Plant Molecular Biology最新文献

{"title":"Frontiers in plant RNA research in ICAR2023: from lab to innovative agriculture","authors":"Ming-Jung Liu, Jhen-Cheng Fang, Ya Ma, Geeng Loo Chong, Chun-Kai Huang, Ami Takeuchi, Natsu Takayanagi, Misato Ohtani","doi":"10.1007/s11103-024-01436-x","DOIUrl":"https://doi.org/10.1007/s11103-024-01436-x","url":null,"abstract":"<p>The recent growth in global warming, soil contamination, and climate instability have widely disturbed ecosystems, and will have a significant negative impact on the growth of plants that produce grains, fruits and woody biomass. To conquer this difficult situation, we need to understand the molecular bias of plant environmental responses and promote development of new technologies for sustainable maintenance of crop production. Accumulated molecular biological data have highlighted the importance of RNA-based mechanisms for plant stress responses. Here, we report the most advanced plant RNA research presented in the 33rd International Conference on Arabidopsis Research (ICAR2023), held as a hybrid event on June 5–9, 2023 in Chiba, Japan, and focused on “Arabidopsis for Sustainable Development Goals”. Six workshops/concurrent sessions in ICAR2023 targeted plant RNA biology, and many RNA-related topics could be found in other sessions. In this meeting report, we focus on the workshops/concurrent sessions targeting RNA biology, to share what is happening now at the forefront of plant RNA research.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140612576","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}

{"title":"Oschib1 gene encoding a GH18 chitinase confers resistance against sheath blight disease of rice caused by Rhizoctonia solani AG1-IA","authors":"Naresh Babu Prathi, Chagamreddy Venkata Durga Rani, Vellaisamy Prakasam, Yeshala Chandra Mohan, Gandikota Mahendranath, G. K. Sri Vidya, C. N. Neeraja, Raman Meenakshi Sundaram, Satendra K. Mangrauthia","doi":"10.1007/s11103-024-01442-z","DOIUrl":"https://doi.org/10.1007/s11103-024-01442-z","url":null,"abstract":"<p>Sheath blight disease of rice caused by <i>Rhizoctonia solani</i> AG1-IA, is a major fungal disease responsible for huge loss to grain yield and quality. The major limitation of achieving persistent and reliable resistance against <i>R. solani</i> is the governance of disease resistance trait by many genes. Therefore, functional characterization of new genes involved in sheath blight resistance is necessary to understand the mechanism of resistance as well as evolving effective strategies to manage the disease through host-plant resistance. In this study, we performed RNA sequencing of six diverse rice genotypes (TN1, BPT5204, Vandana, N22, Tetep, and Pankaj) from sheath and leaf tissue of control and fungal infected samples. The approach for identification of candidate resistant genes led to identification of 352 differentially expressed genes commonly present in all the six genotypes. 23 genes were analyzed for RT-qPCR expression which helped identification of <i>Oschib1</i> showing differences in expression level in a time-course manner between susceptible and resistant genotypes. The <i>Oschib1</i> encoding classIII chitinase was cloned from resistant variety Tetep and over-expressed in susceptible variety Taipei 309. The over-expression lines showed resistance against <i>R. solani</i>, as analyzed by detached leaf and whole plant assays. Interestingly, the resistance response was correlated with the level of transgene expression suggesting that the enzyme functions in a dose dependent manner. We report here the classIIIb chitinase from chromosome10 of rice showing anti-<i>R. solani</i> activity to combat the dreaded sheath blight disease.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140602470","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}

{"title":"Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae","authors":"Li-Qiong Chen, Xin Li, Xin Yao, De-Zhu Li, Craig Barrett, Claude W. dePamphilis, Wen-Bin Yu","doi":"10.1007/s11103-024-01440-1","DOIUrl":"https://doi.org/10.1007/s11103-024-01440-1","url":null,"abstract":"<p>Parasitic lifestyle can often relax the constraint on the plastome, leading to gene pseudogenization and loss, and resulting in diverse genomic structures and rampant genome degradation. Although several plastomes of parasitic <i>Cuscuta</i> have been reported, the evolution of parasitism in the family Convolvulaceae which is linked to structural variations and reduction of plastome has not been well investigated. In this study, we assembled and collected 40 plastid genomes belonging to 23 species representing four subgenera of <i>Cuscuta</i> and ten species of autotrophic Convolvulaceae. Our findings revealed nine types of structural variations and six types of inverted repeat (IR) boundary variations in the plastome of Convolvulaceae spp. These structural variations were associated with the shift of parasitic lifestyle, and IR boundary shift, as well as the abundance of long repeats. Overall, the degradation of <i>Cuscuta</i> plastome proceeded gradually, with one clade exhibiting an accelerated degradation rate. We observed five stages of gene loss in <i>Cuscuta</i>, including NAD(P)H complex → PEP complex → Photosynthesis-related → Ribosomal protein subunits → ATP synthase complex. Based on our results, we speculated that the shift of parasitic lifestyle in early divergent time promoted relaxed selection on plastomes, leading to the accumulation of microvariations, which ultimately resulted in the plastome reduction. This study provides new evidence towards a better understanding of plastomic evolution, variation, and reduction in the genus <i>Cuscuta</i>.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140587345","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}

{"title":"Bacteria from the skin of amphibians promote growth of Arabidopsis thaliana and Solanum lycopersicum by modifying hormone-related transcriptome response","authors":"Yordan J. Romero-Contreras, Francisco González-Serrano, Elena Bello-López, Damien Formey, Wendy Aragón, Miguel Ángel Cevallos, Eria A. Rebollar, Mario Serrano","doi":"10.1007/s11103-024-01444-x","DOIUrl":"https://doi.org/10.1007/s11103-024-01444-x","url":null,"abstract":"<p>Plants and microorganisms establish beneficial associations that can improve their development and growth. Recently, it has been demonstrated that bacteria isolated from the skin of amphibians can contribute to plant growth and defense. However, the molecular mechanisms involved in the beneficial effect for the host are still unclear. In this work, we explored whether bacteria isolated from three tropical frogs species can contribute to plant growth. After a wide screening, we identified three bacterial strains with high biostimulant potential, capable of modifying the root structure of <i>Arabidopsis thaliana</i> plants. In addition, applying individual bacterial cultures to <i>Solanum lycopersicum</i> plants induced an increase in their growth. To understand the effect that these microorganisms have over the host plant, we analysed the transcriptomic profile of <i>A. thaliana</i> during the interaction with the C32I bacterium, demonstrating that the presence of the bacteria elicits a transcriptional response associated to plant hormone biosynthesis. Our results show that amphibian skin bacteria can function as biostimulants to improve agricultural crops growth and development by modifying the plant transcriptomic responses.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140587149","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}

{"title":"Reactive oxygen species (ROS) modulate nitrogen signaling using temporal transcriptome analysis in foxtail millet","authors":"Hui-Xin Meng, Yu-Ze Wang, Xin-Li Yao, Xin-Ran Xie, Shuqi Dong, Xiangyang Yuan, Xiaorui Li, Lulu Gao, Guanghui Yang, Xiaoqian Chu, Jia-Gang Wang","doi":"10.1007/s11103-024-01435-y","DOIUrl":"https://doi.org/10.1007/s11103-024-01435-y","url":null,"abstract":"<p>Reactive oxygen species (ROS) is a chemically reactive chemical substance containing oxygen and a natural by-product of normal oxygen metabolism. Excessive ROS affect the growth process of crops, which will lead to the decrease of yield. Nitrogen, as a critical nutrient element in plants and plays a vital role in plant growth and crop production. Nitrate is the primary nitrogen source available to plants in agricultural soil and various natural environments. However, the molecular mechanism of ROS-nitrate crosstalk is still unclear. In this study, we used the foxtail millet (<i><u>Setaria italica L.</u></i>) as the material to figure it out. Here, we show that excessive NaCl inhibits nitrate-promoted plant growth and nitrogen use efficiency (NUE). NaCl induces ROS accumulation in roots, and ROS inhibits nitrate-induced gene expression in a short time. Surprisingly, low concentration ROS slight promotes and high concentration of ROS inhibits foxtail millet growth under long-term H₂O₂ treatment. These results may open a new perspective for further exploration of ROS-nitrate signaling pathway in plants.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140587135","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}

{"title":"Insights into the cell-wall dynamics in grapevine berries during ripening and in response to biotic and abiotic stresses","authors":"Giulia Malacarne, Jorge Lagreze, Barbara Rojas San Martin, Mickael Malnoy, Marco Moretto, Claudio Moser, Lorenza Dalla Costa","doi":"10.1007/s11103-024-01437-w","DOIUrl":"https://doi.org/10.1007/s11103-024-01437-w","url":null,"abstract":"<p>The cell wall (CW) is the dynamic structure of a plant cell, acting as a barrier against biotic and abiotic stresses. In grape berries, the modifications of pulp and skin CW during softening ensure flexibility during cell expansion and determine the final berry texture. In addition, the CW of grape berry skin is of fundamental importance for winemaking, controlling secondary metabolite extractability. Grapevine varieties with contrasting CW characteristics generally respond differently to biotic and abiotic stresses. In the context of climate change, it is important to investigate the CW dynamics occurring upon different stresses, to define new adaptation strategies. This review summarizes the molecular mechanisms underlying CW modifications during grapevine berry fruit ripening, plant-pathogen interaction, or in response to environmental stresses, also considering the most recently published transcriptomic data. Furthermore, perspectives of new biotechnological approaches aiming at modifying the CW properties based on other crops’ examples are also presented.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140587136","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}

{"title":"A long non-coding RNA functions as a competitive endogenous RNA to modulate TaNAC018 by acting as a decoy for tae-miR6206","authors":"Wei-Bo Xu, Qian-Huan Guo, Peng Liu, Shuang Dai, Chang-Ai Wu, Guo-Dong Yang, Jin-Guang Huang, Shi-Zhong Zhang, Jian-Min Song, Cheng-Chao Zheng, Kang Yan","doi":"10.1007/s11103-024-01448-7","DOIUrl":"https://doi.org/10.1007/s11103-024-01448-7","url":null,"abstract":"<p>Increasing evidence indicates a strong correlation between the deposition of cuticular waxes and drought tolerance. However, the precise regulatory mechanism remains elusive. Here, we conducted a comprehensive transcriptome analysis of two wheat (<i>Triticum aestivum</i>) near-isogenic lines, the glaucous line G-JM38 rich in cuticular waxes and the non-glaucous line NG-JM31. We identified 85,143 protein-coding mRNAs, 4,485 lncRNAs, and 1,130 miRNAs. Using the lncRNA–miRNA–mRNA network and endogenous target mimic (eTM) prediction, we discovered that <i>lncRNA35557</i> acted as an eTM for the miRNA tae-miR6206, effectively preventing tae-miR6206 from cleaving the NAC transcription factor gene <i>TaNAC018</i>. This lncRNA–miRNA interaction led to higher transcript abundance for <i>TaNAC018</i> and enhanced drought-stress tolerance. Additionally, treatment with mannitol and abscisic acid (ABA) each influenced the levels of tae-miR6206, lncRNA35557, and <i>TaNAC018</i> transcript. The ectopic expression of <i>TaNAC018</i> in Arabidopsis also improved tolerance toward mannitol and ABA treatment, whereas knocking down <i>TaNAC018</i> transcript levels via virus-induced gene silencing in wheat rendered seedlings more sensitive to mannitol stress. Our results indicate that lncRNA35557 functions as a competing endogenous RNA to modulate <i>TaNAC018</i> expression by acting as a decoy target for tae-miR6206 in glaucous wheat, suggesting that non-coding RNA has important roles in the regulatory mechanisms responsible for wheat stress tolerance.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140587137","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}

{"title":"Utilizing plasma-generated N2O5 gas from atmospheric air as a novel gaseous nitrogen source for plants","authors":"Taro Yamanashi, Shouki Takeshi, Shota Sasaki, Keisuke Takashima, Toshiro Kaneko, Yasuhiro Ishimaru, Nobuyuki Uozumi","doi":"10.1007/s11103-024-01438-9","DOIUrl":"https://doi.org/10.1007/s11103-024-01438-9","url":null,"abstract":"<p>Fixing atmospheric nitrogen for use as fertilizer is a crucial process in promoting plant growth and enhancing crop yields in agricultural production. Currently, the chemical production of nitrogen fertilizer from atmospheric N₂ relies on the energy-intensive Haber–Bosch process. Therefore, developing a low-cost and easily applicable method for fixing nitrogen from the air would provide a beneficial alternative. In this study, we tested the utilization of dinitrogen pentoxide (N₂O₅) gas, generated from oxygen and nitrogen present in ambient air with the help of a portable plasma device, as a nitrogen source for the model plant <i>Arabidopsis thaliana</i>. Nitrogen-deficient plants supplied with medium treated with N₂O₅, were able to overcome nitrogen deficiency, similar to those provided with medium containing a conventional nitrogen source. However, prolonged direct exposure of plants to N₂O₅ gas adversely affected their growth. Short-time exposure of plants to N₂O₅ gas mitigated its toxicity and was able to support growth. Moreover, when the exposure of N₂O₅ and the contact with plants were physically separated, plants cultured under nitrogen deficiency were able to grow. This study shows that N₂O₅ gas generated from atmospheric nitrogen can be used as an effective nutrient for plants, indicating its potential to serve as an alternative nitrogen fertilization method for promoting plant growth.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140602876","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}

{"title":"Genome-wide identification and in-silico expression analysis of CCO gene family in sunflower (Helianthus annnus) against abiotic stress","authors":"Adnan Sami, Muhammad Zeeshan Haider, Muhammad Shafiq, Saleh Sadiq, Farooq Ahmad","doi":"10.1007/s11103-024-01433-0","DOIUrl":"https://doi.org/10.1007/s11103-024-01433-0","url":null,"abstract":"<p>Carotenoid cleavage oxygenases (CCOs) enzymes play an important role in plant growth and development by producing a wide array of apocarotenoids and their derivatives. These compounds are vital for colouring flowers and fruits and synthesizing plant hormones such as abscisic acid and strigolactones. Despite their importance, the gene family responsible for CCO enzymes in sunflowers has not been identified. In this study, we identify the <i>CCO</i> genes of the sunflower plant to fill this knowledge gap. Phylogenetic and synteny analysis indicated that the <i>Helianthus annnus CCO (HaCCO)</i> genes were conserved in different plant species and they could be divided into three subgroups based on their conserved domains. Analysis using MEME tool and multiple sequence alignment identified conserved motifs in the <i>HaCCO</i> gene sequence. <i>Cis</i>-regulatory elements (CREs) analysis of the <i>HaCCO</i> genes indicated the presence of various responsive elements related to plant hormones, development, and responses to both biotic and abiotic stresses. This implies that these genes may respond to plant hormones, developmental cues, and drought stress, offering potential applications in the development of more resistant crops. Genes belonging to the 9-cis-epoxy carotenoid dioxygenases (NCED) subgroups predominantly exhibited chloroplast localization, whereas the genes found in other groups are primarily localized in the cytoplasm. These 21 identified <i>HaCCOs</i> were regulated by 60 miRNAs, indicating the crucial role of microRNAs in gene regulation in sunflowers. Gene expression analysis under drought stress revealed significant up-regulation of <i>HaNCED16</i> and <i>HaNCED19</i>, genes that are pivotal in ABA hormone biosynthesis. During organ-specific gene expression analysis, <i>HaCCD12</i> and <i>HaCCD20</i> genes exhibit higher activity in leaves, indicating a potential role in leaf pigmentation. This study provides a foundation for future research on the regulation and functions of the <i>CCO</i> gene family in sunflower and beyond. There is potential for developing molecular markers that could be employed in breeding programs to create new sunflower lines resistant to biotic and abiotic stresses.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140587139","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}

{"title":"Artificial intelligence models for validating and predicting the impact of chemical priming of hydrogen peroxide (H₂O₂) and light emitting diodes on in vitro grown industrial hemp (Cannabis sativa L.).","authors":"Muhammad Aasim, Buşra Yıldırım, Ahmet Say, Seyid Amjad Ali, Selim Aytaç, Muhammad Azhar Nadeem","doi":"10.1007/s11103-024-01427-y","DOIUrl":"10.1007/s11103-024-01427-y","url":null,"abstract":"<p><p>Industrial hemp (Cannabis sativa L.) is a highly recalcitrant plant under in vitro conditions that can be overcome by employing external stimuli. Hemp seeds were primed with 2.0-3.0% hydrogen peroxide (H₂O₂) followed by culture under different Light Emitting Diodes (LEDs) sources. Priming seeds with 2.0% yielded relatively high germination rate, growth, and other biochemical and enzymatic activities. The LED lights exerted a variable impact on Cannabis germination and enzymatic activities. Similarly, variable responses were observed for H₂O₂ × Blue-LEDs combination. The results were also analyzed by multiple regression analysis, followed by an investigation of the impact of both factors by Pareto chart and normal plots. The results were optimized by contour and surface plots for all parameters. Response surface optimizer optimized 2.0% H₂O₂ × 918 LUX LEDs for maximum scores of all output parameters. The results were predicted by employing Multilayer Perceptron (MLP), Random Forest (RF), and eXtreme Gradient Boosting (XGBoost) algorithms. Moreover, the validity of these models was assessed by using six different performance metrics. MLP performed better than RF and XGBoost models, considering all six-performance metrics. Despite the differences in scores, the performance indicators for all examined models were quite close to each other. It can easily be concluded that all three models are capable of predicting and validating data for cannabis seeds primed with H₂O₂ and grown under different LED lights.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140288772","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}