Genomics, transcriptomics, proteomics and metabolomics of crop plants /

Genomics, Transcriptomics, Proteomics and Metabolomics of Crop Plants presents current operational methods applied to model crop plants.Including subcellular organelles, DNA fingerprinting and barcoding, sRNA, gene expression, rhizosphere engineering, marker assisted and 5G breeding, plant-microorga...

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Bibliographic Details
Corporate Author:	ScienceDirect (Online service)
Other Authors:	Husen, Azamal, Ahmad, Altaf
Format:	eBook
Language:	English
Published:	London, United Kingdom ; San Diego, CA : Academic Press, 2023.
Series:	Plant biology, sustainability and climate change
Subjects:	Crops > Molecular genetics. Cultures > Génétique moléculaire. Electronic books.
Online Access:	Connect to the full text of this electronic book

Table of Contents:

Front Cover
Genomics, Transcriptomics, Proteomics and Metabolomics of Crop Plants
Copyright Page
Contents
List of contributors
About the editors
Preface
1 Genome to phenome: bioinformatics of crop plants
1.1 Introduction
1.2 De novo genome assembly approach
1.3 Genome annotation
1.4 Phenotypes
1.5 Data analysis
1.6 Conclusions
References
Further reading
2 Emerging approach of transcriptomics for crop plants improvements
2.1 Introduction
2.2 Transcriptomic approaches applied in plants
2.2.1 Classical approaches before transcriptome
2.2.1.1 cDNA libraries and expression sequence tags
cDNA-AFLP (cDNA amplified fragment length polymorphism)
Serial analysis of gene expression
2.2.2 High-throughput transcriptome approaches and applications
2.2.2.1 Microarray
2.2.2.2 cDNA microarray
2.2.2.3 Oligonucleotide microarray
2.2.2.4 Microarray applications in plants
2.2.2.5 Next generation sequencing technologies
2.2.2.6 Sequencing by synthesis
ROCHE 454 GS
İon Torrent
Illumina/Solexa
2.2.2.7 Sequencing by ligation
ABI/SOLiD
2.2.2.8 Single molecule sequencing
Pacific biosciences SMRT sequencing
Oxford nanopore sequencing
Helicos single-molecule sequencing
Experimental design of single molecule sequencing
Sample preparation
Library preparation and sequencing
Data processing
Analysis, integration, and validation of data
2.3 Conclusion
References
3 Proteomics as a tool for analyzing plant responses to abiotic and biotic stresses
3.1 Introduction
3.2 Proteomics' significance for agricultural systems
3.3 Various proteomics approaches used in plant studies
3.3.1 Gel-based proteomics approach
3.3.1.1 2D map in different plant tissues
3.3.1.2 Electrophoretic separations of native proteins.
3.3.1.3 One-dimensional gel electrophoresis
3.3.2 Gel-free proteomics approach
3.3.2.1 Mass spectrometry for protein characterization
3.3.2.2 MALDI-TOF/MS
3.3.2.3 Electrospray ionization
3.3.2.4 Chromatographic techniques
3.3.2.5 Protein microarrays
3.3.2.6 Tissue proteome analysis of a biotic stress response in agricultural crops productivity
3.3.2.7 Posttranslational modification in agricultural crops
3.4 Proteomics for crop improvement
3.4.1 Proteomics for addressing biotic stresses
3.4.2 Proteomics for addressing abiotic stresses
3.4.2.1 Drought stress
3.4.2.2 Flood stress
3.4.2.3 Salinity stress
3.4.2.4 Chilling stress
3.4.2.5 Heat stress
3.4.3 Fungicide development
3.5 Concerns of proteomics in plants for the next decade
3.6 Conclusions and prospects
References
Further reading
4 Metabolic engineering of plant primary-secondary metabolism interface
4.1 Introduction
4.2 Metabolic engineering
4.3 Primary and secondary metabolites
4.3.1 Alkaloids
4.3.2 Phenolics
4.3.3 Terpenes/terpenoids
4.4 Plant metabolic engineering
4.4.1 Nitrogen fixation in plants
4.4.2 Nutritional content of plant
4.4.3 Biofuel production from plants
4.4.4 Photorespiration in plants
4.5 Plant primary-secondary metabolism interface
4.6 Conclusion
References
5 Current understanding of genomics, transcriptomics, proteomics, and metabolomics of crop plants under low nutrient stress
5.1 Introduction
5.2 Omics approaches for investigating nutrient response of crop plants
5.3 Nitrogen (N) and its response to plants at omics levels
5.4 Phosphorus (P) and its response to plants at omics levels
5.5 Potassium (K) and its response to plants at omics levels
5.6 Sulfur (S) and its response to plants at omics levels.
5.7 Calcium and its response to plants at omics levels
5.8 Magnesium (Mg) and its response to plants at omics levels
5.9 Boron (B) and its response to plants at omics levels
5.10 Manganese (Mn) and its response to plants at omics levels
5.11 Iron (Fe) and its response to plants at omics levels
5.12 Copper (Cu) and its response to plants at omics levels
5.13 Other micronutrients and their responses to plants at omics levels
5.14 Conclusion
References
Further reading
6 Perspectives of omics and plant microbiome
6.1 Introduction
6.2 Plant-microbe dynamics and their multiomics studies
6.2.1 Bioinformatics approaches in community-based analysis
6.2.2 Proteomics and epigenomics
6.2.3 Computational methods to detect plant microbial pathogenesis
6.3 Industrial view of plant-microbial bioactive compounds extraction
6.3.1 Medicinal plants microbiome
6.3.2 Microorganisms' antibiotic production
6.4 Conclusion and future perspectives
6.4.1 Next-generation agriculture
6.4.2 Biotechnology solutions: bioremediation and biocontrol agents
6.4.3 Biosynthesis of nanoparticles for more sustainable agriculture
References
7 Genome-wide transcriptome profiling of crop plants
7.1 Introduction
7.2 Plant stress-responsive mechanisms
7.3 Transcriptomics
7.3.1 Transcriptomics techniques
7.3.1.1 Microarray
Methods
Result analysis with array mining
7.3.2 SAGE (serial analysis of gene expression)
7.3.2.1 SAGE data analysis
7.3.3 RNA sequencing (RNA-Seq)
7.3.3.1 Principles
7.3.3.2 Advantage of RNA-seq over microarray
7.3.3.3 RNA-Seq data analysis
7.4 Genome-wide transcriptome profiling of some crop plants
7.4.1 Role of transcriptomics in crop improvement against abiotic stress
7.4.2 Role of transcriptomics in crop improvement against biotic stress.
7.5 Gene ontology and KEGG enrichment analysis of DEGs
7.6 Challenges and prospects in transcriptomics
7.7 Conclusion
References
8 Role of noncoding RNA in regulation of biological processes of crop plants
8.1 Introduction
8.2 Classification and function of different types of noncoding RNAs
8.2.1 Role of sRNA in plants
8.2.2 miRNAs
8.2.3 Biogenesis of miRNA
8.2.4 Role of miRNA in nitrogen availability
8.2.5 Role of miRNA throughout bacterial infections
8.2.6 Role of miRNA throughout fungal infections
8.2.7 miRNA role in abiotic stress
8.2.7.1 During salinity and drought stress
8.2.7.2 In Heat and cold stress
8.3 Biogenesis of siRNAs
8.3.1 Biogenesis of nat-siRNA
8.3.2 Biogenesis of hcsiRNA
8.3.3 Biogenesis of vsiRNA
8.3.4 Biogenesis of tasiRNA, phasiRNA, and easiRNA
8.4 Function of siRNA in plants
8.4.1 circRNA function in plants
8.4.1.1 CircRNA involves during stress response in plants
8.4.2 Function of lncRNA in plants
8.4.3 lncRNA in vernalization
8.4.4 lncRNA in fertility
8.4.5 Role in photomorphogenesis
8.4.6 Role in phosphate homeostasis
8.4.7 miRNA mimicry
8.4.8 Role in fruit ripening
8.4.9 Additional role of lncRNA in plant
8.5 Housekeeping ncRNAs
8.6 Conclusion
References
9 DNA barcoding of crop plants
9.1 Introduction
9.2 Plant species and the barcode
9.3 DNA sequences and barcode
9.3.1 Single locus-based DNA barcode markers
9.3.2 Genes and sequences used for Barcoding
9.3.3 Genome-based DNA barcode markers
9.3.4 DNA barcoding of cultivated species
9.4 Herbing of plant species
9.4.1 Molecular methods applied to barcode
9.4.1.1 High quality DNA isolation
9.4.1.2 Polymerase chain reaction (PCR)
9.4.1.3 Sequencing and coupled technologies
9.4.2 Bioinformatic tools applied to barcode.
9.4.3 Deposit and registration of barcode sequences in GenBank
Acknowledgments
Conflict of interest
Abbreviations
References
10 DNA fingerprinting of crop plants
10.1 Introduction
10.2 DNA markers
10.2.1 Non-PCR based DMs
10.2.1.1 Restriction fragment length polymorphism
10.2.1.2 Variable number tandem repeats
10.2.2 PCR-based DMs
10.2.2.1 Random amplified polymorphic DNA
10.2.2.2 Amplified fragment length polymorphism
10.2.2.3 Simple sequence repeats
10.2.2.4 Expressed sequence tag
10.2.2.5 Intersimple sequence repeats
10.2.2.6 Sequence characterized amplified regions
10.2.2.7 Cleaved amplified polymorphic sequence
10.2.2.8 Sequence tagged sites
10.2.2.9 Interretrotransposon amplified polymorphism
10.2.2.10 Retrotransposon microsatellite amplified polymorphism
10.2.2.11 Sequence-specific amplified polymorphism
10.2.3 DNA chip and sequencing based
10.2.3.1 Single nucleotide polymorphism
10.2.3.2 Diversity arrays technology
10.3 Conclusion
References
11 Marker assisted selection and breeding of crop plants
11.1 Introduction
11.2 Variations of MAS
11.2.1 Marker-assisted backcrossing (MABC)
11.2.2 Marker-assisted gene pyramiding (MAGP)
11.2.3 Marker-assisted recurrent selection (MARS)
11.2.4 Genomic selection (GS)
11.3 Application of MAS in plant breeding
11.4 Selection of molecular markers
11.4.1 Hybridization-based markers
11.4.2 PCR-based markers
11.4.3 Sequence-based markers
11.5 Conclusion
References
12 An overview of gene regulations in crop plants
12.1 Introduction
12.2 Gene and genome
12.3 Are genes steady?
12.4 Regulation of gene expression in plants
12.5 Gene regulation in crop plants under stress conditions
12.5.1 Salinity stress
12.5.2 Oxidative stress
12.5.3 Water stress.