Table Of ContentMolecular Markers
in
Plant Genetics
and
Biotechnology
Molecular Markers
in
Plant Genetics
and
Biotechnology
Editor
Dominique de Vienne
Institute National de la Recherche Agronomique
Versailles, France
%
Science Publisher Inc.
Enfield (NH), USA Plymouth, UK
© 2003, Copyright reserved
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ISBN 13: 978-1-57808-239-9 (hbk)
Published by arrangement with INRA, Paris, France.
Ourage publie avec le concours du Ministere frarn;ais charge de la culture-
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This work has been published with the help of the French Ministere de la
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Library of Congress Cataloging-in-Publication Data
Marquerurs moleculaires en genetique et biotechnologies vegtales.
English.
Molecular markers in plant genetics and biotechnology/editor
Dominique de Vienne.
p. cm
Includes bibliographical references (p.).
ISBN 1-57808-239-0
1. Plant genome mapping. 2. Genetic polymorphisms. I. Vienne, D.
de (Dominique) II Title.
QK981.45 M37 2003
52.8'62-dc21
2002036561
Translation of: /es marqueurs moleculaires en genetique et biotechnologies
vegetales, !NRA, Paris, 1998. Text updated by author for the
English edition in 2002
French edition: ©INRA, Paris, 1998
ISBN 2-7380-07766-7
ISSN 1144-7605
Published by Science Publishers, Inc. Enfield, NH, USA
Foreword
Does Science progress essentially by the acquisition of new tools or by the
emergence of new concepts? This debate between Homo faber and Homo
sapiens can be fed with several examples illustrating the relevance of these
two points of view and, above all, the dialectic at work between these two
sources of rejuvenation of approaches. Those who favour universal
attraction, the theory of evolution or general relativity, are opposed to those
who emphasize the decisive role of optic instruments (telescopes and
microscopes of all types) or analytical tools (mass spectrometry, electro(cid:66)
phoresis, magnetic resonance, etc.).
In this debate, molecular markers provide a fresh illustration of the key
role that new tools can play in reviving scientific fields that are rich, even
superabundant, in theoretical concepts but deficient in the capacity for
refined observation of their object. Studies in quantitative genetics, as well
as in population genetics, have progressively constructed a theoretical
apparatus that often allows the explanation of a given fact by several
hypotheses that are not mutually exclusive and that are often difficult to
organize into a hierarchy. The 'genotype', which these disciplines
constantly refer to, can be compared to a puzzle of which one knows only a
few pieces and a very fuzzy overall image. It is clear from this analogy that
debates on what the image represents could get lively!
Now, within a few years, geneticists have been possessed of a
significant number of new pieces of the puzzle, and this new deal allows
them to discriminate between hypotheses, or perhaps discard them all to
construct new ones, illustrating thus the dialectic mentioned above
between tool and concept.
The technological revolution has been extremely rapid. When DNA
fingerprinting in humans was developed in the mid-1980s, many thought
that its cost and complexity would limit it to criminology or specific
applications. Twenty years later, it is difficult to study the genetics of an
animal or plant species, to describe its biodiversity or for genetic
improvement, without using molecular markers.
This volume, edited by Dominique de Vienne, very clearly presents
these different approaches and their fields of application. The challenge
was difficult: the techniques are rapidly developing and are often similar,
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and the definition of their 'field of relevance' requires a fine understanding
of the problems that must be tackled. The authors seem to have succeeded
thoroughly. Beyond its technical value, I am sure that this work will impart
to the reader the present feverish enthusiasm of geneticists, who are coming
closer and closer to revealing the traits of an object that they have long
manipulated without really having known: the genome of plant and animal
species.
Bernard Chevassus-au-Louis
Preface
The intensive use of molecular markers, even though it does not coincide
with the emergence of a new scientific field, completely overturned several
scopes in biology in the 1990s. One example is positional cloning, by which
a gene with an unknown product can be isolated, just from its position in
the genome. But this aspect, which medical genetics has widely advertised,
must not obscure other equally fundamental applications. In the field of
evolution, comparative mapping allows us to locate the genomic structural
alterations that have occurred during the diversification of a genus or
family. In formal genetics, the factors that influence the recombination rate
can be analysed systematically. In population genetics, diversity and gene
flow can be measured. The field most rejuvenated by molecular markers is
quantitative genetics. Considered at first a "science for engineers", because
it was used more by plant and animal breeders than by researchers, it is
today successful in areas ranging from the analysis of genetic bases of
morphological variation to the development of strategies for characterizing
"quantitative" genes (the well-known QTL, for quantitative trait loci), and
marker-assisted selection has become a powerful tool for plant and animal
improvement. The recent complete genome sequencing of two model
species, Arabidopsis (a dicot) and rice (a monocot) will greatly increase the
potential of marker approaches in all higher plants, due to gene homology
and synteny conservation in the plant kingdom.
To the extent that the set of methods known as 'molecular markers'
apply to widely varying fields in genetics and plant biotechnology, it has
not been possible to present the fundamentals of all the fields concerned. In
each case we have wanted to show what specific inputs markers offer, the
new questions they enable us to resolve, and possibly the problems they
raise. The reader will need to refer, wherever necessary, to the fundamental
works in genetics (formal, quantitative, or population genetics). Sound
notions of molecular biology and statistics will also be useful. One
exception is nevertheless made for the construction of genetic maps, the
theory of which has been detailed for two reasons. First, the maps are the
basis of most applications of markers; inadequate knowledge of their
nature and way of construction would limit the reader's understanding of
the rest of the book. Second, even though their principles have been well
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understood for 70 years, their teaching at the university level has been
limited for decades for lack of new applications. Finally, the use of
informatics offers new perspectives that merit attention.
The book is thus organized in the following manner. The first chapter
details the different techniques of molecular markers, emphasizing genetic
aspects, because these determine the type of use one can put it to. The
construction of genetic linkage maps is the subject of the second chapter,
where the advantages and disadvantages of the most common mapping
populations are specified. The particular case of mapping of major genes,
especially for the purpose of positional cloning, is addressed in the third
chapter. Detection and applications of QTL controlling the expression of
quantitative traits are presented in the fourth chapter, which also tackles
the complex question of their identification. The fifth chapter underscores
the major contribution of molecular markers in analysis of the structure and
evolution of natural populations. Finally, the advantages of markers in
selection, for studies of diversity and in the context of marker-assisted
selection, are discussed in the last chapter. Throughout the book we have
tried not only to expose in detail the principle of the numerous possibilities
offered by markers, but also to illustrate them systematically with relevant
bibliographical results. We have sought to give some unity to the work
while respecting the spirit of each chapter, which is determined by the
personality of the authors as well as the specificity of the field explored.
We hope that the work will therefore answer the needs of students as
well as teachers, and that it will be a valuable tool for all researchers using
markers, no matter what their objectives are.
Dominique de Vienne
Contents
Foreword v
Preface vii
Introduction 1
Definitions 1
What is a 'good' genetic marker?
1. Principal sources of molecular markers 3
D. de Vienne, S. Santoni and M. Falque
Criteria of classification 3
Codominant markers detected individually 4
Sequence polymorphism 4
Differences at restriction enzyme sites: the RFLP technique 5
A particular case of RFLP: CAPS 15
Differences of conformation: SSCP 17
Differences of stability: D/TGGE 17
SNP genotyping techniques 19
Polymorphism of number of sequence repeats: SSR 29
Patterns of multiple dominant markers: genetic fingerprinting 31
Sequence polymorphism 31
Differences in hybridization sites of an arbitrary primer, or
techniques of MAAP, RAPD, AP-PCR and DAF 31
Differences of restriction sites and hybridization sites of
specific primers: AFLP™ 35
Polymorphism of number of tandem repeats 37
ISSR techniques 37
Minisatellites 38
Gene markers: cDNA and proteins 39
What markers are suitable for what purpose? 39
Glossary 41
2. Construction of genetic linkage maps 47
D. de Vienne
The concept of genetic distance 48
The Haldane distance 49
