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Applications and Potentials of Marker Assisted Selection (MAS) in Plant Breeding Sarah Brumlop and Maria R. Finckh Applications and potentials of marker assisted selection (MAS) in plant breeding BfN-Skripten 298 2011 Applications and potentials of marker assisted selection (MAS) in plant breeding Final report of the F+E project “Applications and Potentials of Smart Breeding” (FKZ 350 889 0020) On behalf of the Federal Agency for Nature Conservation December 2010 Sarah Brumlop Maria R. Finckh Cover picture: A diverse wheat composite cross population in the F8. Such materials could be used for the development of modern land races using MAS to select for homogeneity in important traits while maintaining overall population diversity (M. Finckh). Authors’ address: Sarah Brumlop Faculty of Organic Agricultural Sciences Prof. Dr. Maria R. Finckh Group Ecological Plant Protection University of Kassel Nordbahnhofstr. 1 a Tel: x-49-5542-98 15 62 D-37213 Witzenhausen Fax: x-49-5542-98 15 64 Germany e-mail: [email protected] http://www.wiz.uni-kassel.de/phytomed/ Scientific Supervision at BfN: Dr. Wolfram Reichenbecher Division II 3.3 “GMO-Regulation, Biosafety” Final report of the F+E project “Applications and Potentials of Smart Breeding” (FKZ 350 889 0020) on behalf of the Federal Agency for Nature Conservation. The Project was completed in December 2010. This publication is included in the literature database “DNL-online” (www.dnl-online.de). The BfN-Skripten are not available in book trade but can be downloaded in a pdf version from the internet at: http://www.bfn.de/0502_skripten.html Publisher: Bundesamt für Naturschutz (BfN) Federal Agency for Nature Conservation Konstantinstrasse 110 53179 Bonn, Germany URL: http://www.bfn.de All rights reserved by BfN. The publisher takes no guarantee for correctness, details and completeness of statements and views in this report as well as no guarantee for respecting private rights of third parties. Views expressed in the papers published in this issue of BfN-Skripten are those of the authors and do not necessarily represent those of the publisher. No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording or by any information storage and retrieval system without written permission from the copyright owner. Printed by the printing office of the Federal Ministry of Environment, Nature Conservation and Nuclear Safety. Printed on 100% recycled paper. ISBN 978-3-89624-033-0 Bonn, Germany 2011 Contents 1 Introduction ........................................................................................................ 1 1.1 The history of MAS ....................................................................................... 3 1.2 Introduction of marker technologies .............................................................. 4 1.2.1 Restriction fragment length polymorphism (RFLP) markers .................. 5 1.2.2 Randomly-amplified polymorphic DNA (RAPD) markers..................... 5 1.2.3 Amplified fragment length polymorphism (AFLP®) markers................ 6 1.2.4 Microsatellite markers ............................................................................. 7 1.2.5 Single nucleotide polymorphism (SNP) markers .................................... 7 1.2.6 Other marker systems .............................................................................. 8 1.3 QTL-identification ......................................................................................... 9 1.3.1 Advanced backcross AB-QTL analysis................................................. 11 2 Genomic selection ............................................................................................. 11 2.1 Array mapping ............................................................................................. 12 2.2 Association mapping.................................................................................... 15 2.3 EcoTILLING................................................................................................ 16 3 Advantages of marker-assisted breeding........................................................ 18 3.1 MAS versus phenotypic selection................................................................ 19 4 Application of markers in breeding programs............................................... 20 4.1 Breeding strategies in marker-assisted breeding.......................................... 21 4.1.1 Selection from breeding lines/populations ............................................ 21 4.1.2 Marker-assisted backcrossing (MABC) ................................................ 22 4.1.3 Marker-assisted recurrent selection (MARS) ........................................ 23 4.1.4 Pyramiding............................................................................................. 23 4.2 Application of markers in germplasm storage, evaluation, and use............. 24 4.2.1 Application of markers in germplasm storage....................................... 25 4.2.2 Application of markers in germplasm evaluation/characterization ....... 25 4.2.3 Application of markers in germplasm use/introgression ....................... 27 4.3 Application of markers in variety distinction and plant cultivar registration.................................................................................................... 29 i 4.4 Breeding objectives and examples for marker application in breeding ....... 30 4.4.1 Breeding objectives ............................................................................... 30 4.4.2 Examples for marker application........................................................... 31 4.4.3 Wheat..................................................................................................... 37 4.4.4 Barley..................................................................................................... 38 4.4.5 Maize ..................................................................................................... 39 4.4.6 Rice........................................................................................................ 39 4.4.7 Potato..................................................................................................... 40 4.4.8 Tomato................................................................................................... 41 4.4.9 Soybean ................................................................................................. 41 4.4.10 Beans and other vegetables.................................................................... 42 4.4.11 Fruits...................................................................................................... 43 5 The discrepancy between marker development and marker application in breeding programs ....................................................................................... 43 5.1 Marker technology development versus conversion into practical applications .................................................................................................. 45 5.2 Publication aspects....................................................................................... 45 5.3 Lack of conversion of publications into practical applications.................... 46 5.4 GxE interactions and effects of genetic background.................................... 46 5.5 Economic aspects of marker application...................................................... 47 5.6 Intellectual property rights (IPR) in marker application .............................. 48 5.7 Influences of private and public sector breeding.......................................... 50 6 Guided expert interviews and workshop with experts .................................. 51 6.1 Results of expert interviews and workshop.................................................. 52 7 MAS and transgenic crops............................................................................... 63 8 Agricultural biodiversity, molecular markers, and legal matters................ 65 8.1 Genetic uniformity in agricultural crops ...................................................... 66 8.1.1 Consequences of genetic uniformity ..................................................... 67 8.1.2 Biodiversity as a buffer against catastrophic losses............................... 67 8.2 The use of markers for the assessment of diversity in modern crop varieties ........................................................................................................ 68 8.2.1 Potential effects of MAS on the diversity of modern crop varieties...... 69 ii 8.3 Diversification strategies.............................................................................. 69 8.3.1 Increasing inter-varietal diversity.......................................................... 69 8.3.2 Increasing intra-specific and intra-varietal diversity ............................. 73 8.3.2.1 Variety mixtures............................................................................. 73 8.3.2.2 Multilines ....................................................................................... 73 8.3.2.3 Evolutionary breeding for diversity and participatory breeding .... 74 8.4 Seed systems, seed legislation and biodiversity........................................... 75 8.4.1 Requirements for variety registration .................................................... 76 8.4.2 Intellectual Property Rights, Plant Breeders’ Rights, and Patents......... 78 8.4.3 Legal aspects of evolutionary breeding and PPB approaches ............... 80 8.4.4
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