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Editorial overview: Spatial and temporal regulation of molecular and cell biological process across biological scales.
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-12-18 DOI: 10.1016/j.pbi.2024.102675
Arun Sampathkumar, Masayoshi Nakamura
{"title":"Editorial overview: Spatial and temporal regulation of molecular and cell biological process across biological scales.","authors":"Arun Sampathkumar, Masayoshi Nakamura","doi":"10.1016/j.pbi.2024.102675","DOIUrl":"https://doi.org/10.1016/j.pbi.2024.102675","url":null,"abstract":"","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"83 ","pages":"102675"},"PeriodicalIF":8.3,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863534","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
Editorial overview: Physiology and metabolism 2024.
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-12-16 DOI: 10.1016/j.pbi.2024.102673
Vincent Courdavault, Anne Osbourn
{"title":"Editorial overview: Physiology and metabolism 2024.","authors":"Vincent Courdavault, Anne Osbourn","doi":"10.1016/j.pbi.2024.102673","DOIUrl":"https://doi.org/10.1016/j.pbi.2024.102673","url":null,"abstract":"","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"83 ","pages":"102673"},"PeriodicalIF":8.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846047","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
Evolving best practices for transcriptome-wide association studies accelerate discovery of gene-phenotype links.
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-12-02 DOI: 10.1016/j.pbi.2024.102670
J Vladimir Torres-Rodríguez, Delin Li, James C Schnable
{"title":"Evolving best practices for transcriptome-wide association studies accelerate discovery of gene-phenotype links.","authors":"J Vladimir Torres-Rodríguez, Delin Li, James C Schnable","doi":"10.1016/j.pbi.2024.102670","DOIUrl":"https://doi.org/10.1016/j.pbi.2024.102670","url":null,"abstract":"<p><p>Transcriptome-wide association studies (TWAS) complement genome-wide association studies (GWAS) by using gene expression data to link specific genes to phenotypes. This review examines 37 TWAS studies across eight plant species, evaluating the impact of methodological choices on outcomes using maize and soybean datasets. Large sample sizes and synchronized sample collection for gene expression measurement appear to significantly increase power for discovering gene-phenotype linkages, while matching tissue, stage, and environment may matter much less than previously believed, making it feasible to reuse large and well-collected expression datasets across multiple studies. The development of statistical approaches and computational tools specifically optimized for plant TWAS data will ultimately be needed, but further potential remains to adapt advances developed in GWAS to TWAS contexts.</p>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"83 ","pages":"102670"},"PeriodicalIF":8.3,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142767329","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
Corrigendum to “Epigenetics in plant organismic interactions” [Curr Opin Plant Biol 61 (2021) 102060] 植物有机体相互作用中的表观遗传学》[Curr Opin Plant Biol 61 (2021) 102060] 勘误。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-12-01 DOI: 10.1016/j.pbi.2024.102660
Daniela Ramos-Cruz , A. Niloya Troyee , Claude Becker
{"title":"Corrigendum to “Epigenetics in plant organismic interactions” [Curr Opin Plant Biol 61 (2021) 102060]","authors":"Daniela Ramos-Cruz ,&nbsp;A. Niloya Troyee ,&nbsp;Claude Becker","doi":"10.1016/j.pbi.2024.102660","DOIUrl":"10.1016/j.pbi.2024.102660","url":null,"abstract":"","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102660"},"PeriodicalIF":8.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616346","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
Current progress in deciphering the molecular mechanisms underlying plant salt tolerance 破译植物耐盐分子机制的最新进展
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-27 DOI: 10.1016/j.pbi.2024.102671
Yunfei Hu , Dan Wang , Xiaohua Zhang , Xiaodong Lv , Bo Li
{"title":"Current progress in deciphering the molecular mechanisms underlying plant salt tolerance","authors":"Yunfei Hu ,&nbsp;Dan Wang ,&nbsp;Xiaohua Zhang ,&nbsp;Xiaodong Lv ,&nbsp;Bo Li","doi":"10.1016/j.pbi.2024.102671","DOIUrl":"10.1016/j.pbi.2024.102671","url":null,"abstract":"<div><div>Enhancing crop salt tolerance through genetics and genomics is important for food security. It is environmentally friendly and cost-effective in maintaining crop production in farmlands affected by soil salinization and can also facilitate the utilization of marginal saline land. Despite the limited success achieved so far, it is becoming possible to bridge the gap between fundamental research and crop breeding owing to a deeper understanding of plant salt tolerance at both physiological and molecular levels. Therefore, we review the recent key progress in identifying the molecular mechanisms contributing to plant salt tolerance with a focus on balancing growth and salt resilience. With the accruing knowledge and the rapidly evolving tools (e.g. genome editing and artificial intelligence), it is reasonable to expect the future salt-tolerant crops in a few decades.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"83 ","pages":"Article 102671"},"PeriodicalIF":8.3,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142720488","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
Unlocking crops’ genetic potential: Advances in genome and epigenome editing of regulatory regions 释放作物的遗传潜力：基因组和表观基因组编辑调控区的进展
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-26 DOI: 10.1016/j.pbi.2024.102669
Namra Ali, Shubhangi Singh, Rohini Garg
{"title":"Unlocking crops’ genetic potential: Advances in genome and epigenome editing of regulatory regions","authors":"Namra Ali,&nbsp;Shubhangi Singh,&nbsp;Rohini Garg","doi":"10.1016/j.pbi.2024.102669","DOIUrl":"10.1016/j.pbi.2024.102669","url":null,"abstract":"<div><div>Genome editing tools could precisely and efficiently target plant genomes leading to the development of improved crops. Besides editing the coding regions, researchers can employ editing technologies to target specific gene regulatory elements or modify epigenetic marks associated with distal regulatory regions, thereby regulating gene expression in crops. This review outlines several prominent genome editing technologies, including CRISPR-Cas9, TALENs, and ZFNs and recent advancements. The applications for genome and epigenome editing especially of regulatory regions in crop plants is also discussed, including efforts to enhance abiotic stress tolerance, yield, disease resistance and plant phenotype. Additionally, the review addresses the potential of epigenetic modifications, such as DNA methylation and histone modifications, to alter gene expression for crop improvement. Finally, the limitations and future scope of utilizing various genome editing tools to manipulate regulatory elements for gene regulation to unlock the full potential of these tools in plant breeding has been discussed.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"83 ","pages":"Article 102669"},"PeriodicalIF":8.3,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142720489","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 rice genomes towards green super rice 改造水稻基因组，打造绿色超级稻
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-25 DOI: 10.1016/j.pbi.2024.102664
Jianwei Zhang , Jian Che , Yidan Ouyang
{"title":"Engineering rice genomes towards green super rice","authors":"Jianwei Zhang ,&nbsp;Jian Che ,&nbsp;Yidan Ouyang","doi":"10.1016/j.pbi.2024.102664","DOIUrl":"10.1016/j.pbi.2024.102664","url":null,"abstract":"<div><div>Rice, cultivated for millennia across diverse geographical regions, has witnessed tremendous advancements in recent decades, epitomized by the emergence of Green Super Rice. These efforts aim to address challenges such as climate change, pest and disease threats, and sustainable agriculture. Driven by the advent of multiomics big data, breakthroughs in genomic tools and resources, hybrid rice breeding techniques, and the extensive utilization of green genes, rice genomes are undergoing delicate modifications to produce varieties with high yield, superior quality, enhanced nutrient efficiency, and resilience to pests and environmental stresses, leading to the development of green agriculture in China. Additionally, the utilization of wild relatives and the promotion of genomic breeding approaches have further enriched our understanding of rice improvement. In the future, international efforts to develop next-generation green rice varieties remain both challenging and imperative for the whole community.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102664"},"PeriodicalIF":8.3,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142703697","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
Light and high temperatures control epigenomic and epitranscriptomic events in Arabidopsis 光照和高温控制拟南芥的表观基因组和表观转录组事件
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-24 DOI: 10.1016/j.pbi.2024.102668
Tianyuan Xu, Eirini Patitaki, Anna Zioutopoulou, Eirini Kaiserli
{"title":"Light and high temperatures control epigenomic and epitranscriptomic events in Arabidopsis","authors":"Tianyuan Xu,&nbsp;Eirini Patitaki,&nbsp;Anna Zioutopoulou,&nbsp;Eirini Kaiserli","doi":"10.1016/j.pbi.2024.102668","DOIUrl":"10.1016/j.pbi.2024.102668","url":null,"abstract":"<div><div>Light and temperature are two key environmental factors that control plant growth and adaptation by influencing biomolecular events. This review highlights the latest milestones on the role of light and high temperatures in modulating the epigenetic and epitranscriptomic landscape of <em>Arabidopsis</em> to trigger developmental and adaptive responses to a changing environment. Recent discoveries on how light and high temperature signals are integrated in the nucleus to modulate gene expression are discussed, as well as highlighting research gaps and future perspectives in further understanding how to promote plant resilience in times of climate change.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"83 ","pages":"Article 102668"},"PeriodicalIF":8.3,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 gene function prediction challenge: Large language models and knowledge graphs to the rescue 基因功能预测挑战：大型语言模型和知识图谱的拯救。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-22 DOI: 10.1016/j.pbi.2024.102665
Rohan Shawn Sunil, Shan Chun Lim, Manoj Itharajula, Marek Mutwil
{"title":"The gene function prediction challenge: Large language models and knowledge graphs to the rescue","authors":"Rohan Shawn Sunil,&nbsp;Shan Chun Lim,&nbsp;Manoj Itharajula,&nbsp;Marek Mutwil","doi":"10.1016/j.pbi.2024.102665","DOIUrl":"10.1016/j.pbi.2024.102665","url":null,"abstract":"<div><div>Elucidating gene function is one of the ultimate goals of plant science. Despite this, only ∼15 % of all genes in the model plant <em>Arabidopsis thaliana</em> have comprehensively experimentally verified functions. While bioinformatical gene function prediction approaches can guide biologists in their experimental efforts, neither the performance of the gene function prediction methods nor the number of experimental characterization of genes has increased dramatically in recent years. In this review, we will discuss the status quo and the trajectory of gene function elucidation and outline the recent advances in gene function prediction approaches. We will then discuss how recent artificial intelligence advances in large language models and knowledge graphs can be leveraged to accelerate gene function predictions and keep us updated with scientific literature.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102665"},"PeriodicalIF":8.3,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695162","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
Advancing plant single-cell genomics with foundation models 利用基础模型推进植物单细胞基因组学。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-22 DOI: 10.1016/j.pbi.2024.102666
Tran N. Chau , Xuan Wang , John M. McDowell , Song Li
{"title":"Advancing plant single-cell genomics with foundation models","authors":"Tran N. Chau ,&nbsp;Xuan Wang ,&nbsp;John M. McDowell ,&nbsp;Song Li","doi":"10.1016/j.pbi.2024.102666","DOIUrl":"10.1016/j.pbi.2024.102666","url":null,"abstract":"<div><div>Single-cell genomics, combined with advanced AI models, hold transformative potential for understanding complex biological processes in plants. This article reviews deep-learning approaches in single-cell genomics, focusing on foundation models, a type of large-scale, pretrained, multi-purpose generative AI models. We explore how these models, such as Generative Pre-trained Transformers (GPT), Bidirectional Encoder Representations from Transformers (BERT), and other Transformer-based architectures, are applied to extract meaningful biological insights from diverse single-cell datasets. These models address challenges in plant single-cell genomics, including improved cell-type annotation, gene network modeling, and multi-omics integration. Moreover, we assess the use of Generative Adversarial Networks (GANs) and diffusion models, focusing on their capacity to generate high-fidelity synthetic single-cell data, mitigate dropout events, and handle data sparsity and imbalance. Together, these AI-driven approaches hold immense potential to enhance research in plant genomics, facilitating discoveries in crop resilience, productivity, and stress adaptation.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102666"},"PeriodicalIF":8.3,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695087","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
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