Next Generation Sequencing and Whole Genome Selection in Aquaculture

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 Castaño Sánchez, 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