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, Mariângela Cristofani-Yaly, Marinês 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 Gómez-Garay, Ma Ángeles 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-Sánchez, Michelle C.C. Brandi, and Marcelo U. Ferreira

18. Informativeness of Microsatellite Markers

M. Humberto Reyes-Valdés

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