دانلود کتاب Guleria, P: Plant Small RNA

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Cover Plant Small RNA: Biogenesis, Regulation and Application Copyright Contributors Section 1: Basics 1 Introduction to plant small RNAs Introduction Discovery history of small RNAs Diversity of small RNAs miRNAs Biogenesis of plant miRNAs miRNA turnover Mode of action of miRNAs miRNA-guided transcript cleavage miRNA-mediated translation repression miRNAs in plant development miRNA-mediated regulation of meristem organization and cell polarity miRNA-mediated regulation of flower development miRNA-mediated regulation of root architecture miRNA-mediated regulation of seed development siRNAs Biogenesis of siRNAs Mode of action of siRNAs Biological functions of 24-nt transposable element (TE)-derived siRNAs phasiRNAs Biogenesis of phasiRNAs Biological functions of phasiRNAs Movement of small RNAs Future perspectives Acknowledgment References Further reading 2 Diversity and types of small RNA Small regulatory RNAs: Historical milestones Classifying endogenous small RNA in plants Hairpin sRNA and microRNA Natural antisense transcript siRNA Secondary and trans-acting siRNA Heterochromatic siRNA References 3 Biogenesis of small RNA: Molecular pathways and regulatory mechanisms DNA-dependent RNA polymerase RNA-dependent RNA polymerase Dicer Argonaute proteins in plants Ago1 Ago10 Ago5 Ago7 AGO2 and AGO3 Ago4 Ago6 AGO8 and AGO9 Determinants for AGO-sRNA sorting and biological function Small RNA in transgenerational epigenetic inheritance Interrelationship between sRNA pathways Analyzing sRNA: Computational challenges from the “dry lab” References 4 Transcriptome-based identification of small RNA in plants: The need for robust prediction algorithms Introduction The need for small RNA Seq in plants Types of RNA Seq strategies dUTP-based strand-specific RNA Seq Bulked segregant analysis (BSA) using RNA Seq Double-stranded RNA Seq Differential RNA Seq Elements of RNA Seq data and analyses Raw read Read alignment Quantification Transcript identification Alignment Differential gene expression analyses Alternative splicing identification Identifying gene fusions Challenges and solutions for annotating small RNAs in plants Empirical toolkits and databases Fastx miRCat SiloCo miRBASE TAPIR [ http://bioinformatics.psb.ugent.be/webtools/tapir/ ] Emerging algorithms Validation of expression using time course data Normalization and log ratio transformation method Tools and databases available according to the basic steps of RNA Seq data analyses Quality control Trimming and adapters removal Error correction Bias correction Other tasks/preprocessing data Alignment tools De novo splice aligners Normalization, quantitative analysis, and differential expression Open (free) source solutions Alternative splicing analysis Differential isoform/transcript usage Fusion genes/chimeras/translocation finders/structural variations Single-cell RNA Seq Integrated packages Genome-guided assemblers [88, 89] Co-expression networks Visualization tools Functional, network, and pathway analysis tools Links to databases used for analysis of plant transcriptome data A case study: Transcriptome analyses from Vigna mungo and identification of miRNAs Background of the work Sample preparation and sequencing Screening and identification of miRNAs from sequenced data Identification of established and novel miRNA sequences miRNA target prediction, gene ontology classification, and quantification of target genes Quantification of miRNAs in different tissues to study their tissue-specific expression Expression patterns of miRNAs from both mock control (MC) and MYMIV-inoculated (MI) datasets qPCR validation of miRNA targets in MYMIV-susceptible and -resistant background References Further reading Section 2: Expression and regulation mechanism of small RNA 5 Role of RNA interference in seed germination Introduction Mechanism of seed germination Phases in seed germination Factors regulating seed germination The phenomenon of RNA silencing Mechanism of RNA silencing miRNAs Tasi-RNAs Role of small RNAs in seed germination miRNA serve as convergence regulatory nodes Conclusion Acknowledgment References 6 Importance of small RNA in plant seed germination Brief introduction of seed germination miRNAs related to seed germination in Arabidopsis miRNAs related to seed germination in crops siRNAs related to seed germination References Further reading 7 Importance of small RNA in plant metabolism Introduction Major types of plant sRNA Biogenesis of small RNA in plants: microRNA and small interference RNA Diverse functions of sRNA in controlling plant metabolism during stress condition Role of miRNAs in ABA-mediated stress responses miRNA-mediated adaptive response to drought and salt stress conditions Regulation of cold and heat stress tolerance by miRNAs expression miRNAs expression to hypoxia and oxidative stress miRNA in response to nutrient homeostasis Regulating plant metabolism: Role of sRNAs miRNA-mediated regulation plant phytohormone signaling miRNA: Transcription factors in regulating plant metabolism Functional role of miRNA in plant secondary metabolism biosynthesis Regulatory role of siRNAs in plant stress responses Conclusion and future prospectus References Further reading 8 Small RNA in tolerating various biotic stresses Small RNA: Discovery, classifications, and biogenesis Classification MicroRNAs and isomiRs Ta-siRNAs Nat siRNA Heterochromatic-siRNA Pathogen-derived sRNAs and miRNA-like molecules Biogenesis Methodologies applied for sRNA research Parameters applied for sRNA prediction Plant miRNAs and pathogen milRs Plant ta-siRNAs Plant isomiRs Databases available for sRNAs SRNA-mediated biotic stress responses in plants SRNA-mediated responses against insects SRNA-mediated responses against fungi SRNA-mediated responses against virus SRNA-mediated responses against bacteria SRNA-mediated responses against abiotic stress SRNAs and agricultural improvement Small RNA as a spray Conclusion References Further reading 9 Role of small RNA in regulating plant viral pathogenesis Introduction Illustrations of siRNA-mediated and miRNA-mediated antivirus pathway mechanisms Role of miRNA in plant antiviral defense Application of siRNA against plant antiviral defense Regulation of siRNA for plant viral pathogenesis siRNA response against bacterial diseases Role of siRNA to prevent fungal disease References 10 Salt stress tolerance and small RNA Introduction Plant sRNAs: Types and biogenesis miRNA siRNA Trans-acting siRNAs (ta-siRNAs) Natural antisense siRNAs (nat-siRNAs) Heterochromatic siRNAs (hec-siRNAs) Role of sRNAs in salt stress response Conclusion and future perspective Acknowledgment References Further reading 11 Small RNAs and cold stress tolerance Introduction Cold stress sensing and second messengers Mechanism of cold acclimatization Small RNAs and cold stress tolerance Biogenesis of miRNAs and siRNAs Role of miRNAs in cold stress tolerance Role of siRNAs in cold stress tolerance Genes involved in cold stress Conclusion References Further reading 12 Toward elucidating the functions of miRNAs in drought stress tolerance Introduction Drought and drought tolerance mechanisms Drought escape Drought avoidance Drought tolerance Physiological and biochemical mechanisms of drought tolerance Stomatal aperture regulation Reactive oxygen species accumulation Metabolism maintenance Molecular basis of drought tolerance Transcription factors MiRNAs Discovery of miRNAs Biogenesis of miRNAs Functional modes of miRNAs MiRNA responses to drought stress Targets of drought-responsive miRNAs Contribution of miRNAs to drought stress tolerance Conclusion and future perspectives References 13 Regulation of photosynthesis and vegetative growth of plants by small RNAs Introduction Roles of small RNAs in vegetative growth Regulation of shoot apical meristem genes Abaxial-adaxial polarity Morphology and size of leaves Guard cell patterning Leaf senescence Vegetative phase transition Regulation of root traits Roles of small RNAs in photosynthesis Possible applications of small RNAs in modulating photosynthesis and vegetative growth Rice Tobacco Potato Maize Legume Wheat Poplar Tomato Conclusion References 14 Heat stress tolerance through small RNA Introduction Biogenesis How do miRNAs regulate stress response? Heat-responsive miRNAs in plants MiRNA families in cereal crops and their regulatory pathways miR156 family miR159 family miR160 family miR164 family miR166 family miR167 family miR168 family miR169 family miR172 family miR319 family miR393 family miR395 family miR397 family miR398 family miR408 family Manipulation of miRNAs for crop improvement Target mimics Artificial miRNAs miRNA manipulation by genome editing technologies Conclusion Acknowledgment References Further reading 15 Role of small RNA in plant interaction with microbes Introduction Structural diversity of sRNAs in plants miRNAs siRNAs miRNAs regulation in response to beneficial microorganism-plant interactions MicroRNAs-based regulation in plants submitted to beneficial bacteria MicroRNAs-based regulation in plants submitted to beneficial fungi sRNAs in response to pathogenic microorganism-plant interactions Plant defense strategies Counteracting pathogen strategies Conclusion and future perspectives References 16 Plant growth regulation by small RNA-mediated plant-biotic interactions Introduction Mode of action of sRNAs in plant defense Function of small RNA Small RNAs and pathogenesis Pathogen-endogenous sRNAs Pathogen-induced sRNAs Small RNAs and plant defense Bacterial infection Fungal infection Viral infection Small RNAs and symbiotic relationships Summary References 17 Small RNA and DNA methylation in plants Brief overview of small RNAs Transcriptional gene silencing DNA methylation and demethylation DNA methylation Active DNA demethylation Argonaute proteins and their functions Argonaute protein family Argonaute function in Arabidopsis Mobile small RNAs Small RNAs and epigenetic reprogramming in plant sexual production miRNA and DNA methylation A Dicer-independent pathway for biogenesis of siRNAs that direct DNA methylation in Arabidopsis sRNA and hybrid vigor DNA methylation and fleshy fruit ripening Simpson’s paradox on DNA methylation comparison Concluding remarks Acknowledgments References Section 3: Application of small RNA 18 Small RNA manipulation in plants: Techniques and recent developments Introduction Small RNA silencing pathways MicroRNA (miRNA) pathway Small interfering RNA (siRNA) pathway Other RNA silencing-related pathways Trans-acting siRNA (tasiRNA) pathway RdDM pathway in plants The natsiRNA pathway Exogenic nucleic acid-based RNA silencing Recent RNA silencing techniques in plants Hairpin RNA transgene (HpRNA)-induced RNA silencing Artificial miRNA (amiRNA) technology Designing of amiRNAs Virus-induced gene silencing (VIGS) Different methods of VIGS induction Transformation using Agrobacterium tumefaciens VIGS for potato silencing through Potato Virus X (PVX) VIGS for Arabidopsis silencing through TRV TYMV-derived silencing in Arabidopsis Applications of RNA interference Crop improvement and nutritional value RNAi-induced rice and barley RNAi induced in banana RNAi induced in jute and cotton Application of RNAi in biotic stress RNAi in secondary metabolite biosynthetic pathway RNAi in seedless fruit production Application of RNAi developing valuable industrial products RNAi to induce prolonged shelf life RNAi to silence toxic compounds and allergens in edible fruits RNAi for non-hazardous oil production Limitations of RNAi Biosafety concerns of RNAi technology Conclusion References 19 MicroRNA-mediated regularity functions under salinity stress in plants Introduction: Role of microRNAs in abiotic stresses in plants miRNA abundance and dynamics under salinity stress Regulation of miRNAs and associated target genes under salt stress Development of microRNA-mediated salinity tolerance in plants Conclusions and perspectives References 20 Biotic stress-tolerant plants through small RNA technology Plant biotic stress Plant immunity responses against biotic stress factors Biotic stress response related to small RNAs Role of small RNAs in virus-plant interactions Role of small RNAs in bacteria-plant interactions Role of small RNAs in fungi-plant interactions Role of small RNAs in nematode-plant interactions Role of small RNAs in herbivore-plant interactions Small RNA applications for biotic resistance Artificial miRNA applications Site-specific genome editing applications References 21 Application of miRNA in fruit quality improvement Introduction MicroRNA and fruit texture MicroRNA and fruit coloration MicroRNA and fruit development MicroRNA and fruit ripening Concluding remarks and future prospects References 22 Physiological modification of plants through small RNA Foundations of plant physiology Regulation of the physiological development Discovery of plant small RNAs Classification on the basis of RNA source Classification on the basis of RNA synthesis General mode of action Small RNAs in physiological development regulations Chromatin modification Target degradation Lowering translational efficiency Small RNA-mediated physiological and developmental control Vegetative growth Shoot apical meristem development and maintenance Leaf development Root development Phase transition Floral development Flower patterning Flower development Seed development, maturation, and germination Seed development and trigger for embryo formation Seed maturation and storage of products Seed size control Seed germination Conclusions and perspectives References 23 Small RNA technology for plant abiotic stress tolerance Introduction Application of sRNA technology in plants General mechanism of RNAi The biology of miRNAs in plants siRNA-mediated abiotic stress tolerance in plants MicroRNA-mediated abiotic stress tolerance in plants Conclusion References Section 4: Future scope 24 Challenges of small RNA technology Small RNAs in plants: An expanding world RNA interference: Basis of small RNA technology Small RNA technology: Enormous potential Disease resistance Metabolic engineering Abiotic stress Male sterility Small RNA technology: Its challenges and pitfalls Off-target effects Stability of transgene Persistence of double-stranded RNAs (dsRNAs) Food risk assessment of genetically modified (GM) plants Biosafety evaluation of genetically modified (GM) plants Future prospects Bioinformatics approaches to achieve better gene silencing Spray-induced gene silencing CRISPR/Cas9: A platform for editing plant genomes Conclusions References 25 Future scope of small RNA technology in crop science Introduction Overview of diverse small RNA pathways in plants Perspectives on small RNA sequencing and trafficking Developments and challenges of sRNA-mediated gene silencing for crop improvement Stress memory and forgetfulness in plants Small RNA-mediated epigenetic engineering and RNA editing in plants Small RNA trafficking between kingdoms and applications for plant disease control Conclusion Acknowledgments References Index A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Back Cover