Pub Date : 2024-11-25DOI: 10.1016/j.pbi.2024.102664
Jianwei Zhang , Jian Che , Yidan Ouyang
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.
{"title":"Engineering rice genomes towards green super rice","authors":"Jianwei Zhang , Jian Che , 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}
Pub Date : 2024-11-24DOI: 10.1016/j.pbi.2024.102668
Tianyuan Xu, Eirini Patitaki, Anna Zioutopoulou, Eirini Kaiserli
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 Arabidopsis 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.
{"title":"Light and high temperatures control epigenomic and epitranscriptomic events in Arabidopsis","authors":"Tianyuan Xu, Eirini Patitaki, Anna Zioutopoulou, 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}
Pub Date : 2024-11-22DOI: 10.1016/j.pbi.2024.102665
Rohan Shawn Sunil, Shan Chun Lim, Manoj Itharajula, Marek Mutwil
Elucidating gene function is one of the ultimate goals of plant science. Despite this, only ∼15 % of all genes in the model plant Arabidopsis thaliana 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.
{"title":"The gene function prediction challenge: Large language models and knowledge graphs to the rescue","authors":"Rohan Shawn Sunil, Shan Chun Lim, Manoj Itharajula, 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}
Pub Date : 2024-11-22DOI: 10.1016/j.pbi.2024.102666
Tran N. Chau , Xuan Wang , John M. McDowell , Song Li
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.
{"title":"Advancing plant single-cell genomics with foundation models","authors":"Tran N. Chau , Xuan Wang , John M. McDowell , 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}
G protein-coupled receptors (GPCRs) represent the largest superfamily of cell surface membrane receptors in eukaryotes. Unlike plants, fungi do not have receptor kinases or receptor-like kinases. Instead, GPCRs play critical roles in fungi to sense signals crucial for their survival and interspecies interactions to activate downstream cAMP and mitogen-activated protein kinase pathways via heterotrimeric G proteins. Some fungal GPCRs have relatively conserved roles in nutrient sensing and pheromone recognition to facilitate growth and sexual reproduction. For fungal pathogens with expanded families of classical or fungal-specific GPCRs, including those with the CFEM (common in fungal extracellular membrane) domain, distinctive GPCRs are involved in recognizing different signals from their hosts and surroundings. Although only a few ligands recognized by fungal GPCRs have been identified, recent studies have advanced our knowledge of GPCR biology in plant pathogenic and nematode-trapping fungi.
G 蛋白偶联受体(GPCR)是真核生物中最大的细胞表面膜受体超家族。与植物不同,真菌没有受体激酶或类似受体的激酶。相反,GPCR 在真菌中发挥着关键作用,它们能感知对真菌生存和种间相互作用至关重要的信号,并通过异三聚 G 蛋白激活下游 cAMP 和有丝分裂原激活蛋白激酶通路。一些真菌 GPCR 在营养传感和信息素识别方面具有相对保守的作用,可促进生长和有性生殖。对于经典或真菌特异性 GPCR 家族扩大的真菌病原体,包括具有 CFEM(真菌胞外膜常见)结构域的真菌病原体,独特的 GPCR 参与识别来自宿主和周围环境的不同信号。虽然真菌 GPCR 识别的配体为数不多,但最近的研究增进了我们对植物致病真菌和线虫诱捕真菌 GPCR 生物学的了解。
{"title":"Sensing host and environmental cues by fungal GPCRs","authors":"Cong Jiang , Aliang Xia , Daiying Xu , Jin-Rong Xu","doi":"10.1016/j.pbi.2024.102667","DOIUrl":"10.1016/j.pbi.2024.102667","url":null,"abstract":"<div><div>G protein-coupled receptors (GPCRs) represent the largest superfamily of cell surface membrane receptors in eukaryotes. Unlike plants, fungi do not have receptor kinases or receptor-like kinases. Instead, GPCRs play critical roles in fungi to sense signals crucial for their survival and interspecies interactions to activate downstream cAMP and mitogen-activated protein kinase pathways via heterotrimeric G proteins. Some fungal GPCRs have relatively conserved roles in nutrient sensing and pheromone recognition to facilitate growth and sexual reproduction. For fungal pathogens with expanded families of classical or fungal-specific GPCRs, including those with the CFEM (common in fungal extracellular membrane) domain, distinctive GPCRs are involved in recognizing different signals from their hosts and surroundings. Although only a few ligands recognized by fungal GPCRs have been identified, recent studies have advanced our knowledge of GPCR biology in plant pathogenic and nematode-trapping fungi.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102667"},"PeriodicalIF":8.3,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680855","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}
Pub Date : 2024-11-16DOI: 10.1016/j.pbi.2024.102663
Annis Richardson , Heather Jones , Madelaine Bartlett
Grasses dominate agriculturally and ecologically. One hypothesized driver of this dominance is grasses' facility for grain dispersal and rapid seedling establishment. Dispersal and establishment are aided by the awned lemma - a modified bract associated with grass flowers. Awns have diverse forms, many proposed functions, and have been gained and lost repeatedly in grass evolution. Here we hypothesize that the evolution of awn emergence is underpinned by deep conservation of developmental genes. Awns are likely homologous to leaf blades. Because leaf blades are essential, every grass species likely has a latent developmental program available for awn development. This developmental program may be repeatedly reactivated in lemmas, resulting in the frequent appearance of awns. Because awns are inessential, they can be lost and modified without dire consequences to fitness, resulting in the frequent loss and diversity of awns. Replicated awn evolution reveals how developmental conservation can potentiate the evolution of diversity. Awns also present a powerful opportunity to dissect mechanisms of leaf development.
{"title":"Grass awns: Morphological diversity arising from developmental constraint","authors":"Annis Richardson , Heather Jones , Madelaine Bartlett","doi":"10.1016/j.pbi.2024.102663","DOIUrl":"10.1016/j.pbi.2024.102663","url":null,"abstract":"<div><div>Grasses dominate agriculturally and ecologically. One hypothesized driver of this dominance is grasses' facility for grain dispersal and rapid seedling establishment. Dispersal and establishment are aided by the awned lemma - a modified bract associated with grass flowers. Awns have diverse forms, many proposed functions, and have been gained and lost repeatedly in grass evolution. Here we hypothesize that the evolution of awn emergence is underpinned by deep conservation of developmental genes. Awns are likely homologous to leaf blades. Because leaf blades are essential, every grass species likely has a latent developmental program available for awn development. This developmental program may be repeatedly reactivated in lemmas, resulting in the frequent appearance of awns. Because awns are inessential, they can be lost and modified without dire consequences to fitness, resulting in the frequent loss and diversity of awns. Replicated awn evolution reveals how developmental conservation can potentiate the evolution of diversity. Awns also present a powerful opportunity to dissect mechanisms of leaf development.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102663"},"PeriodicalIF":8.3,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643728","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}
Pub Date : 2024-11-15DOI: 10.1016/j.pbi.2024.102658
Ivana Kaňovská, Jana Biová, Mária Škrabišová
Crop breeding advancement is hindered by the imperfection of methods to reveal genes underlying key traits. Genome-wide Association Study (GWAS) is one such method, identifying genomic regions linked to phenotypes. Post-GWAS analyses predict candidate genes and assist in causative mutation (CM) recognition. Here, we assess post-GWAS approaches, address limitations in omics data integration and stress the importance of evaluating associated variants within a broader context of publicly available datasets. Recent advances in bioinformatics tools and genomic strategies for CM identification and allelic variation exploration are reviewed. We discuss the role of markers and marker panel development for more precise breeding. Finally, we highlight the perspectives and challenges of GWAS-based CM prediction for complex quantitative traits.
由于揭示关键性状基因的方法不完善,农作物育种的进展受到阻碍。全基因组关联研究(GWAS)就是这样一种方法,它能确定与表型相关的基因组区域。全基因组关联研究(GWAS)后分析可预测候选基因,并帮助识别致病突变(CM)。在此,我们将评估后GWAS方法,解决omics数据整合的局限性,并强调在更广泛的公开数据集背景下评估相关变异的重要性。我们回顾了用于 CM 鉴定和等位基因变异探索的生物信息学工具和基因组策略的最新进展。我们还讨论了标记的作用以及为实现更精确育种而进行的标记组开发。最后,我们强调了基于 GWAS 的复杂数量性状 CM 预测的前景和挑战。
{"title":"New perspectives of post-GWAS analyses: From markers to causal genes for more precise crop breeding","authors":"Ivana Kaňovská, Jana Biová, Mária Škrabišová","doi":"10.1016/j.pbi.2024.102658","DOIUrl":"10.1016/j.pbi.2024.102658","url":null,"abstract":"<div><div>Crop breeding advancement is hindered by the imperfection of methods to reveal genes underlying key traits. Genome-wide Association Study (GWAS) is one such method, identifying genomic regions linked to phenotypes. Post-GWAS analyses predict candidate genes and assist in causative mutation (CM) recognition. Here, we assess post-GWAS approaches, address limitations in omics data integration and stress the importance of evaluating associated variants within a broader context of publicly available datasets. Recent advances in bioinformatics tools and genomic strategies for CM identification and allelic variation exploration are reviewed. We discuss the role of markers and marker panel development for more precise breeding. Finally, we highlight the perspectives and challenges of GWAS-based CM prediction for complex quantitative traits.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102658"},"PeriodicalIF":8.3,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643731","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}
Pub Date : 2024-11-14DOI: 10.1016/j.pbi.2024.102659
Vibha Srivastava, Christian De Guzman, Samuel B. Fernandes
High nighttime temperature (HNT) is a major obstacle in rice production worldwide. It severely impacts spikelet fertility and induces grain chalk, the two undesirable factors leading to yield and quality decline in rice. Recently, major efforts have been undertaken to understand the genetic mechanisms underlying HNT tolerance. Here, we highlight phenotypic diversity and recent studies on breeding, genomics, and gene editing targeting this trait. These studies point to the challenges in the process as HNT tolerance has so far been found only in non-adapted varieties, and no known modern cultivar bred in the United States is able to withstand exposure to HNT during the reproductive stage. At the same time, identification of the tolerant genotypes enabled genomics, opened up tortuous but promising approaches for breeding, and showed a path for gene editing towards HNT tolerance. The recent advances have set a strong foundation for addressing this current and looming threat.
{"title":"Beat the heat: Breeding, genomics, and gene editing for high nighttime temperature tolerance in rice","authors":"Vibha Srivastava, Christian De Guzman, Samuel B. Fernandes","doi":"10.1016/j.pbi.2024.102659","DOIUrl":"10.1016/j.pbi.2024.102659","url":null,"abstract":"<div><div>High nighttime temperature (HNT) is a major obstacle in rice production worldwide. It severely impacts spikelet fertility and induces grain chalk, the two undesirable factors leading to yield and quality decline in rice. Recently, major efforts have been undertaken to understand the genetic mechanisms underlying HNT tolerance. Here, we highlight phenotypic diversity and recent studies on breeding, genomics, and gene editing targeting this trait. These studies point to the challenges in the process as HNT tolerance has so far been found only in non-adapted varieties, and no known modern cultivar bred in the United States is able to withstand exposure to HNT during the reproductive stage. At the same time, identification of the tolerant genotypes enabled genomics, opened up tortuous but promising approaches for breeding, and showed a path for gene editing towards HNT tolerance. The recent advances have set a strong foundation for addressing this current and looming threat.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102659"},"PeriodicalIF":8.3,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616440","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}
Pub Date : 2024-11-13DOI: 10.1016/j.pbi.2024.102662
Mukesh Jain
Understanding intricate gene regulatory networks (GRNs) orchestrating responses to abiotic stresses is crucial for enhancing climate resilience in crop plants. Recent advancements in single-cell and spatial technologies have revolutionized our ability to dissect the GRNs at unprecedented resolution. Here, we explore the progress, challenges, and opportunities these state-of-the-art technologies offer in delineating the cellular intricacies of plant responses to abiotic stress. Using scRNA-seq, the transcriptome landscape of individual plant cells along with their lineages and regulatory interactions can be unraveled. Moreover, coupling scRNA-seq with spatial transcriptomics provides spatially resolved gene expression and insights into cell-to-cell interactions. In addition, the chromatin accessibility assays can discover the regulatory regions governing abiotic stress responses. An integrated multi-omics approach can facilitate discovery of cell-type-specific GRNs to reveal the key components that coordinate adaptive responses to different stresses. These potential regulatory factors can be harnessed for genetic engineering to enhance stress resilience in crop plants.
{"title":"Gene regulatory networks in abiotic stress responses via single-cell sequencing and spatial technologies: Advances and opportunities","authors":"Mukesh Jain","doi":"10.1016/j.pbi.2024.102662","DOIUrl":"10.1016/j.pbi.2024.102662","url":null,"abstract":"<div><div>Understanding intricate gene regulatory networks (GRNs) orchestrating responses to abiotic stresses is crucial for enhancing climate resilience in crop plants. Recent advancements in single-cell and spatial technologies have revolutionized our ability to dissect the GRNs at unprecedented resolution. Here, we explore the progress, challenges, and opportunities these state-of-the-art technologies offer in delineating the cellular intricacies of plant responses to abiotic stress. Using scRNA-seq, the transcriptome landscape of individual plant cells along with their lineages and regulatory interactions can be unraveled. Moreover, coupling scRNA-seq with spatial transcriptomics provides spatially resolved gene expression and insights into cell-to-cell interactions. In addition, the chromatin accessibility assays can discover the regulatory regions governing abiotic stress responses. An integrated multi-omics approach can facilitate discovery of cell-type-specific GRNs to reveal the key components that coordinate adaptive responses to different stresses. These potential regulatory factors can be harnessed for genetic engineering to enhance stress resilience in crop plants.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102662"},"PeriodicalIF":8.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616342","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}
Pub Date : 2024-11-12DOI: 10.1016/j.pbi.2024.102656
Azeddine Driouich , Marie-Laure Follet Gueye , Maïté Vicré , John P. Moore
Plants have evolved a number of defense mechanisms to protect themselves against biotic stresses. Each cell, tissue, and organ is able to perceive and fight off attackers using a combination of chemical and physical defense mechanisms. Root cells employ similar defense response patterning. They develop immune responses upon pathogen attack and release a variety of compounds able to defend the root proper as well as the entire plant body. Currently, one of the most effective mechanisms of root defense involves the root extracellular trap (RET) that is produced at the tip of the root. The RET consists of root cap–derived cells embedded in mucilaginous secretions containing cell wall–derived polysaccharides, defense-related (glyco)proteins, phytoalexins, histones, and extracellular DNA (eDNA). The RET network plays a central role in root immunity and fulfills biological functions similar to those performed by neutrophil extracellular traps in mammals.
{"title":"The root extracellular trap; a complex and dynamic biomatrix network essential for plant protection","authors":"Azeddine Driouich , Marie-Laure Follet Gueye , Maïté Vicré , John P. Moore","doi":"10.1016/j.pbi.2024.102656","DOIUrl":"10.1016/j.pbi.2024.102656","url":null,"abstract":"<div><div>Plants have evolved a number of defense mechanisms to protect themselves against biotic stresses. Each cell, tissue, and organ is able to perceive and fight off attackers using a combination of chemical and physical defense mechanisms. Root cells employ similar defense response patterning. They develop immune responses upon pathogen attack and release a variety of compounds able to defend the root proper as well as the entire plant body. Currently, one of the most effective mechanisms of root defense involves the root extracellular trap (RET) that is produced at the tip of the root. The RET consists of root cap–derived cells embedded in mucilaginous secretions containing cell wall–derived polysaccharides, defense-related (glyco)proteins, phytoalexins, histones, and extracellular DNA (eDNA). The RET network plays a central role in root immunity and fulfills biological functions similar to those performed by neutrophil extracellular traps in mammals.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102656"},"PeriodicalIF":8.3,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616345","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}