Aquaculture Genome Technologies

Zhanjiang (John) Liu is a Distinguished Alumni Professor, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, and Director, Aquatic Genomics Unit at Auburn University.

"A good and comprehensive overview of the principles of genomic tools … .[It] will be an important reference for quite some time, and I welcome its arrival." (Aquaculture International, August 2008) “Aquaculture Genome Technologies is the quintessential What, When, Why and How-to book for aquatic genome research…an important addition to any science classroom, laboratory or office.”(Aquatic Association of Canada Newsletter) "This most impressive text tells very clearly and comprehensively how and why." (Ausmarine)

• 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