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