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Next Generation Sequencing and Whole Genome Selection in Aquaculture



Next Generation Sequencing and Whole Genome Selection in Aquaculture

Zhanjiang (John) Liu

ISBN: 978-0-813-80637-2 March 2011 Wiley-Blackwell 232 Pages


Recent developments in DNA marker technologies, in particular the emergence of Single Nucleotide Polymorphism (SNP) discovery, have rendered some of the traditional methods of genetic research outdated. 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 SNP 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.

Special Features: 

  • Unique linking of SNP technologies, next generation sequencing technologies, and whole genome selection in the context of aquaculture research
  • Thorough review of Single Nucleotide Polymorphism and existing research
  • 8-page color plate section featuring detailed illustrations

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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