Next-generation Sequencing and Bioinformatics for Plant Science.
- 1st ed.
- 1 online resource (204 pages)
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 -- Introduction -- 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 -- Introduction -- 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 -- Introduction -- 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 -- Introduction -- 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 -- Introduction -- ChIP-seq workflow for plants -- Applications of ChIP-seq in plants -- Perspective -- 11 Cataloguing Plant Genome Structural Variations -- Introduction -- 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.
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.