Plant Genotyping: Methods and Protocols

317 Pages·2015·8.99 MB·English

by  Jacqueline Batley (eds.)

Methods in
Molecular Biology 1245
Jacqueline Batley Editor
Plant
Genotyping
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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Plant Genotyping
Methods and Protocols
Edited by
Jacqueline Batley

School of Plant Biology, The University of Western Australia,
Crawley, WA, Australia
Editor
Jacqueline B atley
School of Plant Biology, The University of Western Australia
Crawley, WA, Australia
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-4939-1965-9 ISBN 978-1-4939-1966-6 (eBook)
DOI 10.1007/978-1-4939-1966-6
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Prefa ce
Plant genotyping is a rapidly advancing fi eld. The ability to produce vast amounts of DNA
sequence data has enabled the discovery of molecular markers in a vast array of plant s pecies,
meaning that genotyping rather marker development becomes the rate limiting factor. This
volume is aimed at plant biologists working on plants from model organisms and crops, to
orphan species and focuses on all the different marker types available. The volume would
also be of interest to researchers who would benefi t from an introduction to the different
marker systems available for plant research.
Plant genotyping is required for a variety of end uses including marker-assisted selec-
tion, associating phenotype with polymorphism, DNA barcoding, genetic diversity analysis,
conservation genetics, and improving genome assemblies. The most suitable genotyping
system to use depends on the throughput requirements, facilities available, and questions
to be answered. Chapters within this volume focus on the diverse range of genotyping
methods available, with guidelines as to what methods may be suitable for the different
needs of the researchers. Overviews are provided in the early chapters. Given the issues with
polyploidy in some plant species, information is included describing how to handle this
data. Information is also provided on bioinformatics tools for marker discovery, databases
hosting existing markers, and software for data analysis. Chapters providing details on spe-
cifi c genotyping methods are then included.
Scientifi c research progresses rapidly and the technologies for genotyping evolve with
this. In this volume we have covered the different methods available to date, many of which
will continue to increase in throughput as these technologies increase and researchers are
encouraged to frequently review which may be the most applicable method for their
research.
Crawley, WA, Australia J acqueline Batley
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 Advances in Plant Genotyping: Where the Future Will Take Us. . . . . . . . . . . . 1
Dhwani A. Patel, Manuel Zander, J essica Dalton-Morgan,
and Jacqueline B atley
2 M olecular Marker Applications in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3
Alice C . Hayward, R eece T ollenaere, J essica D alton-Morgan
and Jacqueline Batley
3 Bioinformatics: Identification of Markers
from Next-G eneration Sequence Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Pradeep R uperao and D avid E dwards
4 Molecular Marker Databases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Kaitao Lai, Michał T adeusz Lorenc, and David E dwards
5 Plant Genotyping Using Fluorescently Tagged Inter-Simple
Sequence Repeats (ISSRs): Basic Principles and Methodology. . . . . . . . . . . . . 63
Linda M. Prince
6 S SR Genotyping. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Annaliese S . M ason
7 G enotyping Analysis Using an RFLP Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1
Shutao D ai and Yan L ong
8 D NA Barcoding for Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 01
Natasha de Vere, T im C . G. R ich, S arah A . Trinder,
and Charlotte L ong
9 M ultiplexed Digital Gene Expression Analysis
for Genetical Genomics in Large Plant Populations. . . . . . . . . . . . . . . . . . . . . 119
Christian Obermeier, B ertha M . Salazar-Colqui, Viola Spamer,
and R od S nowdon
10 SNP Genotyping by Heteroduplex Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . 1 41
Norma P aniego, C orina Fusari, V erónica Lia, and A ndrea P uebla
11 Application of the High-Resolution Melting Technique
for Gene Mapping and SNP Detection in Plants . . . . . . . . . . . . . . . . . . . . . . . 1 51
David Chagné
12 C hallenges of Genotyping Polyploid Species . . . . . . . . . . . . . . . . . . . . . . . . . . 1 61
Annaliese S . M ason
13 Genomic Reduction Assisted Single Nucleotide Polymorphism
Discovery Using 454-Pyrosequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Peter J. Maughan, J oshua A . U dall, and E ric N . J ellen
vii
viii Contents
14 Inter-SINE Amplified Polymorphism (ISAP) for Rapid
and Robust Plant Genotyping. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Torsten W enke, K athrin M . S eibt, T homas Döbel,
Katja Muders, and Thomas S chmidt
15 S creening of Mutations by TILLING in Plants . . . . . . . . . . . . . . . . . . . . . . . . 1 93
Nian W ang and Lei S hi
16 Gene Analysis Using Mass Spectrometric Cleaved Amplified
Polymorphic Sequence (MS-CAPS) with Matrix-A ssisted
Laser Desorption Ionization Time-of-Flight Mass Spectrometry
(MALDI-TOF). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Hideyuki Kajiwara
17 Quantitative SNP Genotyping of Polyploids
with MassARRAY and Other Platforms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Marcelo Mollinari and O liver S erang
18 S NP Genotyping Using KASPar Assays. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Scott M. Smith and Peter J. Maughan
19 Skim-Based Genotyping by Sequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Agnieszka A. G olicz, Philipp E . B ayer, and David Edwards
20 T he Restriction Enzyme Target Approach to Genotyping
by Sequencing (GBS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 71
Elena H ilario
21 M ethods for the Design, Implementation, and Analysis
of Illumina Infinium™ SNP Assays in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . 2 81
David Chagné, L uca B ianco, C indy L awley, D iego M icheletti,
and Jeanne M . E. Jacobs
22 U se of the Illumina GoldenGate Assay for Single Nucleotide
Polymorphism (SNP) Genotyping in Cereal Crops . . . . . . . . . . . . . . . . . . . . . 299
Shiaoman Chao and Cindy Lawley
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
Contributors
JACQUELINE BATLEY • School of Agriculture and Food Sciences, University of Queensland ,
Brisbane, Q LD , A ustralia ; Centre for Integrative Legume Research, U niversity
of Queensland , B risbane, QLD, Australia ; S chool of Plant Biology, T he University of Western
Australia , C rawley , W A , A ustralia
PHILIPP E. BAYER • School of Agriculture and Food Sciences, U niversity of Queensland ,
Brisbane, Q LD , Australia ; A ustralian Centre for Plant Functional Genomics, U niversity
of Queensland , B risbane, QLD, Australia
LUCA BIANCO • Computational Biology Platform-HPC, FEM Research and Innovation
Center , S an Michele all’Adige, T N , I taly
DAVID C HAGNÉ • The New Zealand Institute for Plant & Food Research Limited,
Palmerston North Research Centre , P almerston, N ew Zealand
SHIAOMAN CHAO • USDA-ARS, Biosciences Research Lab , Fargo, N D , U SA
SHUTAO DAI • National Key Laboratory of Crop Genetic Improvement, H uazhong
Agricultural University , W uhan , C hina
JESSICA DALTON-MORGAN • School of Agriculture and Food Sciences, University of
Queensland , B risbane, QLD , A ustralia ; Centre for Integrative Legume Research,
University of Queensland , Brisbane, Q LD , A ustralia
THOMAS D ÖBEL (cid:129) Department of Dermatology, U niversity of Heidelberg , Heidelberg,
Germany
DAVID E DWARDS • School of Agriculture and Food Sciences, U niversity of Queensland ,
Brisbane, Australia ; A ustralian Centre for Plant Functional Genomics, U niversity
of Queensland , B risbane, Australia
CORINA FUSARI • Instituto de Biotecnología , Centro de Investigación en Ciencias
Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria
(INTA), Nicolas Repeto y Los Reseros, Hurlingham, Buenos Aires, Argentina ; S ystem
Regulation Group, Metabolic Networks Department, Max Planck Institute of Molecular
Plant Physiology , Hurlingham, Buenos Aires, A rgentina
AGNIESZKA A. GOLICZ • School of Agriculture and Food Sciences, University
of Queensland , B risbane, A ustralia ; Australian Centre for Plant Functional Genomics,
University of Queensland , Brisbane, A ustralia
ALICE C. HAYWARD • School of Agriculture and Food Sciences, U niversity of Queensland ,
Brisbane, Q LD , Australia ; C entre for Integrative Legume Research, U niversity
of Queensland , B risbane, QLD, Australia
ELENA HILARIO • The New Zealand Institute for Plant and Food Research ,
Auckland, N ew Zealand
JEANNE M . E . JACOBS • The New Zealand Institute for Plant & Food Research Ltd. ,
Christchurch, N ew Zealand
ERIC N. JELLEN • 4105B LSB, Department of Plant and Wildlife Sciences,
Brigham Young University , P rovo , U T , USA
ix