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Nanofertilizers: smart solutions for sustainable agriculture and the global water crisis. 纳米肥料:可持续农业和全球水危机的智能解决方案。
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-13 DOI: 10.1007/s00425-025-04737-7
Abdelrahman R Ahmed, Heba I Mohamed
{"title":"Nanofertilizers: smart solutions for sustainable agriculture and the global water crisis.","authors":"Abdelrahman R Ahmed, Heba I Mohamed","doi":"10.1007/s00425-025-04737-7","DOIUrl":"https://doi.org/10.1007/s00425-025-04737-7","url":null,"abstract":"<p><strong>Main conclusion: </strong>Nanofertilizers can enhance the efficiency of water and nutrient use. This study will explore the potential benefits of nanofertilizers in the context of the global water crisis. Water is essential for all living things to support biodiversity, food security, human life, and societal progress. The world is experiencing a water crisis due to the increasing scarcity of freshwater supplies caused by climate change. Reports indicate that both conventional and unconventional methods are being employed to address the global water crisis. The use of natural resources is under stress because of the massive growth in the human population over the past few decades. To meet this need, chemical fertilizers are being used to enhance crop yields, but this has negative ecological consequences. Thus, the time has come to replace conventional farming methods with sensible ones that will boost food production and nutritional content without threatening our ecosystem. In this regard, achieving sustainability can be accomplished by applying innovative, cutting-edge technologies such as nanotechnology. Nanofertilizers (NFs) are among the most promising synthetic materials for sustaining agricultural yields through intelligent agrochemical release. Unlike the global water crisis, nanofertilizers possess unique properties that can enhance the efficiency of water use in cultivated crops, particularly under stressful conditions. This study offers a wealth of information about the direct and indirect characteristics of nanofertilizers and their potential impacts on the water crisis. In conclusion, there is a pressing need for more research on this significant global issue, especially considering the serious concerns surrounding climate change.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 2","pages":"26"},"PeriodicalIF":3.6,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144286131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Deciphering melatonin biosynthesis pathway in Chenopodium quinoa: genome-wide analysis and expression levels of the genes under salt and drought. 藜麦褪黑素生物合成途径的解读:盐和干旱条件下基因的全基因组分析和表达水平。
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-12 DOI: 10.1007/s00425-025-04741-x
Seher Yolcu, Ece Fidan, Muhammed Fatih Kaya, Emre Aksoy, Ismail Turkan
{"title":"Deciphering melatonin biosynthesis pathway in Chenopodium quinoa: genome-wide analysis and expression levels of the genes under salt and drought.","authors":"Seher Yolcu, Ece Fidan, Muhammed Fatih Kaya, Emre Aksoy, Ismail Turkan","doi":"10.1007/s00425-025-04741-x","DOIUrl":"10.1007/s00425-025-04741-x","url":null,"abstract":"<p><strong>Main conclusion: </strong>In this study, we identified a total of ten melatonin biosynthesis genes (3 TDCs, 2 TSHs, 3 SNATs, and 2 ASMTs) in Chenopodium quinoa through bioinformatics methods, and analyzed physiological traits and gene expression levels in drought- and salt-treated plants with or without melatonin. Gene expression levels showed variations depending on tissues, genotypes, and abiotic stress. Melatonin is involved in distinct biological processes, such as growth, development, and stress response in plants. The tryptophan decarboxylase (TDC), tryptamine 5-hydroxylase (T5H), serotonin N-acetyltransferase (SNAT), and N-acetylserotonin O-methyltransferase (ASMT) enzymes are involved in melatonin biosynthesis. Exogenous melatonin reduces the adverse effects of salt stress in different plants, but the roles of melatonin biosynthesis pathway in quinoa (Chenopodium quinoa) remain elusive. This study aims to identify and characterize the melatonin biosynthetic genes encoding TDCs, T5Hs, SNATs, and ASMTs in C. quinoa genome through bioinformatics methods and determine their transcript abundances under salt and drought stress. In total, ten genes were identified in C. quinoa genome, including 3 TDCs, 2 TSHs, 3 SNATs, and 2 ASMTs. TDCs have a pyridoxal-dependent decarboxylase domain, T5Hs possess a cytochrome P450, SNAT proteins contain the Acetyltransf_1 domain, and ASMTs include the O-methyltransferase domain. We also examined some physiological characteristics such as growth and water relations along with electrolyte leakage. For that purpose, two quinoa genotypes (Salcedo and Ames 1377) were subjected to salt and drought stress, with or without melatonin. Exogenous melatonin remarkably reduced the negative effects of salt and drought on shoot length, RWC, and electrolyte leakage in the sensitive Salcedo genotype. However, it showed limited impact on the stress-tolerant Ames 1377 genotype. Expression patterns showed variations depending on tissues, genotypes, and the type of abiotic stress. Promoter analysis indicated that the cis-elements in TDC, T5H, and SNAT promoters were mostly associated with stress-response, while those in ASMT promoters were related to light response.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"23"},"PeriodicalIF":3.6,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162789/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The ankyrin repeat-containing protein OsANK3 affects grain size and quality in rice. 含有锚蛋白重复序列的蛋白OsANK3影响水稻籽粒大小和品质。
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-10 DOI: 10.1007/s00425-025-04734-w
Jinhui Zhao, Yi Xin, Weiwei Cui, Pengxi Li, Jia Su, Lina Zhao, Quanxiu Wang
{"title":"The ankyrin repeat-containing protein OsANK3 affects grain size and quality in rice.","authors":"Jinhui Zhao, Yi Xin, Weiwei Cui, Pengxi Li, Jia Su, Lina Zhao, Quanxiu Wang","doi":"10.1007/s00425-025-04734-w","DOIUrl":"10.1007/s00425-025-04734-w","url":null,"abstract":"<p><strong>Main conclusion: </strong>Mutation of OsANK3 increases grain length, grain weight, and chalkiness. OsANK3 influences grain size and quality by regulating genes involved in the cell cycle and starch metabolism. Grain size and endosperm starch content are key determinants of rice yield and quality. In this study, we investigated the function of OsANK3, a gene encoding ankyrin repeats, in regulating grain development traits. This gene was initially identified through mass spectrometry analysis as a potential upstream regulator of rice chalkiness in our previous screening. Using CRISPR/Cas9 technology, we generated OsANK3 knockout mutants (cr-osank3-2, cr-osank3-6, and cr-osank3-7) and found that OsANK3 is predominantly expressed in stems and leaves, with subcellular localization in the cytoplasm and plasma membrane. Disruption of OsANK3 increased plant height, grain length, grain weight, and chalkiness while reducing total starch content, amylose content (AC), and gel consistency (GC). Cytological analysis revealed that the elongated grains in cr-osank3 mutants resulted from enhanced cell proliferation and elongation in the outer lemma. qRT-PCR data demonstrated that OsANK3 regulates cell cycle-related genes, thereby influencing cell division and expansion. In addition, starch biosynthesis genes (OsGBSSI, OsAGPL1) were down-regulated in mutants, whereas starch hydrolase genes (OsAmy1 A, OsAmy3B) were up-regulated. Our findings demonstrate that OsANK3 knockout enhances grain size but compromises grain quality by altering cell dynamics and starch metabolism. This study elucidates the molecular role of OsANK3 in grain development and provides a valuable target for rice breeding programs.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"21"},"PeriodicalIF":3.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Identification and expression of the AREB/ABF/ABI5 subfamily genes in chickpea and lentil reveal major players involved in ABA-mediated defense response to drought stress. 鹰嘴豆和扁豆中AREB/ABF/ABI5亚家族基因的鉴定和表达揭示了aba介导的干旱防御反应的主要参与者。
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-10 DOI: 10.1007/s00425-025-04740-y
Marcos Fernando Basso, Paolo Iovieno, Maurizio Capuana, Felice Contaldi, Francesca Ieri, Felicia Menicucci, Fabrizio Lo Celso, Giampaolo Barone, Federico Martinelli
{"title":"Identification and expression of the AREB/ABF/ABI5 subfamily genes in chickpea and lentil reveal major players involved in ABA-mediated defense response to drought stress.","authors":"Marcos Fernando Basso, Paolo Iovieno, Maurizio Capuana, Felice Contaldi, Francesca Ieri, Felicia Menicucci, Fabrizio Lo Celso, Giampaolo Barone, Federico Martinelli","doi":"10.1007/s00425-025-04740-y","DOIUrl":"10.1007/s00425-025-04740-y","url":null,"abstract":"<p><strong>Main conclusion: </strong>This study identified and evaluated the expression of the AREB/ABF/ABI5 subfamily genes in chickpea and lentil, and revealed the major players involved in defense response to PEG-induced drought stress. Abscisic acid (ABA)-responsive element-binding protein/ABRE-binding factor/ABA-INSENSITIVE 5 (AREB/ABF/ABI5) subfamily proteins are major players in the ABA-mediated signaling pathway triggered by multiple stresses. AREB/ABF/ABI5 subfamily proteins belong to the basic-leucine zipper transcription factors that regulate the expression of several downstream defense genes to abiotic and biotic stresses. This protein set is highly targeted when trying to understand plant defense against abiotic stress or to improve plant tolerance to drought, cold, and salinity stresses. However, there is still very little information available about the genes of the AREB/ABF/ABI5 subfamily in chickpea and lentil. Herein, 8 chickpea and 9 lentil genes of the AREB/ABF/ABI5 subfamily were identified based on sequence analysis, and their expression levels were tested in a polyethylene glycol-induced drought experiment (20% PEG in Hoagland solution) using real-time RT-PCR and metadata analysis. Sequence analysis showed that members of this subfamily are highly conserved among themselves and with their orthologous genes in other closely related plant species. Overall, sequence data suggested that these genes may possess close or overlapping biological roles in regulating the transcription of abiotic stress-related defense genes. The meta-analysis from RNA-Seq datasets of unstressed plants showed that some members of this gene subfamily have a tissue-specific expression in both chickpea and lentil. Drought-contrasting chickpea and lentil cultivars showed that most AREB/ABF/ABI5 genes are modulated by PEG-induced drought. Furthermore, AREB/ABF/ABI5 genes had also a tendency for higher expression as cultivar tolerance increases. Therefore, this study identified the AREB/ABF/ABI5 subfamily genes in chickpea and lentil, and provides a comprehensive characterization of these members to support further focused research.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"22"},"PeriodicalIF":3.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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: Simultaneous quantification of cell wall elasticity and turgor pressure in live plant cells by elastic shell theory analysis and AFM. 校正:用弹性壳理论分析和原子力显微镜同时定量测定活植物细胞的细胞壁弹性和胀压。
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-09 DOI: 10.1007/s00425-025-04738-6
Yuki Yamasaki, Kazunori Okano, Tetsuro Mimura, Satoru Tsugawa, Yoichiroh Hosokawa
{"title":"Correction: Simultaneous quantification of cell wall elasticity and turgor pressure in live plant cells by elastic shell theory analysis and AFM.","authors":"Yuki Yamasaki, Kazunori Okano, Tetsuro Mimura, Satoru Tsugawa, Yoichiroh Hosokawa","doi":"10.1007/s00425-025-04738-6","DOIUrl":"10.1007/s00425-025-04738-6","url":null,"abstract":"","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"19"},"PeriodicalIF":3.6,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12149014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Regulation of HvASN1 expression by bZIP transcription factors during barley embryo development and germination. bZIP转录因子对大麦胚发育和萌发过程中HvASN1表达的调控
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-09 DOI: 10.1007/s00425-025-04730-0
Estefanía Contreras, Rosario Alonso, Elena Pastor-Mora, Mar G Ceballos, Jesús Vicente-Carbajosa, Raquel Iglesias-Fernández
{"title":"Regulation of HvASN1 expression by bZIP transcription factors during barley embryo development and germination.","authors":"Estefanía Contreras, Rosario Alonso, Elena Pastor-Mora, Mar G Ceballos, Jesús Vicente-Carbajosa, Raquel Iglesias-Fernández","doi":"10.1007/s00425-025-04730-0","DOIUrl":"10.1007/s00425-025-04730-0","url":null,"abstract":"<p><strong>Main conclusion: </strong>Our findings provide new insights into the molecular mechanisms that regulate N metabolism in barley and potentially other cereal crops, offering valuable perspectives for enhancing N use efficiency in agricultural practices. Efficient nitrogen (N) utilization is essential for plant growth, especially during seed development and germination. In barley (Hordeum vulgare), the asparagine synthetase gene HvASN1 is essential for nitrogen transport and storage, synthesizing asparagine, a key molecule in N recycling. The phylogenetic analysis indicates that HvASN1 clusters with Arabidopsis AtASN1 and shares high similarity with HvASN2, suggesting a conserved role in N metabolism. A detailed characterization of a ~ 500 bp HvASN1 promoter region revealed a conserved GCN-like cis-element. Transient expression assays in Nicotiana benthamiana demonstrated that the wild-type promoter significantly increases luciferase activity under dark conditions, whereas mutation of the GCN-like element reduces this activity, highlighting its role in light-responsive gene regulation. Further investigation identified the bZIP transcription factor HvbZIP53 as an activator of the HvASN1 promoter through binding to the GCN-like element. This activation is finely tuned by sucrose via a conserved upstream open reading frame (uORF) in HvbZIP53's 5' UTR, which mediates sucrose-induced repression of translation. Additionally, yeast two-hybrid assays and transient expression studies in Arabidopsis provided evidence that HvbZIP53 physically interacts with HvBLZ1, a C group bZIP factor, resulting in a synergistic enhancement of HvASN1 expression. The spatial and temporal expression analyses further revealed that HvASN1, HvbZIP53, and HvBLZ1 are co-expressed in key seed tissues during development and germination. These findings indicate a complex regulatory network integrating environmental and metabolic signals to modulate N metabolism in barley, with implications for improving N use efficiency in cereal crops.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"20"},"PeriodicalIF":3.6,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12148973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
OsHsp20-25, a small heat shock protein, from long-lived mRNA regulates seed size and germination rate in rice. OsHsp20-25是一种来自长寿命mRNA的小热休克蛋白,调控水稻种子大小和发芽率。
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-08 DOI: 10.1007/s00425-025-04733-x
Xiaobo Zhu, Zhang Dong, Yihan Liu, Qingshan Mou, Jin Hu, Jiaxin Liu, Min Chen, Yajing Guan
{"title":"OsHsp20-25, a small heat shock protein, from long-lived mRNA regulates seed size and germination rate in rice.","authors":"Xiaobo Zhu, Zhang Dong, Yihan Liu, Qingshan Mou, Jin Hu, Jiaxin Liu, Min Chen, Yajing Guan","doi":"10.1007/s00425-025-04733-x","DOIUrl":"10.1007/s00425-025-04733-x","url":null,"abstract":"<p><strong>Main conclusion: </strong>The small heat shock protein OsHsp20-25, from long-lived mRNA, negatively regulates seed germination but positively regulates seed length. The mRNAs stored for a longer period in mature and dry seeds are called long-lived mRNA, which encodes diverse protein families and plays important roles in seed vigor. However, the specific contributions of individual mRNA populations to germination regulation remain poorly defined. In this study, we analyzed four small heat shock proteins, OsHsp20-17, OsHsp20-18, OsHsp20-20, and OsHsp20-25, from RNA sequencing data of rice seed. They were specifically expressed in the late stage of seed development and early stage of seed germination. Intriguingly, their transcripts retained detectable expression levels in one-year-old stored seeds. Four transgenic lines of OsHsp20s were generated, and only the OsHsp20-25 overexpression lines exhibited lower germination rates compared to the wild-type, accompanied by upregulated expression of OsABI5 and OsMFT2, and enhanced ABA sensitivity. Furthermore, OsHsp20-25-CRISPR mutants produced seeds of shorter length, but the overexpression line showed longer seeds. Biochemical and molecular evidence demonstrates that OsHsp20-25 interacted with OsHsp20-18, which also interacted with an F-box domain protein OsFBL45 in vivo and in vitro. Overall, OsHsp20, as a long-lived mRNA, plays important roles in seed development and seed germination.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"18"},"PeriodicalIF":3.6,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 analyses of the complete chloroplast genomes of four Caragana species, a specific genus distributed in arid and semi-arid area. 分布于干旱和半干旱区的锦鸡儿属四种叶绿体全基因组的比较分析。
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-05 DOI: 10.1007/s00425-025-04729-7
Wenyan Chen, Xue Zhang, Qin Li, Liqiong Jiang, Miaomiao Jiang, Xiaohong Bai, Lei Wang
{"title":"Comparative analyses of the complete chloroplast genomes of four Caragana species, a specific genus distributed in arid and semi-arid area.","authors":"Wenyan Chen, Xue Zhang, Qin Li, Liqiong Jiang, Miaomiao Jiang, Xiaohong Bai, Lei Wang","doi":"10.1007/s00425-025-04729-7","DOIUrl":"10.1007/s00425-025-04729-7","url":null,"abstract":"<p><p>Caragana species, perennial deciduous shrubs of Leguminosae, are significant to illustrate the synchronous evolution of floristics, vegetation, and climate change in arid Central Asia, cold arid alpine Qinghai-Tibetan plateau (QTP), and mesophytic East Asia. The objective of this study was to assemble and annotate the complete cp genome of four Caragana species, including C. opulens, C. roborovskyi, C. stenophylla, C. tibetica, and to compare their various characteristics with previously published data of Caragana species. High-quality DNA was paired-end sequenced utilizing the Illumina NovaSeq platform, followed by de novo assembly with the NOVOPlasty. The four cp genomes of Caragana lacked the IR region and ranged in length from 129,303 to 132,895 bp. The cp genome encoded 112-113 genes, consisting of 77 protein coding genes, 31-32 tRNA genes and four rRNA genes. Similar to other IRLC species, the genes rpl22 and rps16, as well as the intron of rpl2 and rps12 were found to be absent. A total of 77-94 simple sequence repeats (SSRs) were identified with the proportion of SSRs ≥ 10 bp ranging from 55.32 to 66.23%. Comparative analyses indicated that five genes (clpP, matK, rbcL, rpoC and ycf1) underwent positive selection during evolution, and 13 hypervariable regions were recommended as potential molecular markers for distinguishing Caragana species. Phylogenetic analyses showed that the Caragana species were classified into two distinct clades and exhibited a close relationship with Hedysareae. These findings will greatly facilitate the further exploration of the phylogenetic development and adaptive evolution of Caragana species and also IRLC at the genomic scale.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"16"},"PeriodicalIF":3.6,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 review on modeling approaches for the transcriptional regulatory network intricacies of circadian clock genes in plants. 植物生物钟基因转录调控网络复杂性建模方法综述。
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-05 DOI: 10.1007/s00425-025-04735-9
Alokita Roy, Dev Mani Pandey, Anjana Dwivedi
{"title":"A review on modeling approaches for the transcriptional regulatory network intricacies of circadian clock genes in plants.","authors":"Alokita Roy, Dev Mani Pandey, Anjana Dwivedi","doi":"10.1007/s00425-025-04735-9","DOIUrl":"10.1007/s00425-025-04735-9","url":null,"abstract":"<p><strong>Main conclusion: </strong>This review highlights the diverse modeling approaches essential for understanding the dynamics of plant circadian clock genes, which are key to optimizing plant growth, development, and resilience to environmental stress. The circadian clock in plants is a complex system governed by intricate transcriptional regulatory networks that orchestrate gene expression in response to environmental cues. These networks are crucial for understanding plant adaptation to daily changes and optimizing growth. This review provides a comprehensive account of various modeling approaches used to study plants' transcriptional regulatory network of circadian clock genes. Here, we review different computational methodologies like ordinary differential equation-based approaches, stochastic models, and spatial techniques that can be evaluated on their ability to capture the dynamics, variability, and interactions inherent to the circadian clock system. Moreover, the circadian clock's responsiveness to environmental cues, such as light, temperature, and other stressors plays a pivotal role in ensuring plant development. The modeling approaches must consider environmental factors influencing the transcriptional regulatory networks, which potentially alter the clock's phase, amplitude, and photoperiod. These adaptations are critical for plant survival, as they align physiological processes with specific hours of the day, enhancing resource use efficiency, and stress resilience. We highlight the respective strengths and limitations of different models emphasizing the importance of an integrative approach that combines multiple techniques which capture the essence of interactions of circadian clock components and their implications for plant growth, development and survival.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"17"},"PeriodicalIF":3.6,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
CRISPR/Cas9: efficient and emerging scope for Brassica crop improvement. CRISPR/Cas9:油菜作物改良的高效和新兴领域
IF 3.6 3区 生物学
Planta Pub Date : 2025-06-04 DOI: 10.1007/s00425-025-04727-9
Shiv Shankar Sharma, Ashwani Pandey, Anamika Kashyap, Lakshay Goyal, Pooja Garg, Ranjeet Kushwaha, Jyoti Sharma, Shikha Tripathi, Sujata Kumari, George Thomas, Malkhey Verma, Navin C Gupta, Ashish Kumar Gupta, Ramcharan Bhattacharya, Sandhya Sharma, Mahesh Rao
{"title":"CRISPR/Cas9: efficient and emerging scope for Brassica crop improvement.","authors":"Shiv Shankar Sharma, Ashwani Pandey, Anamika Kashyap, Lakshay Goyal, Pooja Garg, Ranjeet Kushwaha, Jyoti Sharma, Shikha Tripathi, Sujata Kumari, George Thomas, Malkhey Verma, Navin C Gupta, Ashish Kumar Gupta, Ramcharan Bhattacharya, Sandhya Sharma, Mahesh Rao","doi":"10.1007/s00425-025-04727-9","DOIUrl":"10.1007/s00425-025-04727-9","url":null,"abstract":"<p><strong>Main conclusion: </strong>CRISPR/Cas9 revolutionizes Brassica crop improvement by enhancing yield, quality, and stress resistance, providing a precise and versatile tool for genetic and agronomic advancements. The rapidly advancing CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9) technologies are being employed in both diploid and polyploid species of Brassica for gene functions and precise genetic improvements. CRISPR/Cas technology has sparked significant attention among the scientific community due to its affordability, precision, and effectiveness compared to other genome editing techniques. The recent discoveries highlight the diverse applications of the CRISPR/Cas9 genome editing tool in enhancing agriculturally important traits in Brassica species. This technology has been utilized to improve yield, quality, and resistance to both biotic and abiotic stresses globally. Here, we present an overview that encourages researchers to explore and improve the functionality and genetic progress of Brassica U-triangle species utilizing genome editing technologies. In addition, ethical considerations and concerns associated with CRISPR technologies are addressed, providing valuable insight into how CRISPR/Cas9 tools and have revolutionized crop improvement with special emphasis on Brassica for various agronomically and nutritionally important traits.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"262 1","pages":"14"},"PeriodicalIF":3.6,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
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