers. To gain insight into the key \"triggers\" and \"forward players\" that induce negative gravitropic reactions, transcriptome profiling of phloem fibers and xylem tissues from the pulling and opposite stem sides was conducted 1 and 8 h after gravistimulation. The first observed reaction was the activation of processes associated with RNA synthesis and protein folding in both tissues and stem sides, followed by the activation of kinases and transferases. Transcriptomic data revealed rapid and substantial shifts in chloroplast metabolism across all analyzed tissues, including the temporal activation of the branched-chain amino acid pathway, adjustments to light-harvesting complexes, and jasmonic acid biosynthesis. Notably, auxin transporter genes were activated only in the xylem, while other auxin-related genes showed minimal upregulation 1 h after stem inclination in any analyzed sample. Asymmetric changes between stem sides included the sharp activation of ethylene-related genes in the phloem fibers of the opposite stem side, as well as tertiary cell wall deposition in both the phloem and xylem fibers of the pulling stem side during the later stages of the graviresponse. These results provide valuable insights into the mechanisms underlying plant response to gravity.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 3","pages":"61"},"PeriodicalIF":3.9,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144064467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unveiling the power of PavGID1s: the critical player in sweet cherry flower bud dormancy release. 揭开甜樱桃花蕾休眠释放关键因子PavGID1s的威力。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-04-23 DOI: 10.1007/s11103-025-01589-3

Xunju Liu, Li Wang, Muhammad Aamir Manzoor, Wanxia Sun, Yan Xu, Muhammad Salman Haider, Zhengxin Lv, Jiyuan Wang, Ruie Liu, Songtao Jiu, Caixi Zhang

{"title":"Unveiling the power of PavGID1s: the critical player in sweet cherry flower bud dormancy release.","authors":"Xunju Liu, Li Wang, Muhammad Aamir Manzoor, Wanxia Sun, Yan Xu, Muhammad Salman Haider, Zhengxin Lv, Jiyuan Wang, Ruie Liu, Songtao Jiu, Caixi Zhang","doi":"10.1007/s11103-025-01589-3","DOIUrl":"10.1007/s11103-025-01589-3","url":null,"abstract":"Exogenous hormones can regulate bud dormancy release, particularly in cases where inadequate winter chill accumulation due to global warming affects perennial plants. Gibberellin (GA) is recognized as a critical signal for dormancy release in woody perennials. This study explores the influence of GA and its signaling components on the dormancy release in sweet cherry. The external application of GA4 + 7 significantly promoted the bud break rate and dormancy release. Notably, there was a substantial accumulation of GA3, GA4, and GA7 in the buds, accompanied by a reduced concentration of abscisic acid (ABA) following GA treatment. RNA-Seq identified 8,610 differentially expressed transcripts in GA-treated buds compared to the Mock group. Transcriptome sequencing revealed differential expressions of PavGID1s, the GA receptor GID1, in sweet cherry flower buds after GA treatment. These findings were further verified across different seasons in sweet cherry. In both PavGID1b and PavGID1c, the open reading frame (ORF) is 1,032 bases long and encodes 344 amino acids. Overexpression of PavGID1b and PavGID1c resulted in early flowering and higher plants in Arabidopsis. However, these genes have opposing roles in seed germination in Arabidopsis. Furthermore, PavWRKY31 may regulate the stabilization and release of dormancy by modulating the transcriptional level of PavGID1c. PavGA20ox-2 and PavGID2 may also influence sweet cherry dormancy release by interacting with GID1s and affecting DELLA protein stability. These results provide a theoretical basis for understanding the regulatory effect of gibberellin on the bud dormancy of plants.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 3","pages":"60"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction: Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L. 更正：大麻Sativa L.天然反义转录物的全基因组观察和表征。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-04-16 DOI: 10.1007/s11103-025-01579-5

Chang Zhang, Mei Jiang, Jingting Liu, Bin Wu, Chang Liu

引用次数: 0

ROOT INITIATION DEFECTIVE 1 regulates seed germination through transcription rather than alternative splicing in a temperature-dependent manner. 根起始缺陷1通过转录而不是选择性剪接以温度依赖的方式调节种子萌发。

IF 3.8 2区生物学

Plant Molecular Biology Pub Date : 2025-04-16 DOI: 10.1007/s11103-025-01587-5

Shuaishuai Zhou, Miaomiao Wang, Ruoyi Chen, Wengeng Yu, Mengmeng Li, Siwen Meng, Ziru Zhang, Congcong Xia, Hongtao Zhao, Lei Liu

{"title":"ROOT INITIATION DEFECTIVE 1 regulates seed germination through transcription rather than alternative splicing in a temperature-dependent manner.","authors":"Shuaishuai Zhou, Miaomiao Wang, Ruoyi Chen, Wengeng Yu, Mengmeng Li, Siwen Meng, Ziru Zhang, Congcong Xia, Hongtao Zhao, Lei Liu","doi":"10.1007/s11103-025-01587-5","DOIUrl":"10.1007/s11103-025-01587-5","url":null,"abstract":"Timely seed germination is a crucial process for plant survival and subsequent propagation, which is significantly impacted by high temperatures. ROOT INITIATION DEFECTIVE 1 (RID1), an Arabidopsis DEAH/RHA RNA helicase, has been previously reported to modulate the cellular specification of mature female gametophyte and callus initiation from hypocotyl explants through proper alternative splicing. However, the role of RID1 in the regulation of seed germination remains largely unexplored. Here, we identified that mutations in RID1 delayed seed germination more severely at 28℃ compared to 22℃. Notably, we found that the rid1-1 mutation did not significantly alter genome-wide alternative splicing patterns during seed germination compared to the wild type. Further evidences demonstrated that RID1 regulates seed germination via the abscisic acid (ABA) pathway by physically and genetically interacting with the SKIP-associated transcriptional complex. These results suggest that RID1 regulates seed germination in response to ambient temperature at the transcriptional level rather than through alternative splicing regulation. This study provides novel insights into the mechanisms underlying the regulation of seed germination.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 3","pages":"58"},"PeriodicalIF":3.8,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Glycine rich proline rich protein from Sorghum bicolor serves as an antimicrobial protein implicated in plant defense response. 作者更正：富含甘氨酸的富含脯氨酸的高粱双色蛋白是一种抗菌蛋白，与植物防御反应有关。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-04-08 DOI: 10.1007/s11103-025-01585-7

Tanmoy Halder, Gouranga Upadhyaya, Shuddhanjali Roy, Ria Biswas, Arup Das, Angshuman Bagchi, Tanushree Agarwal, Sudipta Ray

引用次数: 0

Cutting-edge computational approaches to plant phenotyping. 植物表型的尖端计算方法。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-04-07 DOI: 10.1007/s11103-025-01582-w

Venkatesha Kurumayya

{"title":"Cutting-edge computational approaches to plant phenotyping.","authors":"Venkatesha Kurumayya","doi":"10.1007/s11103-025-01582-w","DOIUrl":"10.1007/s11103-025-01582-w","url":null,"abstract":"Precision agriculture methods can achieve the highest yield by applying the optimum amount of water, selecting appropriate pesticides, and managing crops in a way that minimises environmental impact. A rapidly emerging advanced research area, computer vision and deep learning, plays a significant role in effective crop management, such as superior genotype selection, plant classification, weed and pest detection, root localization, fruit counting and ripeness detection, and yield prediction. Also, phenotyping of plants involves analysing characteristics of plants such as chlorophyll content, leaf size, growth rate, leaf surface temperature, photosynthesis efficiency, leaf count, emergence time, shoot biomass, and germination time. This article presents an exhaustive study of recent techniques in computer vision and deep learning in plant science, with examples. The study provides the frequently used imaging parameters for plant image analysis with formulae, the most popular deep neural networks for plant classification and detection, object counting, and various applications. Furthermore, we discuss the publicly available plant image datasets for disease detection, weed control, and fruit detection with the evaluation metrics, tools and frameworks, future advancements and challenges in machine learning and deep learning models.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"56"},"PeriodicalIF":3.9,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide exploration of soybean domestication traits: integrating association mapping and SNP × SNP interaction analyses. 大豆驯化性状的全基因组探索：整合关联图谱和SNP × SNP互作分析。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-04-03 DOI: 10.1007/s11103-025-01583-9

Abhinandan S Patil, Manoj D Oak, Shreyash Gijare, Aditya Gobade, Santosh Jaybhay, Vilas D Surve, Suresha P G, Dattatraya Salunkhe, Balasaheb N Waghmare, Bhanudas Idhol, Ravindra M Patil, Deepak Pawar

{"title":"Genome-wide exploration of soybean domestication traits: integrating association mapping and SNP × SNP interaction analyses.","authors":"Abhinandan S Patil, Manoj D Oak, Shreyash Gijare, Aditya Gobade, Santosh Jaybhay, Vilas D Surve, Suresha P G, Dattatraya Salunkhe, Balasaheb N Waghmare, Bhanudas Idhol, Ravindra M Patil, Deepak Pawar","doi":"10.1007/s11103-025-01583-9","DOIUrl":"10.1007/s11103-025-01583-9","url":null,"abstract":"Soybean domestication has been essential for crop evolution, adaptation, and modern breeding. Despite advancements in understanding soybean genetics, the genetic basis of DRTs has yet to be fully explored, particularly in the context of genome-wide association studies (GWASs) and gene interaction analyses (epistasis). This study evaluated 198 diverse soybean accessions using 23,574 high-quality SNPs obtained via ddRAD-seq. Nine key DRTs-including those related to seed size (length, width, and thickness), seed coat color, cotyledon color, hypocotyl color, stem growth habit, flower color, pod color, pubescence, and pod-shattering-were phenotyped in two environments. A GWASs conducted via the FarmCPU and BLINK models identified 78 significant SNPs, 14 consistently detected across both environments and models, demonstrating stability. Notably, the SNP rs.Gm16.29778273 linked to pod-shattering resistance. The functional annotation linked three known quantitative trait loci /genes and revealed 11 novel candidate genes associated with DRTs, providing insights into their roles via Gene Ontology (GO) terms. The main effect SNP × SNP interaction analysis revealed that the significant SNP rs.Gm13.16695800 exhibits a pleiotropic effect, controlling both hypocotyl and flower color. Furthermore, 324 epistatic interactions were identified, influencing the expression of DRTs, thereby highlighting the complex genetic architecture underlying these traits. These findings offer valuable insights into domestication and the traits linked to higher yield. They provide a solid foundation for developing marker-assisted selection (MAS) strategies and functional studies to improve soybean breeding for resilient, high-yielding varieties.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"55"},"PeriodicalIF":3.9,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A large-scale gene co-expression network analysis reveals Glutamate Dehydrogenase 2 (GhGDH2_D03) as a hub regulator of salt and salt-alkali tolerance in cotton. 大规模基因共表达网络分析表明，谷氨酸脱氢酶2 （GhGDH2_D03）是棉花耐盐性和盐碱性的枢纽调节因子。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-04-02 DOI: 10.1007/s11103-025-01586-6

Rui Hao, Zhan Gao, Xianliang Zhang, Xingxing Wang, Wuwei Ye, Xiugui Chen, Xiongfeng Ma, Xianpeng Xiong, Guanjing Hu

{"title":"A large-scale gene co-expression network analysis reveals Glutamate Dehydrogenase 2 (GhGDH2_D03) as a hub regulator of salt and salt-alkali tolerance in cotton.","authors":"Rui Hao, Zhan Gao, Xianliang Zhang, Xingxing Wang, Wuwei Ye, Xiugui Chen, Xiongfeng Ma, Xianpeng Xiong, Guanjing Hu","doi":"10.1007/s11103-025-01586-6","DOIUrl":"10.1007/s11103-025-01586-6","url":null,"abstract":"Salt stress and salt-alkali stress significantly inhibit the normal growth and development of plants. Understanding the molecular mechanisms of cotton responses to these stresses is crucial for improve yield and fiber quality. In this study, we conducted a comprehensive analysis of the transcriptome dynamics under salt and salt-alkali stress conditions, utilizing 234 RNA-seq datasets compiled from 11 previous studies. After systematic evaluation and correction for batch effects, we observed that root transcriptomes clustered more consistently than leaf transcriptomes across stress treatment and time points. Weighted gene co-expression network analysis (WGCNA) on 123 root transcriptomes identified three key modules, with their hub genes significantly associated with salt and salt-alkali tolerance. Virus-induced gene silencing assay and RNA-seq analysis indicated that GhGDH2_D03 (Gohir.D03G104800), a module hub gene encoding Glutamate Dehydrogenase 2, positively regulates salt and salt-alkali tolerance in cotton by modulating multiple signaling pathways and metabolic processes, including the ethylene signaling pathway. This study underscores the pivotal role of GhGDH2_D03 in conferring tolerance to salt and salt-alkali stress, in addition to its previous reported involvement in biotic stress defense, providing valuable insights and genetic resources for cotton breeding.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"54"},"PeriodicalIF":3.9,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative transcriptomic analysis of heterotic maize development during kernel filling. 杂种玉米灌浆期发育的比较转录组学分析。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-04-02 DOI: 10.1007/s11103-025-01584-8

Wenyu Li, Xiangkun Guo, Wen Yao, Keke Li, Qi Zheng, Yongbiao Yu, Zhiwei Zhang, Yan Wang, Weigang Yao, Ju Wu, Huan Hu, Lingwei Hu, Long Zhang, Xinyu Li, Yongbin Dong, Yuling Li

{"title":"Comparative transcriptomic analysis of heterotic maize development during kernel filling.","authors":"Wenyu Li, Xiangkun Guo, Wen Yao, Keke Li, Qi Zheng, Yongbiao Yu, Zhiwei Zhang, Yan Wang, Weigang Yao, Ju Wu, Huan Hu, Lingwei Hu, Long Zhang, Xinyu Li, Yongbin Dong, Yuling Li","doi":"10.1007/s11103-025-01584-8","DOIUrl":"10.1007/s11103-025-01584-8","url":null,"abstract":"Heterosis, characterized by enhanced performance of a hybrid relative to its parental lines, has been a fundament of plant breeding strategies. Despite the application of heterosis, its molecular mechanisms remain elusive. Here, we focused on the maize heterotic hybrid Yudan132, which showed enhanced agronomic traits compared to its parental lines, including ear and kernel size, kernel weight, and overall yield. Notably, Yudan132 showed increased accumulation of storage substances, characterized by starch, protein contents and grain-filling rates, all of which collectively contribute to the augmented kernel weight. Through gene expression profiling, we identified differentially expressed genes (DEGs) in Yudan132 and its parental lines across four distinct kernel developmental stages (12, 20, 28, and 40 days after pollination). These DEGs displayed both additive and non-additive expression patterns, each contributing to heterosis in maize kernels. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis highlighted their involvement in metabolic pathways, biosynthesis of secondary metabolites, carbon metabolism, starch and sucrose metabolism processes. Within these pathways, the enriched DEGs predominantly associated with the gene categories of peroxidase, cytochrome P450, ketoacyl-CoA synthase, and phospholipase D. Furthermore, we identified the transcription factor bZIP88 among the DEGs, which was involved in the regulation of seed size and weight in transgenic Arabidopsis. These results suggested a potential role for bZIP88 in modulating kernel development, thereby further implicating the involvement of the identified DEGs in the molecular mechanisms of heterosis. These findings provide the genetic role of heterosis in kernel and the molecular mechanism regulating kernel development.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"53"},"PeriodicalIF":3.9,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Simulation study of factors affecting the accuracy of transcriptome models under complex environments. 复杂环境下影响转录组模型准确性因素的模拟研究。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-03-28 DOI: 10.1007/s11103-025-01578-6

Dan Eiju, Yoichi Hashida, Taro Maeda, Koji Iwayama, Atsushi J Nagano

{"title":"Simulation study of factors affecting the accuracy of transcriptome models under complex environments.","authors":"Dan Eiju, Yoichi Hashida, Taro Maeda, Koji Iwayama, Atsushi J Nagano","doi":"10.1007/s11103-025-01578-6","DOIUrl":"10.1007/s11103-025-01578-6","url":null,"abstract":"Characterization of molecular responses in real and complex field environments is essential for understanding the environmental response of plants. Field transcriptomics prediction consists of modeling of transcriptomes in outdoor fields with various environmental variables: Meteorological parameters, atmospheric gases, soil conditions, herbivores, management, etc. It is the most comprehensive method of studying gene expression dynamics in complex environments. However, it is not clear what factors influence the accuracy of field transcriptome models. In this study, a novel simulation system was developed. Using the system, we performed a large-scale simulation to reveal the factors affecting the accuracy of the models. We found that the factors that had the greatest impact on the accuracy are, in order of importance, the expression pattern of the gene, the number of samples in the training data, the diurnal coverage of the training data, and the temperature coverage of the training data. Validation using actually measured transcriptome data showed similar results to the simulations. Our simulation system and the analysis results will be helpful for developing efficient sampling strategies for training data and for generating simulated data for benchmarking new modelling methods. It will also be valuable to dissect the relative importance of various factors behind transcriptome dynamics in the real environment.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 2","pages":"52"},"PeriodicalIF":3.9,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143736203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0