DNA SEQUENCING – METHODS AND APPLICATIONS

1 DNA SEQUENCING METHODS AND APPLICATIONS Edited by Anjana Munshi DNA SEQUENCING METHODS and APPLICATIONS Edited by Anjana Munshi Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications.

2 After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications.

3 Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, METHODS or ideas contained in the book. Publishing Process Manager Bojan Rafaj Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published April, 2012 Printed in Croatia A free online edition of this book is available at Additional hard copies can be obtained from DNA SEQUENCING METHODS and APPLICATIONS , Edited by Anjana Munshi p.

4 Cm. ISBN 978-953-51-0564-0 Contents Preface VII Section 1 METHODS of DNA SEQUENCING 1 Chapter 1 DNA Representation 3 Bharti Rajendra Kumar Chapter 2 Hot Start 7-Deaza-dGTP Improves Sanger Dideoxy SEQUENCING Data of GC-Rich Targets 15 Sabrina Shore, Elena Hidalgo Ashrafi and Natasha Paul Section 2 APPLICATIONS of DNA SEQUENCING 33 Chapter 3 SEQUENCING Technologies and Their Use in Plant Biotechnology and Breeding 35 Victor Llaca Chapter 4 DNA SEQUENCING and Crop Protection 61 Rosemarie Tedeschi Chapter 5 Improvement of Farm Animal Breeding by DNA SEQUENCING 85 G.

5 Darshan Raj Chapter 6 The Input of DNA Sequences to Animal Systematics: Rodents as Study Cases 103 Laurent Granjon and Claudine Montgelard Chapter 7 The Application of Pooled DNA SEQUENCING in Disease Association Study 141 Chang-Yun Lin and Tao Wang Chapter 8 Nucleic Acid Aptamers as Molecular Tags for Omics Analyses Involving SEQUENCING 157 Masayasu Kuwahara and Naoki Sugimoto Preface More than a quarter of a century earlier the story of DNA SEQUENCING began when Sanger s studies of insulin first demonstrated the importance of sequence in biological

6 Macromolecules. Although two different DNA SEQUENCING METHODS have been developed during the same period, Sanger s dideoxy chain-termination SEQUENCING method has became the method of choice over the Maxam Gilbert method. The complete sequence of oX-174 was published in 1977 and then revised slightly in the following year by dideoxy method. It demonstrated that the DNA sequence could tell a fascinating story based upon the interpretation of the sequence in terms of the genetic code.

7 Recently several next generation high throughput DNA SEQUENCING techniques have arrived on the scene and are opening fascinating opportunities in the fields of biology and medicine. This book, DNA SEQUENCING - METHODS and APPLICATIONS illustrates METHODS of DNA SEQUENCING and its application in plant, animal and medical sciences. This book has two distinct sections. The first one includes 2 chapters devoted to the DNA SEQUENCING METHODS and the second one includes 6 chapters focusing on various APPLICATIONS of this technology.

8 The content of the articles presented in the book is guided by the knowledge and experience of the contributing authors. This book is intended to serve as an important resource and review to the researchers in the field of DNA SEQUENCING . An overview of DNA SEQUENCING technologies right from the Sanger s method to the next generation high throughput DNA SEQUENCING techniques including massively parallel signature SEQUENCING , polony SEQUENCING , pyrosequencing, Illumina SEQUENCING , SOLiD SEQUENCING etc.

9 Has been presented in chapter 1. Chapter 2 reviews how Hot Start-7-deaza-dGTP improves Sanger s dideoxy SEQUENCING data of GC rich template DNA. Chapter 3 demonstrates how the use of SEQUENCING METHODS in combination with strategies in breeding and molecular genetic modifications has contributed to our knowledge of plant genetics and remarkable increase in agricultural productivity. Chapter 4 provides information on APPLICATIONS of DNA SEQUENCING in crop protection.

10 This chapter highlights the perspectives for new sustainable and environmental friendly strategies for controlling pests and diseases of crop plants. VIII Preface Chapter 5 has discussed the application of DNA SEQUENCING in improving the breeding strategies of farm animals. The development of molecular markers using DNA SEQUENCING serves as an underlying tool, for geneticists and breeders to create desirable farm animals. Chapter 6 aims at showing how DNA SEQUENCING technology has reboosted rodent systematics leading to a much better supported classification of this order.