Bioinformatics for agriculture: High-throughput approaches

✍ Scribed by Atul Kumar Upadhyay (editor), R Sowdhamini (editor), Virupaksh U. Patil (editor)

• Publisher: Springer
• Year: 2021
• Tongue: English
• Leaves: 160
• Edition: 1st ed. 2021
• Category: Library

✦ Synopsis

This book illustrates the importance and significance of bioinformatics in the field of agriculture. It first introduces the basic concepts of bioinformatics, such as homologous sequence and gene function analyses, determination of protein structures, and discusses machine learning applications for an in-depth understanding of the desired genes and proteins based on commonly used bioinformatics software and tools, e.g. BLAST, molecular modelling, molecular-docking and simulations, protein-protein and domain-domain interactions.

The book also describes recent advances in the high-throughput analysis of whole genome and transcriptome using next-generation sequencing platforms, and functional proteome studies. It also examines the role of computational biology in understanding and improving the nutrient quality and yield of crops. Lastly, the book explores a comprehensive list of applications of bioinformatics to improve plant yield, biomass, and health, and the challenges involved.

✦ Table of Contents

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