Note: Front Cover -- Plant Small RNA: Biogenesis, Regulation and Application -- Copyright -- Contents -- Contributors -- Section: 1 Basics -- Chapter 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 -- Chapter 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 -- Chapter 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. , Chapter 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 -- Chapter 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 -- Chapter 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 -- Chapter 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 -- Chapter 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 -- Chapter 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 -- Chapter 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 -- Chapter 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 -- Chapter 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 -- Chapter 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 -- Chapter 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.