Plant Molecular Biology最新文献_第7页

Transcriptomic analysis of wrinkled leaf development of Tai-cai (Brassica rapa var. tai-tsai) and its synthetic allotetraploid via RNA and miRNA sequencing. 通过RNA和miRNA测序分析太菜（Brassica rapa var. tai-tsai）皱叶发育及其合成异体四倍体的转录组学分析。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-05-06 DOI: 10.1007/s11103-025-01592-8

Xinli Zhang, Wen Zheng, Zhiyu Zhu, Xiaocan Guo, Jinbao Hu, Li'ai Xu, Huihui Fang, Yunshuai Huang, Zhengyan Ling, Zhujun Zhu, Yunxiang Zang, Jianguo Wu

{"title":"Transcriptomic analysis of wrinkled leaf development of Tai-cai (Brassica rapa var. tai-tsai) and its synthetic allotetraploid via RNA and miRNA sequencing.","authors":"Xinli Zhang, Wen Zheng, Zhiyu Zhu, Xiaocan Guo, Jinbao Hu, Li'ai Xu, Huihui Fang, Yunshuai Huang, Zhengyan Ling, Zhujun Zhu, Yunxiang Zang, Jianguo Wu","doi":"10.1007/s11103-025-01592-8","DOIUrl":"10.1007/s11103-025-01592-8","url":null,"abstract":"The allotetraploid (AACC) was synthesized through wide hybridization between 'Mottle-leaf Tai-cai' (Brassica rapa var. tai-tsai Hort. AA) and 'Big Yellow Flower Chinese Kale' (B. oleracea var. alboglabra Bailey. CC) in earlier study, which owns a stronger wrinkled leaf and wave margin than Tai-cai. To analyze the structure and developmental mechanism of wrinkled leaf and wave edge, four leaf development stages were chosen for RNA-seq and their key stages for anatomical observation. As a result, the number of cell layers and compactness of AA and AACC were significantly increased in folded parts, and the enlargement of epidermal cells causes the leaf edge to curve inward. The gene expression bias of AACC showed no difference in the cotyledon stage, favored the A genome in the first leaf stage, however, favored the C genome in the third leaf and fifth leaf stages, showing an expression level advantage over the C genome parent. During the leaf development, the plant hormone signaling pathway were significantly enriched, PIN1 (BraC07g037600), AUX1 (BraC05g007870), AUX/IAA (BraC03g037630), and GH3 (BraC10g026970), which maintained high expression during the euphylla leaf stage of AA and AACC. And these genes performed different patterns in CC. In addition, the expression levels of miR319 and miR156 of AA were significantly higher than those of CC, and the expression levels of their target genes TCP and SPL were lower. These genes were jointly involved in the development of AA and AACC leaves and may be closely related to the formation of leaf folds and waves.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 3","pages":"66"},"PeriodicalIF":3.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144064474","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

Engineering plant photoreceptors towards enhancing plant productivity. 工程植物光感受器提高植物生产力。

IF 3.9 2区生物学

Plant Molecular Biology Pub Date : 2025-05-06 DOI: 10.1007/s11103-025-01591-9

Ramyani Bhattacharjee, Highland Kayang, Eros V Kharshiing

{"title":"Engineering plant photoreceptors towards enhancing plant productivity.","authors":"Ramyani Bhattacharjee, Highland Kayang, Eros V Kharshiing","doi":"10.1007/s11103-025-01591-9","DOIUrl":"10.1007/s11103-025-01591-9","url":null,"abstract":"Light is a critical environmental factor that governs the growth and development of plants. Plants have specialised photoreceptor proteins, which allow them to sense both quality and quantity of light and drive a wide range of responses critical for optimising growth, resource use and adaptation to changes in environment. Understanding the role of these photoreceptors in plant biology has opened up potential avenues for engineering crops with enhanced productivity by engineering photoreceptor activity and/or action. The ability to manipulate plant genomes through genetic engineering and synthetic biology approaches offers the potential to unlock new agricultural innovations by fine-tuning photoreceptors or photoreceptor pathways that control plant traits of agronomic significance. Additionally, optogenetic tools which allow for precise, light-triggered control of plant responses are emerging as powerful technologies for real-time manipulation of plant cellular responses. As these technologies continue to develop, the integration of photoreceptor engineering and optogenetics into crop breeding programs could potentially revolutionise how plant researchers tackle challenges of plant productivity. Here we provide an overview on the roles of key photoreceptors in regulating agronomically important traits, the current state of plant photoreceptor engineering, the emerging use of optogenetics and synthetic biology, and the practical considerations of applying these approaches to crop improvement. This review seeks to highlight both opportunities and challenges in harnessing photoreceptor engineering approaches for enhancing plant productivity. In this review, we provide an overview on the roles of key photoreceptors in regulating agronomically important traits, the current state of plant photoreceptor engineering, the emerging use of optogenetics and synthetic biology, and the practical considerations of applying these approaches to crop improvement.","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"115 3","pages":"64"},"PeriodicalIF":3.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144000047","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

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