Crop Breeding: Methods and Protocols

260 Pages·2014·7.959 MB·English

by  Delphine Fleury, Ryan Whitford (eds.)

Methods in
Molecular Biology 1145
Delphine Fleury
Ryan Whitford Editors
Crop Breeding
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
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Crop Breeding
Methods and Protocols
Edited by
Delphine Fleury and Ryan Whitford
Australian Centre for Plant Functional Genomics (ACPFG), University of Adelaide,
Urrbrae, SA, Australia
Editors
Delphine Fleury Ryan Whitford
Australian Centre for Plant Functional Australian Centre for Plant Functional
Genomics (ACPFG) Genomics (ACPFG)
University of Adelaide University of Adelaide
Urrbrae, SA, Australia Urrbrae, SA , A ustralia
Additional material to this book can be downloaded from http://extras.springer.com
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-4939-0445-7 ISBN 978-1-4939-0446-4 (eBook)
DOI 10.1007/978-1-4939-0446-4
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Prefa ce
One of our greatest challenges is to feed several billion people in a changing environment
whereby water and nutrients are predicted to become limiting yet the demands of popula-
tion growth continue. The fi rst green revolution enabled us to increase crop production
through the breeding of new hybrid and semi-dwarf varieties, the use of fertilizers and
modern agronomical practices. The recent advent of molecular technologies has changed
the way plant breeders identify and select their germplasm, genetic variation can now be
assessed at the DNA level, with much of this information fi nding application to their selec-
tion strategies. A small size breeding program can easily utilise 20–50 markers for their
molecular-assisted selection, focusing on known traits such as fl owering time, grain quality
or disease resistance. Large breeding programs are now routinely assessing millions of
molecular data points every year in order to identify new genes and diagnostic markers.
This information facilitates genetic background selection of progenies, therefore allowing
the best choice of plants for the following round of selection. Furthermore, the molecular
identity of gene sequences underlying important traits can now be used in the creation of
novel transgenic varieties.
This volume addresses breeders and pre-breeding researchers in the crop science com-
munity. The fi rst two chapters give guidelines on how to design a breeding strategy for the
selection of an ideal variety or genetic ideotype, and how to transform gene sequence infor-
mation into practical diagnostic markers. The second section (Chapters 3–7) provides pro-
tocols for breeders using molecular markers in selection programs and for laboratories
providing molecular services to breeding programs. The methodologies collated were
selected based on cost, effi ciency and applicability to both medium- and large-scale breed-
ing systems. These protocols can therefore suit different needs and capacity: from small
laboratories analysing molecular markers on a one-by-one basis to the increasingly popular
high-throughput protocols for high-capacity laboratories. Molecular biology and breeding
now involve considerable analysis in silico, from data collection, storage to complex statisti-
cal analysis. The third section (Chapters 8–12) describes statistical programs and software
to aid implementation of molecular data into breeding programs. The fourth and fi nal sec-
tion (Chapters 13–19) describes methodologies that facilitate the generation of genetic
diversity and its characterisation, for example creating new alleles by introgression, muta-
genesis and plant transformation, as well as capturing and fi xing this variation through
doubled haploidy.
We would like to thank the authors for their kind contribution. The described methods
are those that they have either developed or used within their own breeding programs. The
detailed guidelines and tutorials were developed so that the methods could be easily adopted
by breeders. We hope this volume will help in expanding the use of molecular technologies
for the creation of tomorrow’s crop varieties.
Urrbrae, SA, Australia Delphine Fleury
Ryan W hitford
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 Defining a Genetic Ideotype for Crop Improvement. . . . . . . . . . . . . . . . . . . . 1
Richard M . Trethowan
2 F rom Genes to Markers: Exploiting Gene Sequence Information
to Develop Tools for Plant Breeding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Melissa G arcia and D iane E . M ather
3 Temperature Switch PCR (TSP): A Gel-Based Molecular Marker
Technique for Investigating Single Nucleotide Polymorphisms . . . . . . . . . . . . 3 7
Le P huoc Thanh and K elvin Khoo
4 M ultiplex-Ready Technology for Mid-Throughput
Genotyping of Molecular Markers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Julien B onneau and Matthew H ayden
5 G enotyping by High-Resolution Melting Analysis. . . . . . . . . . . . . . . . . . . . . . 5 9
Elise J . Tucker and Bao L am Huynh
6 B i-Allelic SNP Genotyping Using the TaqMan® Assay. . . . . . . . . . . . . . . . . . . 67
John W oodward
7 SNP Genotyping: The KASP Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 5
Chunlin He, J ohn Holme, and Jeffrey Anthony
8 R indsel: An R Package for Phenotypic and Molecular
Selection Indices Used in Plant Breeding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Sergío Perez-Elizalde, J esús J . C erón-Rojas, J osé C rossa,
Delphine F leury, and Gregorio A lvarado
9 O ptiMAS: A Decision Support Tool to Conduct
Marker- Assisted Selection Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 7
Fabio V alente, Franck Gauthier, Nicolas Bardol, G uylaine B lanc,
Johann Joets, A lain Charcosset, and Laurence M oreau
10 G enomic Selection in Plant Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 17
Mark A . Newell and J ean -Luc Jannink
11 Simulated Breeding with QU-GENE Graphical User Interface . . . . . . . . . . . . 1 31
Adrian H athorn, S cott Chapman, and Mark Dieters
12 The Control of Recombination in Wheat by Ph1 and Its Use in Breeding . . . . 143
Graham Moore
13 TILLING for Plant Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 55
Peter Sharp and Chongmei D ong
vii
viii Contents
14 In vitro Culture for Doubled Haploids: Tools for Molecular Breeding. . . . . . . 1 67
Sue B roughton, P arminder K. S idhu, and Philip A. D avies
15 B iolistic Transformation of Wheat with Centrophenoxine
as a Synthetic Auxin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 91
Ainur Ismagul, G ulnur I skakova, John C . Harris, and Serik Eliby
16 A grobacterium -Mediated Transformation
of Barley (Hordeum vulgare L.). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Ainur Ismagul, Iryna M azonka, C orinne C allegari, and S erik Eliby
17 qPCR for Quantification of Transgene Expression
and Determination of Transgene Copy Number . . . . . . . . . . . . . . . . . . . . . . . 2 13
Stephen J. Fletcher
18 High-Throughput Analysis Pipeline for Achieving Simple
Low-Copy Wheat and Barley Transgenics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
Nataliya K ovalchuk

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 53
Contributors
GREGORIO ALVARADO • Biometrics and Statistics Unit of the Crop Research Informatics
Laboratory , I nternational Maize and Wheat Improvement Center (CIMMYT) , Mexico
DF Mexico
JEFFREY ANTHONY • LGC Genomics Ltd , Hoddesdon, Herts, U K
NICOLAS BARDOL • INRA, UMR de Génétique Végétale, Ferme du Moulon , G if sur Yvette,
France ; E uralis Semences, Domaine de Sandreau , M ondonville, F rance
GUYLAINE BLANC • INRA, UMR de Génétique Végétale, Ferme du Moulon , Gif sur Yvette,
France
JULIEN BONNEAU • Australian Centre for Plant Functional Genomics, S chool of Botany,
The University of Melbourne , Melbourne, V IC , A ustralia
SUE BROUGHTON • Department of Agriculture and Food WA , S outh Perth, W A , A ustralia
CORINNE CALLEGARI • Australian Centre for Plant Functional Genomics, University of
Adelaide, Glen Osmond, SA, Australia; School of Agriculture, Food and Wine, Waite
Research Institute, University of Adelaide, Hartley Grove, Urrbrae, SA, Australia
JESÚS J . CERÓN-ROJAS • Biometrics and Statistics Unit of the Crop Research Informatics
Laboratory , I nternational Maize and Wheat Improvement Center (CIMMYT) ,
Mexico DF M exico
SCOTT CHAPMAN • CSIRO Plant Industry , S t. Lucia, Q LD, Australia
ALAIN CHARCOSSET • INRA, UMR de Génétique Végétale, Ferme du Moulon , G if sur
Yvette , France
JOSÉ CROSSA • Biometrics and Statistics Unit of the Crop Research Informatics Laboratory,
International Maize and Wheat Improvement Center (CIMMYT) , Mexico DF , Mexico
PHILIP A. DAVIES • South Australian Research and Development Institute , A delaide,
SA, A ustralia
MARK DIETERS • School of Agriculture & Food Sciences, The University of Queensland ,
St Lucia, Q LD , Australia
CHONGMEI DONG • Plant Breeding Institute, University of Sydney , Narellan, N SW, A ustralia
SERIK ELIBY • Australian Centre for Plant Functional Genomics, University of Adelaide,
Glen Osmond, SA, Australia; School of Agriculture, Food and Wine, Waite Research
Institute, University of Adelaide, Hartley Grove, Urrbrae, SA, Australia
STEPHEN J. FLETCHER • Chemistry and Molecular Biosciences, The School of Biological
Sciences, University of Queensland, Brisbane, QLD, Australia
DELPHINE F LEURY • Australian Centre for Plant Functional Genomics (ACPFG),
University of Adelaide , Urrbrae, SA , A ustralia
MELISSA G ARCIA • Australian Centre for Plant Functional Genomics, The University of
Adelaide , G len Osmond, S A , A ustralia
FRANCK GAUTHIER • INRA, UMR de Génétique Végétale, Ferme du Moulon ,
Gif sur Yvette, F rance
JOHN C . HARRIS • Australian Centre for Plant Functional Genomics, University of
Adelaide, Glen Osmond, SA, Australia; School of Agriculture, Food and Wine, Waite
Research Institute, University of Adelaide, Hartley Grove, Urrbrae, SA, Australia
ADRIAN H ATHORN • CSIRO Plant Industry , St. Lucia, QLD, A ustralia
ix