Bioinformatics for agriculture: High-throughput approaches

Contents
Introduction to the Concepts of Agr-Informatics
	Introduction
	Some Basic Biological Science
		Scale and Time
		Cell
		DNA and Chromosome
		Central Dogma
	Databases
		Types of Biological Databases
			Primary Databases
			Secondary Databases
			Special Databases
	Sequence Alignment
	What Is the Need of Sequence Alignment?
		Alignment Methods
		Online Resources to Perform Global and Local Alignment
		Substitution Matrices
		What Is the Need of Creating Substitution Matrices?
		Types of Substitution Matrices
		Differences Between PAM and BLOSUM Matrices
	Multiple Sequence Alignment
	Phylogenetic Tree
		How to Construct a Phylogenetic Tree?
		UPGMA Method
	References
Genomics Assisted Breeding for Sustainable Agriculture: Meeting the Challenge of Global Food Security
	Introduction
	Genomics Advancements
		Genome Sequencing
		Transcriptome Sequencing and Expression Studies
		Bioinformatics
		Resequencing and SNP Genotyping
		Construction of High-Density Genetic Maps
	Supremacy of GAB
	Technology Involved in GAB
		Marker Assisted Selection (MAS)
		Advanced Backcross QTLs (AB-QTLs)
		Marker Assisted Recurrent Selection (MARS)
		Association Mapping
		Genomic Selection (GS)
		Multiparent Advanced Generation Intercross (MAGIC)
		Targeting Induced Local Lesions IN Genomes (TILLING) and Ecotype-Targeting Induced Local Lesions IN Genomes (Eco-TILING)
	Successful Applications of GAB
		Marker Assisted Selection (MAS)
		AB-QTLs
		Association Mapping
		Genomic Selection
		MAGIC
		TILLING and Eco-TILLING
	Future Prospects
	Concluding Remarks
	References
Role of Computational Biology in Sustainable Development of Agriculture
	Introduction
	Computational Biology and Agriculture
	Bioinformatics Tools Employed in Agriculture
	Conclusions
	References
Big Data and Its Analytics in Agriculture
	Introduction to Big Data
	Transcriptome Data Analysis in Agriculture
	Proteomic Data Analysis in Agriculture
	Databases: Big Data in Agriculture
	Genomics in Agriculture
	Metabolomics in Agriculture
	Big Data Analytics
	Future Scope of Big Data in Agricultural Practices
	Conclusion
	References
The Distinction of Omics in Amelioration of Food Crops Nutritional Value
	Introduction
	Genomics
	Transcriptomics
	Proteomics
	Metabolomics
	Omics Intervention in Sugarcane
	Omics Intervention in Common Bean
	Omics Intervention in Finger Millet
	Omics Intervention in Rice
	Conclusion
	References
Immunoinformatics in Plant-Fungal Disease Management
	Introduction
	Fungal-Plant Interaction
		Fungal Invasion Strategies
	Functional Genomics and Proteomics Tools
		Sequence Retrieving Tools
		Proteomics Tools
		Gene Ontology and Data Retrieval Software´s
		MicroRNA and Transcriptomics Tools or Databases
	Plant-Fungal Management
		Adhesin Prediction Software´s for Plant-Fungal Pathogens
		Secondary Metabolites Prediction and Its Role in the Pathogenesis
		Plant and Fungal Secretomics
		Databases for Integrated Pest Management
	Conclusions
	References
Agri/Bioinformatics: Shaping Next-Generation Agriculture
	Agri/Bio Informatics
	Advancement in Sequencing Approaches Accelerated Bioinformatics
	Illumina Sequencing
	Nanopore DNA Sequencing
	Omic Approach for Crop Improvement
	Genomics
	Transcriptomic
	Proteomics
	Metabolomics
	Agri/Bioinformatics Shaping Future Agriculture
	References
Digital Marketing: A Sustainable Way to Thrive in Competition of Agriculture Marketing
	Introduction
	Agriculture Marketing
	Digitalization of Agriculture Marketing
	Enablers of Digital Marketing of Agricultural Products
	Advantages of Digitalization
	Challenges and Future Course of Action
	Conclusion
	References
Food Allergens and Related Computational Biology Approaches: A Requisite for a Healthy Life
	Introduction
	Identification of Food Allergens
	Impact of Food Processing on Allergenicity Potential of Food Allergens
	Allergen Proteins in Various Pfam (Protein Domain) and Structural Families
	Computational Methods to Predict Food Allergens
	Conclusion
	References