Next Generation Sequencing and Whole Genome Selection in Aquaculture comprehensively covers the current state of research in whole genome selection and applies these discoveries to the aquaculture industry specifically. The text begins with a thorough review of Single Nucleotide Polymorphism and transitions into topics such as next generation sequencing, EST data mining, SNP quality assessment, and whole genome selection principles. Ending with a discussion of the technology's specific applications to the industry, this text will be a valuable reference for those involved in all aspects of aquaculture research.

Table of Contents

Preface vii List of Contributors ix Chapter 1. Genomic Variations and Marker Technologies for Genome-based Selection 3 Zhanjiang (John) Liu Chapter 2. Copy Number Variations 21 Jianguo Lu and Zhanjiang (John) Liu Chapter 3. Next Generation DNA Sequencing Technologies and Applications 35 Qingshu Meng and Jun Yu Chapter 4. Library Construction for Next Generation Sequencing 57 Huseyin Kucuktas and Zhanjiang (John) Liu Chapter 5. SNP Discovery through De Novo Deep Sequencing Using the Next Generation of DNA Sequencers 69 Geoffrey C. Waldbieser Chapter 6. SNP Discovery through EST Data Mining 91 Shaolin Wang and Zhanjiang (John) Liu Chapter 7. SNP Quality Assessment 109 Shaolin Wang, Hong Liu, and Zhanjiang (John) Liu Chapter 8. SNP Genotyping Platforms 123 Eric Peatman Chapter 9. SNP Analysis with Duplicated Fish Genomes: Differentiation of SNPs, Paralogous Sequence Variants, and Multisite Variants 133 Cecilia Castano Sanchez, Yniv Palti, and Caird Rexroad Chapter 10. Genomic Selection for Aquaculture: Principles and Procedures 151 Anna K. Sonesson Chapter 11. Genomic Selection in Aquaculture: Methods and Practical Considerations 165 Ashok Ragavendran and William M. Muir Chapter 12. Comparison of Index Selection, BLUP, MAS, and Whole Genome Selection 185 Zhenmin Bao Index 219 Color plates appear between pages 108 and 109.

About the Author

Zhanjiang (John) Liu is a Distinguished Alumni Professor, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, and Associate Dean for Research, College of Agriculture at Auburn University. He also held appointments to 11 international universities such as Northwestern Agricultural University in China and the Chinese Academy of Fisheries Sciences. Dr. Liu has served as the North American Editor for Marine Biotechnology since 2004, Associate Editor for BMC Genomics and BMC Genetics, and sits on the editorial board for Aquaculture, Animal Biotechnolgy and Reviews in Aquaculture. He published Aquaculture Genome Technologies with Blackwell in 2007, and lectures both nationally and internationally on various topics in fish molecular genetics and biotechnology.