CiNii Books - Microsatellites : methods and protocols

Microsatellites or simple sequence repeats (SSRs) have become the markers of choice for a variety of molecular studies because of their versatility, operational flexibility, and lower cost than other marker systems. Microsatellites: Methods and Protocols brings together experts in the field to cover this significant area of research. Broken in to four convenient parts, this volume delves into classical and modern methods for the discovery and development of microsatellite markers, descriptions of amplification and visualization of SSRs, automated capillary sequencers that are widely used for fragment analysis, as well as a variety of methods for the analysis of data obtained by the use of microsatellites. Written for the highly successful Methods in Molecular Biology (TM) series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and invaluable, Microsatellites: Methods and Protocols aims at researchers that need detailed protocols for incorporating microsatellite markers into their projects and expert scientists looking to expand their knowledge of SSRs discovery, use, and analysis.

Table of Contents

1. Microsatellites: Evolution and Contribution Panagiotis Madesis, Ioannis Ganopoulos, and Athanasios Tsaftaris Part I: Discovery and Development of Microsatellites 2. Screening of Genomic Libraries Valdenice M. Novelli, Mariangela Cristofani-Yaly, Marines Bastianel, Dario A. Palmieri, and Marcos A. Machado 3. PCR-Based Identification of Microsatellite Arrays (PIMA) Heng-Sheng Lin and Song-Bin Chang 4. Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) Kaisa Rikalainen 5. Microsatellite DNA Capture from Enriched Libraries Elena G. Gonzalez and Rafael Zardoya 6. Next-Generation Sequencing for High-Throughput Molecular Ecology: A Step-by-Step Protocol for Targeted Multilocus Genotyping by Pyrosequencing Jonathan B. Puritz and Robert J. Toonen 7. Optimizing Selection of Microsatellite Loci from 454 Pyrosequencing Via Post-Sequencing Bioinformatic Analyses Iria Fernandez-Silva and Robert J. Toonen 8. Identification of DNA-Microsatellite Markers for the Characterization of Somatic Embryos in Quercus suber Arancha Gomez-Garay, M Angeles Bueno, and Beatriz Pintos Part II: Amplification and Visualization 9. Simple Sequence Repeats (SSR) Amplification Kundapura V. Ravishankar and Bommisetty Padmakar 10. Microsatellite Amplification in Plants: Optimization Procedure of Major PCR Components Sana Ghaffari and Nejib Hasnaoui 11. Development of a Multiplex PCR Assay for Characterization of Embryonic Stem Cells Rajarshi Pal, Murali Krishna Mamidi, Anjan Kumar Das, Mahendra Rao, and Ramesh Bhonde 12. Agarose Gel Electrophoresis and Polyacrylamide Gel Electrophoresis for Visualization of Single Sequence Repeats James Anderson, Drew Wright, and Khalid Meksem Part III: Automated Capillary Sequencers 13. Microsatellite Fragment Analysis Using the ABI Prism (R) 377 DNA Sequencer Mark A. Renshaw, Melissa Giresi, and J. Adams 14. Robust and Inexpensive SSR Markers Analyses Using LI-COR DNA Analyzer Maria del Rosario Herrera and Marc Ghislain 15. The Use of the MegaBACE for Sequencing and Genotype Analysis Pamela A. Burger 16. Analyzing Microsatellites Using the QIAxcel System Deborah A. Dean, Phillip A. Wadl, Denita Hadziabdic, Xinwang Wang, and Robert N. Trigiano Part IV: Scoring and Data Analysis 17. Microsatellite Analysis of Malaria Parasites Pamela Orjuela-Sanchez, Michelle C.C. Brandi, and Marcelo U. Ferreira 18. Informativeness of Microsatellite Markers M. Humberto Reyes-Valdes 19. Microsatellite Data Analysis for Population Genetics Kyung Seok Kim and Thomas W. Sappington 20. Molecular Mapping and Breeding with Microsatellite Markers David A. Lightfoot and Muhammad J. Iqbal

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Microsatellites : methods and protocols

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