Next-generation sequencing and bioinformatics for plant science / edited by Vijai Bhadauria.

Format:

Book

Contributor:

Bhadauria, Vijai, editor.

Language:

English

Subjects (All):

Plant biotechnology--Research--Methodology.

Plant biotechnology.

Plant genetics.

Physical Description:

1 online resource (204 pages)

Edition:

1st ed.

Place of Publication:

Norfolk, UK : Caister Academic Press, [2017]

Summary:

In this timely overview of the field, expert scientists review current developments in next-generation sequencing and bioinformatics and discuss their application in understanding and improving agronomic traits such as yield, drought tolerance and disease resistance. The up-to-date reviews cover genome assembly and annotation, omics technologies, structural variations, abnormal chromosome number, chromosomal rearrangement, copy number variation, mobile elements, sequencing of small RNA nucleotides and transcription factor binding sites. Specific topics include the evolution analysis of rice, maize, sorghum and orchids, fruit development and ripening, plant disease resistance, fusarium head blight and stripe rust resistance in wheat and rice, host defence and pathogen virulence, crop design with improved resistance, and biotic and abiotic stress tolerance. This is a useful review of current developments in next-generation sequencing and essential reading for plant geneticists and crop scientists.

Contents:

Intro

Contents

Current Books of Interest

Editorial

1 Status and Prospects of Next-generation Sequencing Technologies in Crop Plants

Introduction

Evolutions of DNA sequencing technology

NGS and plant genomics

Next-generation sequencing and plant transcriptome analysis

NGS and metagenomics of plant-microbe interaction

NGS applications in exome and captured sequencing

Next-genomics sequencing and molecular markers

Conclusion and future prospects of next-generation sequencing

2 Next-generation Sequencing Promoted the Release of Reference Genomes and Discovered Genome Evolution in Cereal Crops

Theories and platforms of NGS technologies

Bioinformatic tools for analysing NGS data

The pathways to assemble a reference genome in cereal crops

The genome evolution and germplasm resources in cereal crops

3 Advanced Applications of Next-generation Sequencing Technologies to Orchid Biology

Sequencing platforms

An overview of current of orchid genome project

Future perspective

4 Bioinformatics Resources for Plant Genomics: Opportunities and Bottlenecks in the -omics Era

The impact of plant genomics

From genome structure to function

Bioinformatics data resources for plant genomics

Bottlenecks and challenges

5 Applications of Bioinformatics to Plant Biotechnology

Gene expression and other omics resource databases

Applications of bioinformatics to enhance fruit development and ripening

Biotechnology and bioinformatics for plant breeding

Bioinformatics for studying stress resistance in plants

Bioinformatics approaches to study resistance to plant pathogens

Conclusions

6 Quantitative Genetics of Disease Resistance in Wheat

7 A Rice Genetic Improvement Boom by Next-generation Sequencing

Introduction.

The available methods for identification of functional genes

Mutant library for functional genomics in rice

Next-generation sequencing-based MutMap strategy for gene mutation

Genome-wide quantitative trait loci mapping

Genomic selection for breeding

Genome editing

Omics integration will push rice genetic improvement forward

8 Dual RNA-seq to Elucidate the Plant-Pathogen Duel

A dual approach in planta

It's all in the design

Weapons in plant-pathogen duels

Next generation of dual approaches

Glossary

9 Next-generation Sequencing Sheds New Light on Small RNAs in Plant Reproductive Development

Plant sRNA biogenesis and classification

NGS accelerating plant sRNAomics

SRAs profiling by NGS in plant reproductive development

Roles of sRNAs in flowering time

Roles of sRNAs in androecium development

Roles of sRNAs in gynoecium development

Roles of sRNAs in fruit/seed development

Conclusions and future perspectives

10 ChIP-seq: A Powerful Tool for Studying Protein-DNA Interactions in Plants

ChIP-seq workflow for plants

Applications of ChIP-seq in plants

Perspective

11 Cataloguing Plant Genome Structural Variations

Large-scale detection of structural variations in plants

Case studies: genetic basis for phenotype diversity contributed by plant SVs

New experimental and computational approaches to detect SVs

Future perspective.

Notes:

Description based on print version record.

ISBN:

1-910190-66-7