About Book

A genome is the name for all genetic material that is characteristically present in one organism. So, all the different chromosomes of an organism together make up organism’s genome. Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genome is present in every individual cell of any living organism. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. Comparative genomics also provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved or common among species, as well as genes that give each organism its unique characteristics. This book highlights important matters in the branch of genomics, ranging from genomic constructs, DNA repair, genomic biomarkers, sequencing technologies, genus salmonella, functional genomics, fiber genomics, salinity tolerance and genetic improvement. This book gives a perspective on primary problems and latest progresses in science and technology in the field of genomics. Therefore, this book provides details to various topics, dealing mainly with their relation to comparative genomics and stresses on its particular uses in bio-medicine, agro-food technologies and zoo techniques. This book unfolds the innovative aspects of genomics that will be crucial for the holistic understanding of the subject matter. Coherent flow of topics, student-friendly language and extensive use of examples make this book an invaluable source of knowledge.

Preface............................................................................................................v

Chapter 1 Genetic Improvement of Sorghum for Biomass Traits Using Genomics Approaches...............................................................................1

Abstract...................................................................................................1

1. Introduction............................................................................................2

2. Genetics of sorghum biomass traits..................................................3

3. Genetic diversity evaluation using quantitative biomass traits of

sorghum..................................................................................................5

4. QTL mapping of quantitative traits in sorghum............................9

5. Association mapping for biomass traits in sorghum .................11

6. Conclusion ...........................................................................................13

Chapter 2 Abiotic Stress Tolerance in Rice (Oryza sativa L.): A Genomics Perspective of Salinity Tolerance..........................................................19

Abstract.................................................................................................19

1. Introduction ........................................................................................20

2. Effects of salinity on rice plant growth and development.........21

3. Molecular mapping approaches: types and methodology.........22

4. Achievements made through molecular mapping approaches

with respect to salinity tolerance in rice ......................................23

5. Future prospects and conclusions...................................................26

Chapter 3 Recent Developments in Fiber Genomics of Tetraploid Cotton Species.........................................................................................................34

Abstract.................................................................................................34

1. Introduction..........................................................................................35

2. Molecular markers..............................................................................36

3. Mapping for fiber-related traits in cotton......................................37

4. Genome-sequencing efforts in cotton..............................................41

5. Fiber-related transcriptome and gene expression studies in

cotton.....................................................................................................43

6. Characterization of specific genes for cotton fiber.......................47

7. Small RNA-mediated gene regulation studies in cotton ...........52

8. Functional genomics and genome-editing technologies in

regulation of fiber genes....................................................................54

9. Conclusion ...........................................................................................56

Acknowledgements.............................................................................57

Chapter 4 Insights from Comparative Genomics of the Genus Salmonella...72

Abstract.................................................................................................72

1. Introduction..........................................................................................73

2. Salmonella comparative genome analyses.....................................74

3. Conclusions..........................................................................................89

Acknowledgements.............................................................................90

Chapter 5 Integration of Next-generation Sequencing Technologies with

Comparative Genomics in Cereals.......................................................93

Abstract.................................................................................................93

1. Introduction..........................................................................................94

2. The need for high-throughput genome and transcriptome

sequencing............................................................................................95

3. Advances in sequencing technologies.............................................96

4. Application of next-generation sequencing in cereal

biotechnology.......................................................................................99

5. Comparative genomics in cereal crops.........................................100

6. Several examples of macro- and microcollinearity in cereal

crops.....................................................................................................102

7. Phenotypic commonality in cereals...............................................104

8. Outlook................................................................................................106

Acknowledgements...........................................................................106

Chapter 6 RNAi Towards Functional Genomics Studies.................................112

1. Introduction........................................................................................112

2. The molecular mechanism of RNA interference in eukaryote

system ................................................................................................114

3. Applications of RNAi in plant systems ......................................124

4. Application of RNAi in animal systems......................................129

5. Conclusions .......................................................................................136

Acknowledgement.............................................................................136

Chapter 7 Novel Tissue Types for the Development of Genomic Biomarkers................................................................................................149

1. Introduction........................................................................................149

2. Clinically important tissues ...........................................................151

3. Factors that impact genomic sample quality and utility ........163

4. Conclusion .........................................................................................166

5. Acknowledgements .........................................................................167

Chapter 8 DNA Repair in Pathogenic Eukaryotic Cells: Insights from Comparative Genomics of Parasitic Protozoan ..............................182

1. Introduction........................................................................................182

2. DNA repair machineries in pathogenic eukaryotic cells..........184

3. Functional categorization of Entamoeba histolytica DNA repair

genes....................................................................................................191

4. Duplicated genes: The case of rad3..............................................192

5. Molecular organization of the MNR complex............................194

6. Molecular organization of the RAD51 recombinase ................198

7. Conclusions .......................................................................................199

8. Acknowledgments ...........................................................................199

Chapter 9 Non-Viral Gene Therapy Vectors Carrying Genomic

Constructs ................................................................................................206

1. Introduction........................................................................................206

2. Advantages of use of genomic constructs in gene therapy.....208

3. Delivery of large DNA molecules ................................................211

4. Extra-chromosomal vectors ............................................................218

5. Vectors integrating at specific sites...............................................222

6. Methods for modification of large DNA molecules..................224

7. Towards gene therapy of cystic fibrosis using a genomic

construct..............................................................................................228

8. Conclusion .........................................................................................229

9. Acknowledgements .........................................................................230

Citation......................................................................................................243

Index...........................................................................................................245

About Author

Adam Yáng pursued his Ph.D. in Molecular Biology from Technological University, Melbourne. He has edited dozens of articles and research papers on structural and functional genomics, transcriptomics, proteomics, and bioinformatics. His researches focus on the genes and genomes, DNA, chromosomes, structural and biochemical mechanisms underlying transcriptional regulation and ubiquitin-mediated signaling. He is an Assistant Professor at a Community College, Manitoba. His work in the field of genetics and functional genomics is noted and acclaimed worldwide. Yáng is a regular contributor to scientific journals, and has also authored numerous articles and books in the field of molecular biology and genetics.