Genome Profiling for Genetic Marker Discovery

Preface Part I. Microarray-assisted DNA marker discovery (6) Genetic discovery by genomics GeneChip microarray for expression and genetic analysis Gene Tanimoto, Affymetrix Inc. Sample preparation for genome profiling Charles Chilcott and Tong Zhu, Syngenta Biotechnology, Inc., Research Triangle Park, NC 27709 SFP detection from genome profiles Justin Borevitz, University of Chicago, Department of Ecology and Evolution, Chicago, IL 60637, USA Single feature polymorphism detection in rice Henry Nguyen, Division of Plant Sciences, University of Missouri-Columbia, Columbia, Missouri, USA Genome resequencing by GeneChip microarrays High resolution SFP detection by tiling arrays David Gresham, Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA Part II. High density marker applications (5) ExTreme array mapping of quantitative trait loci David J. Wolyn, Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2W1, Canada Ultra-high density mapping by genome profiling Christopher Basten, Syngenta Biotechnology, Inc., Research Triangle Park, NC 27709, USA Microarray assisted positional gene cloning Ji-Ming Gong and Julian I. Schroeder, Division of Biological Sciences, Cell and Developmental Biology Section and Center for Molecular Genetics, University of California at San Diego, La Jolla, CA 92093, USA Elucidating genetic diversity with oligonucleotide arrays Elizabeth Winzeler, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA Single-feature polymorphism data for inference in population genetics Simon Tavare Molecular and Computational Biology Program, University of Southern California, CA 90089, USA Part III. Combine genetic and functional information (9) SFP detection from complex transcriptome Robbie Waugh, Scottish Crop Research Institute, Genome Dynamics, Invergowrie, Dundee, DD2 5DA, Scotland, UK Detection and applications of gene expression markers Marilyn West and Richard Michelmore, Department of Plant Sciences and The Genome Center, University of California-Davis, Davis, CA 95616, USA Detecting single-feature polymorphisms by robustified projection pursuit Xinping Cui, Department of Statistics, University of California Riverside, CA 92521, USA Statistical analysis for SFP identification from RNA data Weibo Xie and Qifa Zhang, Huazhong Agricultural University, Wuhan, China Microarray experimental design strategies for genetical genomics studies Guilherme J. M. Rosa, Department of Animal Science and Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824 Statistical methods for expression quantitative trait loci (eQTL) mapping C. M. Kendziorski, Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53703, USA A Bayesian clustering method for analysis of all expressed transcripts and markers jointly in a single model Shizhong Xu, Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA eQTL Viewer: visualizing how sequence variation affects genome-wide transcription Zhao-Bang Zeng, Bioinformatics Research Center, Department of Statistics, and Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA e-QTL case study: Dissect genetic regulation of gene expression in Arabidopsis shoot development Stephen Howell, Plant Sciences Institute, Iowa State University, Ames, IA 50011, USA Part IV. Beyond model systems (4) Rapid and cost-effective polymorphism identification using restriction site associated DNA (RAD) markers Eric Johnson, Institute for Molecular Biology, University of Oregon, Eugene, Oregon 97403 Diversity Arrays Technology (DArT) for whole-genome profiling Andrzej Kilian, Center for the Application of Molecular Biology to International Agriculture and Diversity Arrays Technology Pty. Ltd., Canberra, ACT 2601, Australia Whole genome SNP discovery by pyrosequencing Donald R McCarty, Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA Complexity Reduction of Polymorphic Sequences (CRoPS) technology for SNP marker discovery Michiel J.T. van Eijk, Keygene N.V., Agro Business Park 90, 6700 AE Wageningen, The Netherlands