Preface.
Foreword by James Womack.
Chapter 1. Concept of genome and genomics: Zhanjiang Liu.
Part 1: Marking Genomes.
Chapter 2. Restriction fragment length polymorphism (RFLP): Zhanjiang Liu.
Chapter 3. Randomly amplified polymorphic DNA (RAPD): Zhanjiang Liu.
Chapter 4. Amplified fragment length polymorphism (AFLP): Zhanjiang Liu.
Chapter 5. Microsatellite markers and assessment of marker utility: Zhanjiang Liu.
Chapter 6. Single nucleotide polymorphism (SNP): Zhanjiang Liu.
Chapter 7. Allozyme and mitochondrial markers: Huseyin Kucuktas and Zhanjiang Liu.
Chapter 8. Individual-based genotype methods in aquaculture: Pierre Duchesne and Louis Bernatchez.
Chapter 9. Application of DNA markers for population genetic analysis: Eric M. Hallerman, Paul J. Grobler, and Jess W. Jones.
Part 2: Mapping Genomes.
Chapter 10. Linkage mapping in aquaculture species.
Roy G. Danzmann and Karim Gharbi.
Chapter 11.Detection and analysis of quantitative trait loci (QTLs) for economic traits in aquatic species: Abraham Korol, Andrey Shirak, Avner Cnaani, Eric Hallerman.
Chapter 12. Marker Assisted Selection for Aquaculture Species: Max F. Rothschild and Anatoly Ruvinsky.
Chapter 13. Construction of large-insert bacterial clone libraries and their applications: Limei He, Chunguang Du, Yaning Li, Chantel Scheuring, and Hong-Bin Zhang.
Chapter 14. Bacterial artificial chromosome libraries and BAC-based physical mapping of aquaculture genomes: William S. Davidson.
Chapter 15. Physical characterization of aquaculture genomes through BAC end sequencing: Peng Xu, Shaolin Wang, and Zhanjiang Liu.
Chapter 16. Genomescape: characterizing the repeat structure of the genome: Zhanjiang Liu.
Chapter 17. Genomic analyses using fluorescence in situ hybridization: Ximing Guo, Yongping Wang, and Zhe Xu.
Chapter 18. Radiation hybrid mapping in aquatic species: Caird E. Rexroad III.
Chapter 19. Comparative Genomics and Positional Cloning: Bo-Young Lee and Thomas D. Kocher.
Part 3. Analysis of Genome Expression and Function.
Chapter 20. Transcriptome characterization through the analysis of expressed sequence: Zhanjiang Liu.
Chapter 21. Microarray fundamentals: Basic principles and application in aquaculture: Eric Peatman, and Zhanjiang Liu.
Chapter 22. Salmonid DNA microarrays and other tools for functional genomics research: Matthew L. Rise, Kristian R. von Schalburg, Glenn A. Cooper, and Ben F. Koop.
Chapter 23. Computational challenges for the analysis of large datasets related to aquatic environmental genomics: Gregory W. Warr, Jonas S. Almeida, and Robert W. Chapman.
Chapter 24. Functional genomics: Perry B. Hackett and Karl J. Clark.
Part 4. Preparing for Genome Sequencing.
Chapter 25. DNA sequencing technologies: Zhanjiang Liu.
Chapter 26. Sequencing the genome: Zhanjiang Liu.
Chapter 27. Bioinformatics: Lei Liu.
Part 5. Dealing with the Daunting Genomes of Aquaculture Species.
Chapter 28. Dealing with duplicated genomes of teleosts: Alan Christoffels.
Chapter 29. Bivalve genomics: complications, challenges, and future perspectives: Jason P. Curole and Dennis Hedgecock
