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PLANT GENOTYPING II SNP Technology This page intentionally left blank PLANT GENOTYPING II SNP Technology Edited by Robert J. Henry Centre for Plant Conservation Genetics Southern Cross University Lismore, New South Wales, Australia CABI is a trading name of CAB International CABI Head Office CABI North American Office Nosworthy Way 875 Massachusetts Avenue Wallingford 7th Floor Oxfordshire OX10 8DE Cambridge, Massachusetts 02139 UK USA Tel: +44 (0)1491 832111 Tel: +1 617 395 4056 Fax: +44 (0)1491 833508 Fax: +1 617 354 6875 E-mail: [email protected] E-mail: [email protected] Web site: www.cabi.org ©CAB International 2008. All rights reserved. No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photo- copying, recording or otherwise, without the prior permission of the copyright owners. A catalogue record for this book is available from the British Library, London, UK. Library of Congress Cataloging-in-Publication Data Plant genotyping II : SNP technology / edited by Robert J. Henry. p. cm. Includes bibliographical references and index. ISBN 978-1-84593-382-1 (alk. paper) 1. Plant genome mapping. 2. Genetic polymorphisms. I. Henry, Robert J. QK981.45.P565 2008 581.3'5--dc22 2007041585 ISBN: 978 1 84593 382 1 Typeset by SPi, Pondicherry, India. Printed and bound in the UK by Biddles Ltd, King’s Lynn. Contents Contributors vii Preface ix 1 SNP Discovery in Plants 1 K.J. Edward, R.L. Poole and G.L. Barker 2 SNPs and Their Use in Maize 30 A. Rafalski and S. Tingey 3 Rare SNP Discovery with Endonucleases 44 M.J. Cross 4 Sequence Polymorphisms in the Flanking Regions of 68 Microsatellite Markers G. Ablett and R.J. Henry 5 SNP Discovery by Ecotilling Using Capillary 78 Electrophoresis F. Eliott, G. Cordeiro, P.C. Bundock and R.J. Henry 6 Genotyping by Allele-specifi c PCR 88 D.L.E. Waters, P.C. Bundock and R.J. Henry 7 The MassARRAY System for Plant Genomics 98 D. Irwin 8 Mutation Screening 114 L. Izquierdo v vi Contents 9 Nanotechnology: The Future of Cost-effective 133 Plant Genotyping J.A. Pattemore, M. Trau and R.J. Henry 10 Functionally Associated Molecular Genetic Markers 154 for Temperate Pasture Plant Improvement J.W. Forster, N.O.I. Cogan, M.P. Dobrowolski, M.G. Francki, G.C. Spangenberg and K.F. Smith 11 Genotyping for Rice Eating Qualities 187 L.M.T. Bradbury, D.L.E. Waters and R.J. Henry 12 Towards Universal Loci for Plant Genotyping 195 T. Pacey-Miller 13 DNA Banks as a Resource for SNP Genotyping 207 N. Rice, S. Kasem and R.J. Henry 14 DNA Extraction from Plant Tissue 219 S. Kasem, N. Rice and R.J. Henry 15 Future Prospects for Plant Genotyping 272 R.J. Henry Index 281 Contributors G. Ablett, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] G.L. Barker, University of Bristol, School of Biological Sciences, Woodland Road, Bristol BS8 1UG, UK. E-mail: Gary [email protected] L.M.E. Bradbury, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: l.bradbury.10@ scu.edu.au P.C. Bundock, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] N.O.I. Cogan, Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria, 3083, Australia. E-mail: [email protected] G. Cordeiro, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] M.J. Cross, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] M.P. Dobrowolski, Department of Primary Industries, Biosciences Research Division, Hamilton Centre, Hamilton, Victoria 3300, Australia and Molecular Plant Breeding Cooperative Research Centre, Australia. E-mail: mark. [email protected] K.J. Edward, University of Bristol, School of Biological Sciences Woodland Road, Bristol BS8 1UG, UK. E-mail: [email protected] F. Eliott, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] J.W. Forster, Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria, 3083, Australia. E-mail: [email protected] vii viii Contributors M.G. Francki, Department of Agriculture and Food Western Australia, 3 Baron- Hay Court, South Perth, Western Australia 6151 and State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Western Australia 6983, Australia and Molecular Plant Breeding Cooperative Research Centre, Australia. E-mail: [email protected] R.J. Henry, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] D. Irwin, Sequenom Herston, Queensland, Australia. E-mail: [email protected] L. Izquierdo, Griffith University, Lismore, New South Wales, Australia. E-mail: [email protected] S. Kasem, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] T. Pacey-Miller, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: toni.pacey-miller@ scu.edu.au J.A. Pattemore, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] R.L. Poole, University of Bristol, School of Biological Sciences Woodland Road, Bristol BS8 1UG, UK. E-mail: [email protected] A. Rafalski, DuPont Crop Genetics Research, Experimental Station E353, Route 141 and Henry Clay Road, Wilmington, Delaware. E-mail: antoni.rafalski@cgr. dupont.com N. Rice, Australian Plant DNA Bank, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] K.F. Smith, Department of Primary Industries, Biosciences Research Division, Hamilton Centre, Hamilton, Victoria 3300, Australia and Molecular Plant Breeding Cooperative Research Centre, Australia. E-mail: kevin.f.smith@dpi. vic.gov.au G.C. Spangenberg, Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria, 3083, Australia. E-mail: german.spangenberg@dpi. vic.gov.au S. Tingey, DuPont Crop Genetics Research, Experimental Station E353, Route 141 and Henry Clay Road, Wilmington, Delaware. E-mail: Scott.V.Tingey@USA. dupont.com M. Trau, Centre for Nanotechnology and Biomaterials University of Queensland, St Lucia, Queensland, Australia. E-mail: [email protected] D.L.E. Waters, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, New South Wales, Australia. E-mail: [email protected] Preface Plant Genotyping: The DNA Fingerprinting of Plants was published in 2001. The book was based upon a workshop held at Southern Cross University in 2000 with additional contributions from some authors who did not attend the work- shop. The techniques available for plant DNA analysis have advanced consid- erably in the time since the original volume was published. Plant Genotyping II: SNP Technology aims to describe some of the important recent developments in this field. This book is based upon a second workshop held recently to review progress in this area. Recent developments focus on high- throughput methods and generally target single nucleotide polymorphism (SNP) discovery and analysis. R.J. Henry Centre for Plant Conservation Genetics Southern Cross University ix This page intentionally left blank 1 SNP Discovery in Plants K.J. EDWARD, R.L. POOLE AND G.L. BARKER Introduction Marker-assisted selection (MAS) using DNA-based molecular markers is now used by virtually all commercial plant and animal breeding companies (reviewed in Henry, 2001). Molecular markers can be used to identify both useful genotypes for inclusion in breeding programmes and interesting prog- eny for further study. However, the cost of MAS is a limitation when com- pared to phenotypically driven conventional breeding. In plants microsatellite markers are currently the most popular type of marker system; however, their development is resource-intensive and they are difficult to multiplex. Recently there has been considerable interest in the development of single nucleotide polymorphism (SNP pronounced SNiP)-based marker systems. More recently the use of SNPs has been fuelled by the explosion in the number of expressed sequence tags (ESTs) available in the various databases and this trend is set to continue for the foreseeable future (Varshney et al., 2004). SNPs are the most common form of sequence variation between indi- viduals within a species (reviewed in Brookes, 1999). New SNPs are continu- ally arising within every cell of an organism but most are removed through the action of the enzymatic process known as mismatch repair (MMR), and hence SNPs which become fixed within a germ line and a population are simply those mutations which have escaped the repair process (reviewed in Kunkel and Erie, 2005). As mutations are the source of all SNPs, the number of SNPs within a specific population reflects the forward and reverse muta- tion rates, the number of generations that separate the population from its closest relative and the number of independent progenitors of that popula- tion. The number and distribution of SNPs are also influenced by the past and present selection pressures applied to the population including any bot- tlenecks through which it has passed. Hence, while mutations probably occur at broadly similar frequencies in most species, the number of SNPs present ©CAB International 2008. Plant Genotyping II: SNP Technology (ed. R.J. Henry) 1 2 K.J. Edward et al. within a population will often show considerable variation, and it should come as no surprise to any plant breeder that different plant species will have different SNP frequencies and that these frequencies will vary within different regions of the genome.