Edited byKhalid Meksem and Günter Kahl

The Handbook ofPlant Mutation Screening

Mining of Natural and Induced Alleles

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Edited by

Khalid Meksem and Günter Kahl

The Handbook of

Plant Mutation Screening

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Edited byKhalid Meksem and Günter Kahl

The Handbook ofPlant Mutation Screening

Mining of Natural and Induced Alleles

The Editors

Prof. Dr. Khalid MeksemDepartment of Plant, Soil andAgricultural SystemsSouthern Illinois UniversityCarbondale, IL 62901-4415USA

Prof. Dr. Günter KahlGenXPro GmbHResearch Innovation Center (FIZ) BiotechnologyAltenhöferallee 360438 Frankfurt am MainGermany

All books published by Wiley-VCH are carefullyproduced. Nevertheless, authors, editors, andpublisher do not warrant the information containedin these books, including this book, to be free oferrors. Readers are advised to keep in mind thatstatements, data, illustrations, procedural details orother items may inadvertently be inaccurate.

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# 2010 WILEY-VCH Verlag GmbH & Co. KGaA,Weinheim

All rights reserved (including those of translation intoother languages). No part of this book may bereproduced in any form – by photoprinting,microfilm, or any other means – nor transmitted ortranslated into a machine language without writtenpermission from the publishers. Registered names,trademarks, etc. used in this book, even when notspecifically marked as such, are not to be consideredunprotected by law.

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Printed in the Federal Republic of GermanyPrinted on acid-free paper

ISBN: 978-3-527-32604-4

To my families, without their support, I would have been somewhere else!

Khalid Meksem

I appreciate the atmosphere and innovative work of the GenXPro GmbH

thinktank in the Frankfurt Innovation Center Biotechnology.

Günter Kahl

Contents

Preface XVList of Contributors XVIIList of Abbreviations XXIII

Part I Induced Mutations 1

1 Physically Induced Mutation: Ion Beam Mutagenesis 3Shimpei Magori, Atsushi Tanaka, and Masayoshi Kawaguchi

1.1 Introduction 31.1.1 LET 41.1.2 Mutational Effects of Ion Beams on Plants 51.2 Methods and Protocols 71.2.1 Ion Beam Irradiation 81.2.2 Dose Determination for Ion Beam Irradiation 91.2.3 Plant Radiation Sensitivity 101.2.4 Population Size of the M1 Generation 111.3 Applications 111.3.1 Ion Beams for Forward Genetics 121.3.2 Ion Beams for Plant Breeding 131.3.3 Limitations of Ion Beams 131.4 Perspectives 14

References 14

2 Ds Transposon Mutant Lines for Saturation Mutagenesis of theArabidopsis genome 17Takashi Kuromori and Takashi Hirayama

2.1 Introduction 172.2 Methods and Protocols 182.3 Applications 262.4 Perspectives 28

References 28

VII

3 Use of Mutants from T-DNA Insertion Populations Generated byHigh-Throughput Screening 31Ralf Stracke, Gunnar Huep, and Bernd Weisshaar

3.1 Introduction 313.2 Methods and Protocols 343.2.1 Plant Material and Growth Conditions 343.2.2 Plasmid Design 343.2.3 Agrobacterium Culture 353.2.4 Plant Transformation and T1 Seed Harvesting 353.2.5 Sulfadiazine Selection of Transgenic T1 Plants 363.2.6 DNA Preparation from Sulfadiazine-Selected

T1 Plants 363.2.7 FST Production 373.2.8 Sequencing and Computational Sequence Analysis 403.2.9 Genetic Analysis of T-DNA Insertions 413.2.10 DNA-Preparation for Confirmation of FST Predicted

Insertion Sites 413.2.11 Confirmation PCR 423.2.12 Sequencing and Computational Sequence Analysis 443.2.13 Seed Donation 453.2.14 Identification of Homozygous Mutants 463.3 Applications and Considerations for Work with T-DNA

Insertion Mutants 473.3.1 Unconfirmed T-DNA Insertion Lines 483.3.2 Use of Selectable Marker 483.3.3 Aberrant T-DNA Insertions 483.3.4 Multiple T-DNA Insertions 493.3.5 T-DNA-Induced Dominant Effects 493.3.6 Allelic Series of Mutants 493.3.7 Lethal Knockout Mutants 503.3.8 Search for Knockout Phenotype 503.3.9 Handling of Non-Single-Copy Genes 503.4 Perspectives 51

References 52

4 Making Mutations is an Active Process: Methods to ExamineDNA Polymerase Errors 55Kristin A. Eckert and Erin E. Gestl

4.1 Introduction 554.2 Methods and Protocols 564.2.1 Overview of the Genetic Assay 564.2.2 Overview of the Biochemical Assay for TLS 674.3 Applications 734.3.1 General Features of the In Vitro Genetic Assay 734.3.2 Polymerase Accuracy in the Absence of DNA Damage 74

VIII Contents

4.3.3 Mutational Processing of Alkylation Damage by DNAPolymerases 75

4.3.4 DNA Lesion Discrimination Mechanisms 754.4 Perspectives 78

References 79

5 Tnt1 Induced Mutations in Medicago: Characterizationand Applications 83Pascal Ratet, Jiangqi Wen, Viviane Cosson, Million Tadege,and Kirankumar S. Mysore

5.1 Introduction 835.2 Methods and Protocols 845.2.1 Identification of Tnt1 Insertion Sites 845.2.2 Reverse Genetic Approach 945.2.2.1 FST Sequencing 945.2.2.2 Screening DNA Pools 945.3 Applications 955.3.1 Line with a Mutant Phenotype – No FSTs Identified 965.3.2 Line with a Mutant Phenotype and FSTs Already Identified 965.3.3 FST Sequence in the Tnt1 Database Matches a Gene of

Interest – No Mutant Phenotype is Described in that Line 975.3.4 Have a Gene to Work With – No FST or Mutant Phenotype 975.4 Perspectives 98

References 98

Part II Mutation Discovery 101

6 Mutation Discovery with the Illumina Genome Analyzer 103Abizar Lakdawalla and Gary P. Schroth

6.1 Introduction 1036.1.1 Overview of the Illumina Genome Analyzer Sequencing Process 1036.1.2 Resequencing Strategies 1046.1.2.1 Resequencing Whole Genomes 1056.1.2.2 Targeted Genome Selection 1056.1.2.3 Sequencing Transcriptomes 1076.2 Methods and Protocols 1076.3 Applications 1166.4 Perspectives 118

References 118

7 Chemical Methods for Mutation Detection: The Chemical Cleavageof Mismatch Method 121Tania Tabone, Georgina Sallmann, and Richard G.H. Cotton

7.1 Introduction 1217.2 Methods and Protocols 125

Contents IX

7.3 Applications 1277.4 Perspectives 127

References 128

8 Mutation Detection in Plants by EnzymaticMismatch Cleavage 131Bradley J. Till

8.1 Introduction 1318.2 Methods and Protocols 1368.3 Applications 1438.4 Perspectives 144

References 145

9 Mutation Scanning and Genotyping in Plants by High-ResolutionDNA Melting 149Jason 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 1499.2 Methods and Protocols 1509.2.1 LightScanner Instrument 1519.2.2 LightScanner for Variant Scanning 1519.2.3 LightScanner for LunaprobeTM (Unlabeled Probe)

Genotyping 1569.3 Applications 1599.3.1 Sensitivity and Specificity for SNP Heterozygote

Detection 1599.3.2 Variant Scanning by High-Resolution Melting 1609.3.3 Bell Pepper Multiplex Genotyping with Two Unlabeled

Probes 1619.3.4 Potato Tetraploid Genotyping including Allele Dosage using an

Unlabeled Probe 1619.4 Perspectives 162

References 163

10 In Silico Methods: Mutation Detection Software for SangerSequencing, Genome and Fragment Analysis 167Kevin LeVan, Teresa Snyder-Leiby, C.S. Jonathan Liu, and Ni Shouyong

10.1 Introduction 16710.2 Mutation Detection with Sanger Sequencing using

Mutation Surveyor 16810.3 Mutation Detection with NextGENeTM and Next-Generation

Sequence Technologies 17510.4 Mutation Detection with DNA Fragments Using GeneMarker1 18010.5 Perspectives 182

References 182

X Contents

Part III High-Throughput Screening Methods 185

11 Use of TILLING for Reverse and Forward Genetics of Rice 187Sujay 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 18711.2 Methods and Protocols 18811.3 Perspectives 196

References 197

12 Sequencing-Based Screening of Mutations and NaturalVariation using the KeyPointTM Technology 199Diana Rigola and Michiel J.T. van Eijk

12.1 Introduction 19912.2 Methods and Protocols 20212.3 Applications 20612.3.1 EMS Mutation Screening and Validation 20612.3.2 Natural Polymorphism Screening and Validation 20812.4 Perspectives 211

References 211

Part IV Applications in Plant Breeding 215

13 Natural and Induced Mutants of Barley: Single NucleotidePolymorphisms in Genes Important for Breeding 217William T.B. Thomas, Brian P. Forster, and Robbie Waugh

13.1 Brief Review of Barley Mutants 21713.2 Applications in Breeding 22113.3 Single Nucleotide Polymorphism Genotyping to Identify Candidate

Genes for Mutants 22313.3.1 Resources 22313.3.2 Case Study: Two/Six-Row Locus in Barley 22413.3.3 Case Study: Graphical Genotyping of a Disease Resistance Locus 22713.3.4 General Protocol for using High-Throughput Genotyping to

Localize Mutants 227References 229

14 Association Mapping for the Exploration of Genetic Diversityand Identification of Useful Loci for Plant Breeding 231André Beló and Stanley D. Luck

14.1 Introduction 23114.2 Methods and Protocols 23314.2.1 Population for Association Mapping 233

Contents XI

14.2.2 Genotyping 23414.2.3 Phenotyping 23414.2.4 Statistical Procedures 23514.3 Applications 23814.3.1 QTL Mapping versus Association Mapping 24014.3.2 Limitations 24114.4 Perspectives 242

References 243

15 Using Mutations in Corn Breeding Programs 247Anastasia L. Bodnar and M. Paul Scott

15.1 Introduction 24715.1.1 Factors to Consider Before Starting a Breeding Program 24815.1.2 Alternatives to Breeding 24915.2 Methods and Protocols 24915.2.1 Backcross Breeding 24915.2.2 Forward Breeding 25215.2.3 Supplementary Protocols 25315.2.3.1 Determining How Many Seeds to Plant 25315.2.3.2 Working with Recessive Mutations 25515.2.3.3 Intermating 25615.2.4 Complication: Pleiotropic Effects 25715.3 Applications 25815.3.1 Breeding with a Natural Mutation: QPM 25815.3.2 Breeding with a Transgene: GFP 25915.4 Perspectives 25915.4.1 Marker-Assisted Selection 25915.4.1.1 Marker-Assisted Selection in Backcross Breeding 25915.4.1.2 Marker-Assisted Selection in Forward Breeding 26015.4.2 Doubled Haploids 260

References 261

16 Gene Targeting as a Precise Tool for Plant Mutagenesis 263Oliver Zobell and Bernd Reiss

16.1 Introduction 26316.2 Methods and Protocols 26616.3 Applications 27916.4 Perspectives 280

References 280

Part V Emerging Technologies 287

17 True Single Molecule Sequencing (tSMS)TM by Synthesis 289Scott Jenkins and Avak Kahvejian

17.1 Introduction 28917.2 Methods, Protocols, and Technical Principles 291

XII Contents

17.2.1 Single Molecule Sequencing Technical Challenges and Solutions 29117.2.2 Flow Cell Surface Architecture 29417.2.3 Cyclic SBS 29517.2.4 Optical Imaging of Growing Strands 29717.2.5 Mechanical Operation 30017.2.6 System Components 30017.2.7 Data Analysis 30117.3 Applications 30117.3.1 Single Molecule DGE and RNA-Seq 30117.3.1.1 DNA Sequencing Applications 30317.3.2 Single Molecule Sequencing Techniques under Development 30317.4 Perspectives 304

References 306

18 High-Throughput Sequencing by Hybridization 307Sten Linnarsson 307

18.1 Introduction 30718.2 Methods and Protocol 30818.3 Discussion 31618.4 Applications 316

References 317

19 DNA Sequencing-by-Synthesis using Novel Nucleotide Analogs 319Lin Yu, Jia Guo, Ning Xu, Zengmin Li, and Jingyue Ju

19.1 Introduction 31919.2 General Methodology for DNA SBS 32119.3 Four-Color DNA SBS using CF-NRTs 32319.3.1 Overview 32319.3.2 Design, Synthesis, and Characterization of CF-NRTs 32419.3.3 DNA Chip Construction 32619.3.4 Four-Color SBS using CF-NRTs 32619.4 Hybrid DNA SBS using NRTs and CF-ddNTPs 32919.4.1 Overview 32919.4.2 Design and Synthesis of NRTs and CF-ddNTPs 33119.4.3 Four-Color Hybrid DNA SBS 33319.5 Perspectives 335

References 336

20 Emerging Technologies: Nanopore Sequencing forMutation Detection 339Ryan Rollings and Jiali Li

20.1 Introduction 33920.1.1 Nanopore Detection Principle 34020.1.2 Important Parameters and Nanopore Sensing Resolution 34120.1.3 Biological Nanopore History 34120.1.4 Solid-State Nanopore History 343

Contents XIII

20.1.5 Nanopore Promise 34320.2 Current Developments in Nanopore Sequencing 34420.2.1 Improving Biological Nanopores 34420.2.2 Improving Solid-State Nanopores 34520.2.3 Slowing Translocation and Trapping 34720.2.4 Modification of the DNA 34720.2.5 Resequencing Applications 34920.3 Work Done in Our Lab 35020.4 Perspectives 351

References 352

Glossary 355

Index 427

XIV Contents

Preface

The DNA double helix, as we know it since the seminal paper ofWatson and Crick in1953 (Watson, J.D. and Crick, F.H.C. A structure for deoxyribose nucleic acid.Nature 171: 737–738, 1953), probably a special variant of a primordial RNA, hasbeen (and still is) under heavy environmental pressure. It is exposed to chemical andphysical agents such as drugs and radiation that altogether have altered nucleic acidssince their existence. Therefore, DNA is subject to continuous changes in basecomposition and structure, generally called mutations (Latin mutare: to change).These changes not only shaped the DNA molecule, but eliminated or introducednew information, which was, is, and will be fundamental for evolution. Certainly,evolution would not have been possible without mutation(s). The immense pheno-typic variations, which surprise the alert observer, rest upon genetic variation (i.e.,mutations). Although large subsets of mutations are beneficial for the survival andevolution of a species, certain mutations can have a detrimental impact on indivi-duals – they may indeed lead to a reduced fitness and diseases down to death. Theseambivalent aspects of mutations shape life on Earth.

Mutations range in size from single base exchanges, single base deletions, smalldeletions, inversions, insertions, and duplications of two or a couple of bases more,to large changes of several kilobases to megabases and chromosome aberrationssuch as supernumerary chromosomes, missing chromosomes, translocated partsfrom one chromosome to another one (or others, and vice versa), and aberrantphysical appearance of chromosomes (e.g., in various forms of leukemia or in thecase of ring chromosomes). This listing is by no means a complete description of allpossiblemutations, but outlines the variety of potential changes at themolecular andchromosomal level. Keeping in mind that before the discovery of DNA by thepioneer Friedrich Miescher around 1869 in the nuclei of leukocytes from pus onsurgical bandages (at that time coined nuclein), mutations were already known invarious organisms, but could, of course, not be related to DNA. For example, albinosin plants, animals, and humans were considered exotic and unexplainable erraticforms of life.

Today we know of many chromosomal, genomic, and genic mutations, and asmore and more genomes are sequenced and resequenced, more and more muta-

XV

tions are discovered and will serve to identify genetic differences between indivi-duals or species, or the causes underlying the 6000–8000 inherited disorders inhumans. It is for this reason that the detection of mutations became an importantdiscipline in biology and medicine, and therefore the techniques of discovery anddiagnostics of these changes are rapidly evolving.This book witnesses the importance of mutations. The detailed description of

mutation screening technologies by renowned experts in the field gives a flavor ofthe past and present state of mutation sciences, but also a sense of what is emergingin the area of biophysics, biocomputing, molecular biology, and genomics.

Carbondale (USA) Khalid MeksemFrankfurt am Main (Germany) Günter KahlDecember 2009

XVI Preface

List of Contributors

XVII

Akira AbeIwate Agricultural Research Center20-1 Narita, KitakamiIwate 024-0003Japan

André BelóUniversity of Delaware & DuPontCrop GeneticsDepartment of Plant and Soil Sciences152 Townsend HallNewark, NJ 19716-2103USA

Anastasia L. BodnarIowa State UniversityAgronomy DepartmentG426 Agronomy HallAmes, IA 50011USA

Viviane CossonCNRS, Institut des Sciences du Végétal1 Avenue de la Terrasse91198 Gif sur Yvette CedexFrance

Richard G.H. CottonGenomic Disorders Research CentreLevel 2, 161 Barry StreetCarlton South, Victoria 3053Australia

and

University of MelbourneDepartment of MedicineMelbourne, Victoria 3010Australia

David De KoeyerAgriculture and Agri-Food CanadaPotato Research Centre850 Lincoln Road, FrederictonNew Brunswick E3B 4Z7Canada

Kristin A. EckertPennsylvania State University Collegeof MedicineDepartment of Pathology andBiochemistry & Molecular Biology500 University DriveHershey, PA 17033USA

Brian P. ForsterBiohybrids International LtdPO Box 4211Reading RG6 5FYUK

Takahiro FujibeIwate University21 Century COE3-18-8 Ueda, MoriokaIwate 020-8550Japan

Erin E. GestlWest Chester UniversityDepartment of Biology750N. Church StreetWest Chester, PA 19383USA

Jia GuoColumbia University Collegeof Physicians and SurgeonsColumbia Genome Center1150 St. Nicholas AvenueNew York, NY 10032USA

Takashi HirayamaRIKEN, Membrane Molecular BiologyLaboratory1-7-22 Suehiro, TsurumiYokohama 230-0045Japan

Gunnar HuepUniversität BielefeldFakultät für Biologie/GenomforschungUniversitätsstrasse 2733615 BielefeldGermany

Robert L. JarretUS Department of Agriculture/Agricultural Research ServicePlant Genetic Resources Unit1109 Experiment StreetGriffin, GA 30224USA

Scott JenkinsHelicos BioSciences CorporationOne Kendall Square, Building 700Cambridge, MA 02139USA

Jingyue JuColumbia University Collegeof Physicians and SurgeonsColumbia Genome Center1150 St. Nicholas AvenueNew York, NY 10032USA

Avak KahvejianHelicos BioSciences CorporationOne Kendall Square, Building 700Cambridge, MA 02139USA

Hiroyuki KanzakiIwate Biotechnology Research Centre22-174-4 Narita, KitakamiIwate 024-0003Japan

Masayoshi KawaguchiUniversity of TokyoDepartment of Biological SciencesGraduate School of Science7-3-1 Hongo, Bunkyo-kuTokyo 113-0033Japan

XVIII List of Contributors

Yutaka KiuchiIwate Agricultural Research Center20-1 Narita, KitakamiIwate 024-0003Japan

Takashi KuromoriRIKEN Plant Science CenterGene Discovery Research Group1-7-22 Suehiro, TsurumiYokohama 230-0045Japan

Abizar LakdawallaIllumina, Inc.Sequencing Applications25861 Industrial BoulevardHayward, CA 94545USA

Kevin LeVanSoftGenetics LLCSuite 235, 200 Innovation BoulevardState College, PA 16803USA

Jiali LiUniversity of ArkansasDepartment of Physics825 West Dickson StreetFayetteville, AR 72701USA

Zengmin LiColumbia University Collegeof Physicians and SurgeonsColumbia Genome Center1150 St. Nicholas AvenueNew York, NY 10032USA

Sten LinnarssonKarolinska InstitutetDepartment of Medical Biochemistryand BiophysicsLaboratory for Molecular NeurobiologyScheeles väg 117177 StockholmSweden

C.S. Jonathan LiuSoftGenetics LLCSuite 235, 200 Innovation BoulevardState College, PA 16803USA

Stanley D. LuckUniversity of Delaware & DuPont CropGeneticsDepartment of Plant and Soil Sciences152 Townsend HallNewark, NJ 19716-2103USA

Shimpei MagoriUniversity of TokyoDepartment of Biological SciencesGraduate School of Science7-3-1 Hongo, Bunkyo-kuTokyo 113-0033Japan

Hideo MatsumuraIwate Biotechnology Research Centre22-174-4 Narita, KitakamiIwate 024-0003Japan

Jason T. McKinneyIdaho TechnologyGenotyping Applications Division390 Wakara WaySalt Lake City, UT 84108USA

List of Contributors XIX

Chikako MitsuokaIwate Biotechnology Research Centre22-174-4 Narita, KitakamiIwate 024-0003Japan

Kirankumar S. MysoreThe Samuel Roberts Noble FoundationPlant Biology Division2510 Sam Noble ParkwayArdmore, OK 73401USA

Lyle M. NayIdaho TechnologyGenotyping Applications Division390 Wakara WaySalt Lake City, UT 84108USA

Yudai OkuyamaIwate Biotechnology Research Centre22-174-4 Narita, KitakamiIwate 024-0003Japan

Muluneh OliIwate Biotechnology Research Centre22-174-4 Narita, KitakamiIwate 024-0003Japan

Robert A. PalaisUniversity of UtahDepartment of Mathematics155S. 1400E.Salt Lake City, UT 84112USA

Arunita RakshitNRC on Plant BiotechnologyPusa CampusNew Delhi 110 012India

Sujay RakshitNational Research Centre on SorghumRajendranagarHyderabad 500 030India

Pascal RatetCNRS, Institut des Sciences du Végétal1 Avenue de la Terrasse91198 Gif sur Yvette CedexFrance

Gudrun H. ReedUniversity of UtahDepartment of Pathology50N. Medical DriveSalt Lake City, UT 84109USA

Bernd ReissMax-Planck-Institut fürZüchtungsforschungUnabhängige Forschergruppe DNARekombination der PflanzenCarl-von-Linne-Weg 1050829 KölnGermany

Diana RigolaKeygene NVAgro Business Park 90PO Box 2166700 AE WageningenThe Netherlands

Ryan RollingsUniversity of ArkansasDepartment of Physics825 West Dickson StreetFayetteville, AR 72701USA

XX List of Contributors

Georgina SallmannMonash UniversityDepartment of MedicineCentral and Eastern Clinical School85 Commercial RoadMelbourne, Victoria 3004Australia

Gary P. SchrothIllumina, Inc.Gene Expression R&D25861 Industrial BoulevardHayward, CA 94545USA

M. Paul ScottIowa State UniversityAgronomy Department1407 Agronomy HallAmes, IA 50011USA

Matt ShentonIwate Biotechnology Research Centre22-174-4 Narita, KitakamiIwate 024-0003Japan

Ni ShouyongSoftGenetics LLCSuite 235, 200 Innovation BoulevardState College, PA 16803USA

Teresa Snyder-LeibySoftGenetics LLCSuite 235, 200 Innovation BoulevardState College, PA 16803USA

Ralf StrackeUniversität BielefeldFakultät für Biologie/GenomforschungUniversitätsstrasse 2733615 BielefeldGermany

Tania TaboneRoyal Melbourne HospitalLudwig Institute for Cancer ResearchCentre for Medical ResearchRoyal ParadeParkville, Victoria 3050Australia

Million TadegeThe Samuel Roberts Noble FoundationPlant Biology Division2510 Sam Noble ParkwayArdmore, OK 73401USA

Atsushi TanakaJapan Atomic Energy AgencyRadiation-Applied Biology DivisionQuantum Beam Science Directorate1233 Watanuki-machi, TakasakiGunma 370-1292Japan

Ryohei TerauchiIwate Biotechnology Research Centre22-174-4 Narita, KitakamiIwate 024-0003Japan

William T.B. ThomasScottish Crop Research InstituteGenetics ProgramErrol RoadDundee DD2 5DAUK

List of Contributors XXI

Bradley J. TillPlant Breeding UnitFAO/IAEA Agricultural &Biotechnology LaboratoryInternational Atomic Energy AgencyWagramer Strasse 51400 ViennaAustria

Hiroe UtsushiIwate Biotechnology Research CentreDepartment/Division??22-174-4 Narita, KitakamiIwate 024-0003Japan

Michiel J.T. van EijkKeygene NVAgro Business Park 90PO Box 2166700 AE WageningenThe Netherlands

Mikeal WallIdaho TechnologyGenotyping Applications Division390 Wakara WaySalt Lake City, UT 84108USA

Robbie WaughScottish Crop Research InstituteGenetics ProgramErrol RoadDundee DD2 5DAUK

Bernd WeisshaarUniversität BielefeldFakultät für Biologie/GenomforschungUniversitätsstrasse 2733615 BielefeldGermany

Jiangqi WenThe Samuel Roberts Noble FoundationPlant Biology Division2510 Sam Noble ParkwayArdmore, OK 73401USA

Carl T. WittwerUniversity of UtahDepartment of Pathology50N. Medical DriveSalt Lake City, UT 84109USA

Ning XuColumbia University Collegeof Physicians and SurgeonsColumbia Genome Center1150 St. Nicholas AvenueNew York, NY 10032USA

Kentaro YoshidaIwate Biotechnology Research Centre22-174-4 Narita, KitakamiIwate 024-0003Japan

Lin YuColumbia University College ofPhysicians and SurgeonsColumbia Genome Center1150 St. Nicholas AvenueNew York, NY 10032USA

Oliver ZobellUniversity of OsnabrückBotanyBarbarastrasse 1149076 OsnabrückGermany

XXII List of Contributors

Abbreviations

2,4-D 2,4-dichlorophenoxyacetic acidAc ActivatorAFLP amplified fragment length polymorphismANOVA ANalysis Of VarianceAOD altered organ developmentAVF azimuthally varying fieldBAC bacterial artificial chromosomeBaYMV barley yellow mosaic virusBOPA barley oligo pooled arrayBSA bovine serum albuminCarb carbenicillinCaMV cauliflower mosaic virus[CCM] chemical cleavage of mismatchCJE celery juice extractChIP chromatin immunoprecipitationCF cleavable fluorescentCm chloramphenicolCTAB cetyltrimethylammonium bromideDGAT diacylglycerol acyltransferaseDGE digital gene expressionDHPLC denaturing high-performance liquid chromatographyDMSO dimethylsulfoxideDs DissociatorDSB double-strand breakDSBs double-strand breaksdsDNA double-stranded DNAEELS electron energy loss spectroscopyEMS ethylmethane sulfonateERA-PG European Research Area in Plant GenomicsEST expressed sequence tag5-FAM 5-Carboxyfluorescein6-FAM 6-Carboxyfluorescein5(6)-FAM 5-(and -6)-Carboxyfluorescein

XXIII

FDR false discovery rateFST flanking sequence tagFUdR 5-fluoro-20-deoxyuridineGD gapped duplexGFP green fluorescent proteinGS genome sequencerGSPs gene-specific primersGWA genome-wide associationHEX hexachlorocarboxyfluoresceinHIMAC Heavy Ion Medical Accelerator in ChibaHSV-tk herpes simplex virus type 1 thymidine kinaseI inverseIAA indole-3-acetic acidIndels insertion/deletionsINRA Institut National de la Recherche AgronomiqueIRD infrared dyeJAEA Japan Atomic Energy AgencyKF polymerase Klenow fragment of E. coli DNA polymerase ILB left borderLD linkage disequilibriumLD50 median lethal doseLET linear energy transferLOH loss of heterozygosityLTR long terminal repeatMALDI-TOF MS matrix-assisted laser desorption/ionization-time of flight

mass spectrometryMCMC Markov chain Monte Carlom6G O6-methylguanineMNU N-methyl-N-nitrosoureaMS mutation screeningMSI microsatellite instabilityNA numerical apertureNAM naphthalene acetamideNCBI National Center for Biotechnology InformationNIRS National Institute of Radiological SciencesNRTs nucleotide reversible terminatorsNVS natural variation screeningOC open circleORF open reading framePAGE polyacrylamide gel electrophoresisPCA principal component analysisPCR polymerase chain reactionPEB phenol extraction bufferPEG polyethylene glycolPMSF phenylmethylsulfonate

XXIV Abbreviations

PTP picotiterplatePVP polyvinylpyrrolidoneQPM quality protein maizeQTLs quantitative trait lociRB right borderRIBF RI beam factorySBH sequencing-by-hybridizationSBS sequencing-by-synthesisSDS sodium dodecyl sulfateSNP single nucleotide polymorphismSSC sodium chloride/sodium citrateSSC standard sodium citratessDNA single-stranded DNASSR short sequence repeatSTM scanning tunneling microscopySTRs short tandem repeatsTAIL thermal asymmetric interlacedTCEP tris(2-carboxy-ethyl) phosphineTD transposon displayTEM transmission electron microscopyTIARA Takasaki Ion Accelerators for Advanced Radiation ApplicationTILLING targeting induced local lesions in genomesTIRFM total internal reflection fluorescence microscopyTLS translesion synthesisTm melting temperaturetSMS� True Single Molecule SequencingUTR untranslated regionVB Vogel–BonnerW-MAST Wakasa Wan Energy Research Center Multi-purpose Acceler-

ator with Synchrotron and TandemYAC yeast artificial chromosome

Abbreviations XXV

Part IInduced Mutations