The Handbook Of Plant Mutation Screening Mining Of Natural And Induced Alleles

Induced mutagenesis is a common and promising method for screening for new crops with improved properties. This title introduces the different methods and then focuses on the screening, detection and analysis of the novel mutations. Written by a global team of authors the book is an indispensable tool for all scientists working on crop breeding in industry and academia.

Gunter Kahl is Professor for Plant Molecular Biology at Frankfurt University, Germany. After his Ph.D. in plant biochemistry, he spent two years with Joe Varner, Michigan State University, East Lansing, USA, and James Bonner, California Institute of Technology, Pasadena, USA. Main research areas are
Plant Genome analysis
Transcriptome analyses in eukaryotic organisms
Mutation detection.
Gunter Kahl cooperates with a series of research institutions throughout Europe, in Japan, the USA, Israel, India, and Latin America. He served in expert missions for IAEA, FAO and UNESCO in many countries, and Chief Scientific Officer in GenXPro Gmbh, an SME located at the Frankfurt Innovation Center Biotechnology.
Khalid Meksem is Professor of Genome Biotechnology at Southern Illinois University, USA. He graduated from the University of Casablanca, Morocco, and joined the Plant Molecular and Khalid Meksem gained his doctorate in Botany, Biochemistry and Genetics at the University of Cologne in collaboration with the Max-Planck-Institute, Germany.
His research interest covers both, structural and functional genomics, and his long time area of interest is the molecular dissection of plant disease resistance mechanisms to nematodes and fungi. Khalid Meksem is serving as Associate Editor of the International Journal of Plant Genomics, and as reviewer for a number of international scientific journals as well as for several granting agencies.

Preface.
List of Contributors.
List of Abbreviations.
Part I Induced Mutations.
1 Physically Induced Mutation: Ion Beam Mutagenesis (Shimpei Magori, Atsushi Tanaka, and Masayoshi Kawaguchi).
1.1 Introduction.
1.2 Methods and Protocols.
1.3 Applications.
1.4 Perspectives.
References.
2 Ds Transposon Mutant Lines for Saturation Mutagenesis of the Arabidopsis genome (Takashi Kuromori and Takashi Hirayama).
2.1 Introduction.
2.2 Methods and Protocols.
2.3 Applications.
2.4 Perspectives.
References.
3 Use of Mutants from T-DNA Insertion Populations Generated by High-Throughput Screening (Ralf Stracke, Gunnar Huep, and Bernd Weisshaar).
3.1 Introduction.
3.2 Methods and Protocols.
3.3 Applications and Considerations for Work with T-DNA Insertion Mutants.
3.4 Perspectives.
References.
4 Making Mutations is an Active Process: Methods to Examine DNA Polymerase Errors (Kristin A. Eckert and Erin E. Gestl).
4.1 Introduction.
4.2 Methods and Protocols.
4.3 Applications.
4.4 Perspectives.
References.
5 Tnt1 Induced Mutations in Medicago: Characterization and Applications (Pascal Ratet, Jiangqi Wen, Viviane Cosson, Million Tadege, and Kirankumar S. Mysore).
5.1 Introduction.
5.2 Methods and Protocols.
5.3 Applications.
5.4 Perspectives.
References.
Part II Mutation Discovery.
6 Mutation Discovery with the Illumina Genome Analyzer (Abizar Lakdawalla and Gary P. Schroth).
6.1 Introduction.
6.2 Methods and Protocols.
6.3 Applications.
6.4 Perspectives.
References.
7 Chemical Methods for Mutation Detection: The Chemical Cleavage of Mismatch Method (Tania Tabone, Georgina Sallmann, and Richard G.H. Cotton).
7.1 Introduction.
7.2 Methods and Protocols.
7.3 Applications.
7.4 Perspectives.
References.
8 Mutation Detection in Plants by Enzymatic Mismatch Cleavage (Bradley J. Till).
8.1 Introduction.
8.2 Methods and Protocols.
8.3 Applications.
8.4 Perspectives.
References.
9 Mutation Scanning and Genotyping in Plants by High-Resolution DNA Melting (Jason T. McKinney, Lyle M. Nay, David De Koeyer, Gudrun H. Reed, Mikeal Wall, Robert A. Palais, Robert L. Jarret, and Carl T. Wittwer).
9.1 Introduction.
9.2 Methods and Protocols.
9.3 Applications.
9.4 Perspectives.
References.
10 In Silico Methods: Mutation Detection Software for Sanger Sequencing, Genome and Fragment Analysis (Kevin LeVan, Teresa Snyder-Leiby, C.S. Jonathan Liu, and Ni Shouyong).
10.1 Introduction.
10.2 Mutation Detection with Sanger Sequencing using Mutation Surveyor.
10.3 Mutation Detection with NextGENe and Next-Generation Sequence Technologies.
10.4 Mutation Detection with DNA Fragments Using GeneMarker®.
10.5 Perspectives.
References.
Part III High-Throughput Screening Methods.
11 Use of TILLING for Reverse and Forward Genetics of Rice (Sujay Rakshit, Hiroyuki Kanzaki, Hideo Matsumura, Arunita Rakshit, Takahiro Fujibe, Yudai Okuyama, Kentaro Yoshida, Muluneh Oli, Matt Shenton, Hiroe Utsushi, Chikako Mitsuoka, Akira Abe, Yutaka Kiuchi, and Ryohei Terauchi).
11.1 Introduction.
11.2 Methods and Protocols.
11.3 Perspectives.
References.
12 Sequencing-Based Screening of Mutations and Natural Variation using the KeyPoint™ Technology (Diana Rigola and Michiel J.T. van Eijk).
12.1 Introduction.
12.2 Methods and Protocols.
12.3 Applications.
12.4 Perspectives.
References.
Part IV Applications in Plant Breeding.
13 Natural and Induced Mutants of Barley: Single Nucleotide Polymorphisms in Genes Important for Breeding (William T.B. Thomas, Brian P. Forster, and Robbie Waugh).
13.1 Brief Review of Barley Mutants.
13.2 Applications in Breeding.
13.3 Single Nucleotide Polymorphism Genotyping to Identify Candidate Genes for Mutants.
References.
14 Association Mapping for the Exploration of Genetic Diversity and Identification of Useful Loci for Plant Breeding (André Beló and Stanley D. Luck).
14.1 Introduction.
14.2 Methods and Protocols.
14.3 Applications.
14.4 Perspectives.
References.
15 Using Mutations in Corn Breeding Programs (Anastasia L. Bodnar and M. Paul Scott).
15.1 Introduction.
15.2 Methods and Protocols.
15.3 Applications.
15.4 Perspectives.
References.
16 Gene Targeting as a Precise Tool for Plant Mutagenesis (Oliver Zobell and Bernd Reiss).
16.1 Introduction.
16.2 Methods and Protocols.
16.3 Applications.
16.4 Perspectives.
References.
Part V Emerging Technologies.
17 True Single Molecule Sequencing (tSMS) by Synthesis (Scott Jenkins and Avak Kahvejian).
17.1 Introduction.
17.2 Methods, Protocols, and Technical Principles.
17.3 Applications.
17.4 Perspectives.
References.
18 High-Throughput Sequencing by Hybridization (Sten Linnarsson).
18.1 Introduction.
18.2 Methods and Protocol.
18.3 Discussion.
18.4 Applications.
References.
19 DNA Sequencing-by-Synthesis using Novel Nucleotide Analogs (Lin Yu, Jia Guo, Ning Xu, Zengmin Li, and Jingyue Ju).
19.1 Introduction.
19.2 General Methodology for DNA SBS.
19.3 Four-Color DNA SBS using CF-NRTs.
19.4 Hybrid DNA SBS using NRTs and CF-ddNTPs.
19.5 Perspectives.
References.
20 Emerging Technologies: Nanopore Sequencing for Mutation Detection (Ryan Rollings and Jiali Li).
20.1 Introduction.
20.2 Current Developments in Nanopore Sequencing.
20.3 Work Done in Our Lab.
20.4 Perspectives.
References.
Glossary.
Index.