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GENETICS, GENOMICS
AND BREEDING OF
GRAPES
 Genetics, Genomics and Breeding of Crop Plants

Series Editor
Chittaranjan Kole
Department of Genetics and Biochemistry
Clemson University
Clemson, SC
USA

Books in this Series:

Published or in Press:
• Jinguo Hu, Gerald Seiler & Chittaranjan Kole:
Sunflower
• Kristin D. Bilyeu, Milind B. Ratnaparkhe &
Chittaranjan Kole: Soybean
• Robert Henry & Chittaranjan Kole: Sugarcane
• Kevin Folta & Chittaranjan Kole: Berries
• Jan Sadowsky & Chittaranjan Kole: Vegetable
Brassicas
• James M. Bradeen & Chittaranjan Kole: Potato
• C.P. Joshi, Stephen DiFazio & Chittaranjan Kole:
Poplar
• Anne-Françoise Adam-Blondon, José M. Martínez-
Zapater & Chittaranjan Kole: Grapes
• Christophe Plomion, Jean Bousquet & Chittaranjan
Kole: Conifers
• Dave Edwards, Jacqueline Batley, Isobel Parkin &
Chittaranjan Kole: Oilseed Brassicas
• Marcelino Pérez de la Vega, Ana María Torres,
José Ignacio Cubero & Chittaranjan Kole: Cool
Season Grain Legumes
• Yi-Hong Wang, Tusar Kanti Behera & Chittaranjan
Kole: Cucurbit
 GENETICS, GENOMICS
AND BREEDING OF
GRAPES

Editors
Anne-Françoise Adam-Blondon
INRA
UMR INRA UEVE URL CNRS Genomique végétale (URGV)
Evry Cedex, France
José M. Martínez-Zapater
Instituto de Ciencias de la Vid y del Vino
(CSIC, UR, Gobierno de La Rioja)
Logroño
Spain
Chittaranjan Kole
Department of Genetics and Biochemistry
Clemson University
Clemson, SC
USA

Science Publishers
Jersey, British Isles
Enfield, New Hampshire
Published by Science Publishers, an imprint of Edenbridge Ltd.
• St. Helier, Jersey, British Channel Islands
• P.O. Box 699, Enfield, NH 03748, USA
E-mail: info@[Link] Website: [Link]
Marketed and distributed by:

Copyright reserved © 2011

ISBN 978-1-57808-717-4
Library of Congress Cataloging-in-Publication Data
Genetics, genomics and breeding of grapes / editors, Anne-
Françoise
Adam-Blondon, José-Miguel Martinez-Zapater, Chittaranjan
Kole. -- 1st
ed.
p. cm. -- (Genetics, genomics and breeding of crop
plants)
Includes bibliographical references and index.
ISBN 978-1-57808-717-4 (hardcover)
1. Grapes--Genetics. 2. Grapes--Genome mapping. 3.
Grapes--Breeding. I. Adam-Blondon, Anne-Françoise. II.
Martínez-Zapater, José M. III. Kole, Chittaranjan. IV.
Series:
Genetics, genomics and breeding of crop plants.
SB398.3.G46 2011
634.8’8233--dc22
2011000002
The views expressed in this book are those of the author(s) and the publisher does not assume
responsibility for the authenticity of the findings/conclusions drawn by the author(s). Also
no responsibility is assumed by the publishers for any damage to the property or persons as
a result of operation or use of this publication and/or the information contained herein.
All rights reserved. No part of this publication may be reproduced, stored in
a retrieval system, or transmitted in any form or by any means, electronic,
mechanical, photocopying or otherwise, without the prior permission of the
publisher, in writing. The exception to this is when a reasonable part of the text is
quoted for purpose of book review, abstracting etc.
This book is sold subject to the condition that it shall not, by way of trade
or otherwise be lent, re-sold, hired out, or otherwise circulated without the
publisher’s prior consent in any form of binding or cover other than that in which it is
published and without a similar condition including this condition being imposed
on the subsequent purchaser.
Printed in the United States of America
 Preface to the Series

Genetics, genomics and breeding has emerged as three overlapping and

complimentary disciplines for comprehensive and fine-scale analysis of
plant genomes and their precise and rapid improvement. While genetics
and plant breeding have contributed enormously towards several new
concepts and strategies for elucidation of plant genes and genomes as well
as development of a huge number of crop varieties with desirable traits,
genomics has depicted the chemical nature of genes, gene products and
genomes and also provided additional resources for crop improvement.
In today’s world, teaching, research, funding, regulation and utilization
of plant genetics, genomics and breeding essentially require thorough
understanding of their components including classical, biochemical,
cytological and molecular genetics; and traditional, molecular, transgenic
and genomics-assisted breeding. There are several book volumes and
reviews available that cover individually or in combination of a few of these
components for the major plants or plant groups; and also on the concepts
and strategies for these individual components with examples drawn
mainly from the major plants. Therefore, we planned to fill an existing gap
with individual book volumes dedicated to the leading crop and model
plants with comprehensive deliberations on all the classical, advanced and
modern concepts of depiction and improvement of genomes. The success
stories and limitations in the different plant species, crop or model, must
vary; however, we have tried to include a more or less general outline of
the contents of the chapters of the volumes to maintain uniformity as far
as possible.
Often genetics, genomics and plant breeding and particularly their
complimentary and supplementary disciplines are studied and practiced
by people who do not have, and reasonably so, the basic understanding of
biology of the plants for which they are contributing. A general description
of the plants and their botany would surely instill more interest among
them on the plant species they are working for and therefore we presented
lucid details on the economic and/or academic importance of the plant(s);
historical information on geographical origin and distribution; botanical
origin and evolution; available germplasms and gene pools, and genetic
and cytogenetic stocks as genetic, genomic and breeding resources; and
vi Genetics, Genomics and Breeding of Grapes

basic information on taxonomy, habit, habitat, morphology, karyotype,

ploidy level and genome size, etc.
Classical genetics and traditional breeding have contributed enormously
even by employing the phenotype-to-genotype approach. We included
detailed descriptions on these classical efforts such as genetic mapping
using morphological, cytological and isozyme markers; and achievements
of conventional breeding for desirable and against undesirable traits.
Employment of the in vitro culture techniques such as micro- and megaspore
culture, and somatic mutation and hybridization, has also been enumerated.
In addition, an assessment of the achievements and limitations of the basic
genetics and conventional breeding efforts has been presented.
It is a hard truth that in many instances we depend too much on a few
advanced technologies, we are trained in, for creating and using novel or
alien genes but forget the infinite wealth of desirable genes in the indigenous
cultivars and wild allied species besides the available germplasms in national
and international institutes or centers. Exploring as broad as possible
natural genetic diversity not only provides information on availability of
target donor genes but also on genetically divergent genotypes, botanical
varieties, subspecies, species and even genera to be used as potential parents
in crosses to realize optimum genetic polymorphism required for mapping
and breeding. Genetic divergence has been evaluated using the available
tools at a particular point of time. We included discussions on phenotype-
based strategies employing morphological markers, genotype-based
strategies employing molecular markers; the statistical procedures utilized;
their utilities for evaluation of genetic divergence among genotypes, local
landraces, species and genera; and also on the effects of breeding pedigrees
and geographical locations on the degree of genetic diversity.
Association mapping using molecular markers is a recent strategy to
utilize the natural genetic variability to detect marker-trait association and
to validate the genomic locations of genes, particularly those controlling the
quantitative traits. Association mapping has been employed effectively in
genetic studies in human and other animal models and those have inspired
the plant scientists to take advantage of this tool. We included examples of
its use and implication in some of the volumes that devote to the plants for
which this technique has been successfully employed for assessment of the
degree of linkage disequilibrium related to a particular gene or genome,
and for germplasm enhancement.
Genetic linkage mapping using molecular markers have been discussed
in many books, reviews and book series. However, in this series, genetic
mapping has been discussed at length with more elaborations and examples
on diverse markers including the anonymous type 2 markers such as
RFLPs, RAPDs, AFLPs, etc. and the gene-specific type 1 markers such as
EST-SSRs, SNPs, etc.; various mapping populations including F2, backcross,
 Preface to the Series vii

recombinant inbred, doubled haploid, near-isogenic and pseudotestcross;

computer software including MapMaker, JoinMap, etc. used; and different
types of genetic maps including preliminary, high-resolution, high-density,
saturated, reference, consensus and integrated developed so far.
Mapping of simply inherited traits and quantitative traits controlled
by oligogenes and polygenes, respectively has been deliberated in the
earlier literature crop-wise or crop group-wise. However, more detailed
information on mapping or tagging oligogenes by linkage mapping or
bulked segregant analysis, mapping polygenes by QTL analysis, and
different computer software employed such as MapMaker, JoinMap, QTL
Cartographer, Map Manager, etc. for these purposes have been discussed
at more depth in the present volumes.
The strategies and achievements of marker-assisted or molecular
breeding have been discussed in a few books and reviews earlier. However,
those mostly deliberated on the general aspects with examples drawn mainly
from major plants. In this series, we included comprehensive descriptions
on the use of molecular markers for germplasm characterization, detection
and maintenance of distinctiveness, uniformity and stability of genotypes,
introgression and pyramiding of genes. We have also included elucidations
on the strategies and achievements of transgenic breeding for developing
genotypes particularly with resistance to herbicide, biotic and abiotic
stresses; for biofuel production, biopharming, phytoremediation; and also
for producing resources for functional genomics.
A number of desirable genes and QTLs have been cloned in plants since
1992 and 2000, respectively using different strategies, mainly positional
cloning and transposon tagging. We included enumeration of these and
other strategies for isolation of genes and QTLs, testing of their expression
and their effective utilization in the relevant volumes.
Physical maps and integrated physical-genetic maps are now available
in most of the leading crop and model plants owing mainly to the BAC,
YAC, EST and cDNA libraries. Similar libraries and other required genomic
resources have also been developed for the remaining crops. We have
devoted a section on the library development and sequencing of these
resources; detection, validation and utilization of gene-based molecular
markers; and impact of new generation sequencing technologies on
structural genomics.
As mentioned earlier, whole genome sequencing has been completed
in one model plant (Arabidopsis) and seven economic plants (rice, poplar,
peach, papaya, grapes, soybean and sorghum) and is progressing in an
array of model and economic plants. Advent of massively parallel DNA
sequencing using 454-pyrosequencing, Solexa Genome Analyzer, SOLiD
system, Heliscope and SMRT have facilitated whole genome sequencing in
many other plants more rapidly, cheaply and precisely. We have included
viii Genetics, Genomics and Breeding of Grapes

extensive coverage on the level (national or international) of collaboration

and the strategies and status of whole genome sequencing in plants for
which sequencing efforts have been completed or are progressing currently.
We have also included critical assessment of the impact of these genome
initiatives in the respective volumes.
Comparative genome mapping based on molecular markers and map
positions of genes and QTLs practiced during the last two decades of the
last century provided answers to many basic questions related to evolution,
origin and phylogenetic relationship of close plant taxa. Enrichment of
genomic resources has reinforced the study of genome homology and
synteny of genes among plants not only in the same family but also of
taxonomically distant families. Comparative genomics is not only delivering
answers to the questions of academic interest but also providing many
candidate genes for plant genetic improvement.
The ‘central dogma’ enunciated in 1958 provided a simple picture of gene
function—gene to mRNA to transcripts to proteins (enzymes) to metabolites.
The enormous amount of information generated on characterization of
transcripts, proteins and metabolites now have led to the emergence of
individual disciplines including functional genomics, transcriptomics,
proteomics and metabolomics. Although all of them ultimately strengthen
the analysis and improvement of a genome, they deserve individual
deliberations for each plant species. For example, microarrays, SAGE, MPSS
for transcriptome analysis; and 2D gel electrophoresis, MALDI, NMR,
MS for proteomics and metabolomics studies require elaboration. Besides
transcriptome, proteome or metabolome QTL mapping and application
of transcriptomics, proteomics and metabolomics in genomics-assisted
breeding are frontier fields now. We included discussions on them in the
relevant volumes.
The databases for storage, search and utilization on the genomes, genes,
gene products and their sequences are growing enormously in each second
and they require robust bioinformatics tools plant-wise and purpose-
wise. We included a section on databases on the gene and genomes, gene
expression, comparative genomes, molecular marker and genetic maps,
protein and metabolomes, and their integration.
Notwithstanding the progress made so far, each crop or model plant
species requires more pragmatic retrospect. For the model plants we need
to answer how much they have been utilized to answer the basic questions
of genetics and genomics as compared to other wild and domesticated
species. For the economic plants we need to answer as to whether they
have been genetically tailored perfectly for expanded geographical regions
and current requirements for green fuel, plant-based bioproducts and for
improvements of ecology and environment. These futuristic explanations
have been addressed finally in the volumes.
 Preface to the Series ix

We are aware of exclusions of some plants for which we have

comprehensive compilations on genetics, genomics and breeding in
hard copy or digital format and also some other plants which will have
enough achievements to claim for individual book volume only in distant
future. However, we feel satisfied that we could present comprehensive
deliberations on genetics, genomics and breeding of 30 model and economic
plants, and their groups in a few cases, in this series. I personally feel also
happy that I could work with many internationally celebrated scientists
who edited the book volumes on the leading plants and plant groups and
included chapters authored by many scientists reputed globally for their
contributions on the concerned plant or plant group.
We paid serious attention to reviewing, revising and updating of the
manuscripts of all the chapters of this book series, but some technical and
formatting mistakes will remain for sure. As the series editor, I take complete
responsibility for all these mistakes and will look forward to the readers
for corrections of these mistakes and also for their suggestions for further
improvement of the volumes and the series so that future editions can serve
better the purposes of the students, scientists, industries, and the society of
this and future generations.
Science publishers, Inc. has been serving the requirements of science
and society for a long time with publications of books devoted to advanced
concepts, strategies, tools, methodologies and achievements of various
science disciplines. Myself as the editor and also on behalf of the volume
editors, chapter authors and the ultimate beneficiaries of the volumes
take this opportunity to acknowledge the publisher for presenting these
books that could be useful for teaching, research and extension of genetics,
genomics and breeding.

Chittaranjan Kole
 Preface to the Volume

Grapevine (Vitis vinifera L.) is one of the most economically important

perennial fruit crop species in the world with more than 7.4 million hectares
planted in temperate and tropical climatic regions. Grapes are not only
produced for fruit, juice or raisins but are the basis of high added value
products, mainly wine and spirits. Contrary to other crops where innovation
is primarily based on cultivar improvement, the notable innovation
suffered by viticulture in the last decades has been based on management
techniques, whereas wine grape cultivars have changed slowly or not at
all. Most vineyards in the world are planted with cultivars that have been
perpetuated for centuries by vegetative propagation.
The original wild species from which grapevines were domesticated
can still be found in remnant populations in temperate Eurasian regions.
This species is dioecious, with male and female plants, while most current
cultivars are hermaphrodite plants. Still, as other fruit tree species, grapevine
cultivars are highly heterozygous which require vegetative propagation to
maintain their phenotypic features. While breeding has been very successful
in the generation of new table grape cultivars in the last decades, wine
grape cultivars have not evolved in the same way. The need to be attached
to a few elite cultivars recognized world-wide and the added difficulty of
introducing wine quality evaluation and selection in breeding programs
have resulted in very few new bred wine cultivars being incorporated to
the wine market in the last century.
Two decades ago, the application of molecular markers in the
construction of genetic maps and the analyses of quantitative traits opened
the way to understanding the genetic basis of relevant agronomic and
quality traits in grapevine and related species. More recently, the completion
of its genome sequence has speeded up the development of genomics and is
generating an explosion in grapevine research. The application of these fast
evolving technologies will greatly increase our understanding of grapevine
biology and should pave the way to support the development of new
wine and table grape cultivars more adapted to the needs of a sustainable
viticulture in a changing environment. In addition, these genomics can also
help to improve viticulture techniques by providing information on the
plant status and its relationships with other organisms in the vineyard.
xii Genetics, Genomics and Breeding of Grapes

This volume presents in 14 Chapters the recent advances in grapevine

genetics and genomics. The book begins with basic information on the species
and the crop in the introductory Chapter 1 and dedicates two chapters to
describe the existent natural variation in the Vitis genus (Chapter 2) as well
as the origin and utilization of somatic variation in grapevine (Chapter 3).
Natural genetic variation is the raw material for breeding but it is also a
basic tool to understand gene biological function. Genetic analyses and
molecular breeding are considered in the following four chapters including
association genetics (Chapter 4), genetic maps (Chapter 5), genetic analysis
of complex traits (Chapter 6) and molecular breeding (Chapter 7). The
connection between genetic and physical maps is considered in Chapter
8 which demonstrates the feasibility of positional cloning in grapevine.
The following chapters review the available information on the grapevine
genome sequence (Chapter 9), the application of global gene expression
analytical strategies (Chapters 10 and 11), the development of proteomics
and metabolomics technologies for grapevine (Chapter 12) and the
availability of databases and bioinformatics tools (Chapter 13). The book
ends with a chapter on future prospects of genome research in viticulture
(Chapter 14). We greatly appreciate the effort and time devoted to this
volume by all contributors. We expect that this new knowledge will help
coping with future viticulture challenges.
Finally, we would like to dedicate this book to the memory of Dr Alain
Bouquet, who left us suddenly in May 2009, while we were completing the
preparation of the book. His entire career (nearly 40 years) in the French
National Institute for Agronomical Research (INRA), first at Versailles
(1971–1972), then in Bordeaux (1973–1983) and finally in Montpellier
(1984–2009) was devoted to grapevine genetic improvement, mainly
pathogen resistance but also other important traits, such as seedlessness.
Alain Bouquet was passionate about the challenge to increase and exploit
genetic variation in grapevine for breeding purposes. He shared his wide
knowledge on grapevine and its cultivation by writing the introductory
chapter. He also co-authored Chapter 3 and participated, through the
creation of innovative genetic materials, in the results described in many
other Chapters such as 2, 5, 6, 7 and 8. Alain was a very enthusiastic,
committed and extremely generous scientist whose vision and creativity
has paved the way for many of the breakthroughs in grapevine genetics
that are now being achieved by grape researchers throughout the world.
He will be sadly missed but his legacy lives on.

Anne Françoise Adam Blondon

José Miguel Martínez Zapater
Chittaranjan Kole
 Contents

Preface to the Series v

Preface to the Volume xi
List of Contributors xv
Abbreviations xxiii
1. Grapevines and Viticulture 1
Alain Bouquet
2. Natural Variation in Vitis 30
Patrice This, José M. Martínez Zapater, Jean Pierre Péros,
and Thierry Lacombe
3. Origins and Consequences of Somatic Variation 68
in Grapevine
Laurent Torregrosa, Lucie Fernandez, Alain Bouquet, Jean-Michel
Boursiquot, Frédérique Pelsy and José M. Martínez-Zapater
4. Linkage Disequilibrium and Prospects for 93
Association Mapping in Vitis
Christopher L. Owens
5. Molecular Linkage Maps: Strategies, Resources and 111
Achievements
Guido Cipriani, Gabriele Di Gaspero, Aurélie Canaguier,
Julie Jusseaume, Johan Tassin, Arnaud Lemainque,
Vincent Thareau, Anne-Françoise Adam-Blondon
and Raffaele Testolin
6. Basics of Grapevine Genetic Analysis 137
Leocir J. Welter, M. Stella Grando and Eva Zyprian
7. Molecular Breeding 160
Reinhard Töpfer, Ludger Hausmann and Rudolf Eibach
8. Positional Cloning of Disease Resistance Genes in Grapevine 186
Claire Anderson, Nathalie Choisne, Anne-Françoise
Adam-Blondon and Ian B. Dry
xiv Genetics, Genomics and Breeding of Grapes

9. Genome Sequence Initiatives 211

Anne-Françoise Adam-Blondon, Olivier Jaillon, Silvia Vezzulli,
Andrey Zharkikh, Michela Troggio and Riccardo Velasco
10. Vitis Functional Genomics: Open Systems for 235
Transcriptome Analysis
Richard L. Tillett and John C. Cushman
11. Functional Genomics: Closed System Approaches for 270
Transcriptome Analyses
Charles Romieu, Christian Kappel and Serge Delrot
12. Functional Genomics: Proteomics and Metabolomics 299
Steven T. Lund and Grant R. Cramer
13. Bioinformatics Tools in Grapevine Genomics 317
Jérôme Grimplet, Julie Dickerson, Anne-Françoise Adam-Blondon
and Grant Cramer
14. Future Prospects 332
Anne-Françoise Adam-Blondon, Michel Boulay and
José M. Martinez-Zapater
Index 347
Color Plate Section 361
 List of Contributors

Anne-Françoise Adam-Blondon
UMR INRA UEVE ERL CNRS, Génomique végétale (URGV), 2 rue Gaston
Crémieux, BP5708, 91 057 Evry cedex, France.
Tel: (33) 160874534
Fax: (33) 160874549
Email: adam@[Link] fr
Claire Anderson
School of Forest Resources and Conservation, University of Florida,
Gainsville, FL 32611.
Tel: (1) 3522738122
Fax: (1) 3523921707
Email: anderson@[Link]
Michel Boulay
60, rue de Vaux, 77000 Livry-sur-Seine, France, ex. Responsable du
Développement Viticole, Moët et Chandon, 20 Avenue de Champagne,
51200 Epernay cedex.
Alain Bouquet
UMR INRA1334 CIRAD Montpellier SupAgro AGAP 2, place P. Viala, 34060
Montpellier Cedex, France.
Jean-Michel Boursiquot
UMT Géno-Vigne, 2, place P. Viala, 34060 Montpellier Cedex, France.
Tel: (33) 499612258
Fax: (33) 499612064
Email: boursiquot@[Link]
Aurélie Canaguier
UMR INRA UEVE ERL CNRS, Génomique végétale (URGV), 2 rue Gaston
Crémieux, BP5708, 91 057 Evry cedex, France.
Tel: (33) 160874534
Fax: (33) 160874549
Email: canaguier@[Link]
xvi Genetics, Genomics and Breeding of Grapes

Nathalie Choisne
Unité de Recherches en Génomique-info (URGI), INRA, Route de Saint-Cyr,
78026 Versailles, France.
Tel: (33) 130833000
Fax: (33) 130833458
Email: nchoisne@[Link]
Guido Cipriani
Dipartmento de Scienze Agrarie e Ambientali, University of Udine, via
delle scienze 208, 33100 Udine, Italy.
Tel: (39) 432629911
Fax: (39) 432603887
Email: [Link]@[Link]
John C. Cushman
Department of Biochemistry and Molecular Biology, MS 200, University of
Nevada, Reno, Nevada 89557-0200, USA.
Tel: (1) 7757841419
Fax: (1) 7757841650
Email: jcushman@[Link]
Grant Cramer
1664 North Virginia Street, Department of Biochemistry and Molecular
Biology, University of Nevada, Reno, NY 89557, USA.
Tel: (1) 7757844204
Fax: (1) 7757841650
Email: cramer@[Link]
Serge Delrot
Lab Ecophysiology and Grape Functional Genomics, Institute of Vine and
Wine Sciences, University of Bordeaux, INRA, 210 Chemin de, Leysotte,
CS 2008, 33882 Villenave d’Omon, France.
Tel: (33) 55757900
Fax: (33) 557575923
Email: [Link]@[Link]
Julie Dickerson
Electrical and Computer Engineering, Iowa State University, Ames, IA,
50011-3060, USA.
Tel: (1) 51529947705
Fax: (1) 5152948432
Email: julied@[Link]
 List of Contributors xvii

Gabriele Di Gaspero
Dipartmento de Scienze Agrarie e Ambientali, University of Udine, via
delle scienze 208, 33100 Udine, Italy, Istituto di Genomica Applicata, Parco
Scientifico e Tecnologico, Via Jacopo Linussio 51, 33100 Udine, Italy.
Tel: (39) 432629911
Fax: (39) 432603887
Email: [Link]@[Link]
Ian B. Dry
CSIRO Plant Industry, Waite Campus, Hartley Grove, Urrbrae, SA 5064,
Australia.
Tel: (61) 883038632
Fax: (61) 883038601
Email: [Link]@[Link]
Rudolf Eibach
JKI Institute for Grapevine Breeding, Geilweilerhof, D-76833 Siebeldingen,
Germany.
Tel: (49) 634541118
Fax: (49) 6345919050
Email: [Link]@[Link]
Lucie Fernandez
Instituto de Ciencias de la Vid y del Vino (ICVV), (CSIC, Universidad de La
Rioja, Gobierno de La Rioja), C/Madre de Dios 51, 26006 Logroño, Spain.
Tel: (34) 941299694
Fax: (34) 941299608
Email: [Link]@[Link]
Stella Grando
IASMA Research and Innovation Centre, Fondazione Edmund Mach-
Genomics and Crop Biology Area, Via Mach, 1 38010 San Michele all’Adige
(Trento), Italy.
Tel: (39) 461 615197
Fax: (39) 461 650956
Email: [Link]@[Link]
Jérôme Grimplet
Instituto de Ciencias de la Vid y del Vino (CSIC,UR, Gobierno de La Rioja),
C/Madre de Dios 51, 26006 Logroño, Spain.
Tel: (34) 941299695
Fax: (34) 941299608
Email: [Link]@[Link]
xviii Genetics, Genomics and Breeding of Grapes

Ludger Hausmann
JKI Institute for Grapevine Breeding, Geilweilerhof, D-76833 Siebeldingen,
Germany.
Tel: (49) 63451117
Fax: (49) 634591050
Email: [Link]@[Link]
Olivier Jaillon
CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux,
CP5706, 91057 Evry, France.
Tel: (33) 160872500
Fax: (33) 160872514
Email: ojaillon@[Link]
Julie Jusseaume
UMR INRA UEVE ERL CNRS, Génomique végétale (URGV), 2 rue Gaston
Crémieux, BP5708, 91 057 Evry cedex, France.
Tel: (33) 160874534
Fax: (33) 160874549
Christian Kappel
Lab Ecophysiology and Grape Functional Genomics, Institute of Vine and
Wine Sciences, University of Bordeaux, INRA, 210 Chemin de, Leysotte,
CS 2008, 33882 Villenave d’Omon, France.
Tel: (33) 55757900
Fax: (33) 557575923
Email: [Link]@[Link]
Thierry Lacombe
UMR INRA1334 CIRAD Montpellier SupAgro AGAP 2, place P. Viala, 34060
Montpellier Cedex, France.
Tel: (33) 499612253
Fax: (33) 499612064
Email: lacombe@[Link]
Arnaud Lemainque
Centre National de Génotypage, CNG-IG CEA, 2 rue Gastron Crémieux
CP 5721, 91057 Evry Cedex, France.
Tel: (33) 160878344
Fax: (33) 160878485
 List of Contributors xix

Steven Lund
241-2205 East Mall, Wine Research Centre, Faculty of Land and Food Systems,
University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
Tel: (1) 6048225708
Fax: (1) 6048222016
Email: [Link]@[Link]
José M. Martinez-Zapater
Instituto de Ciencias de la Vid y del Vino (ICVV), (CSIC, Universidad de La
Rioja, Gobierno de La Rioja), C/Madre de Dios 51, 26006 Logroño, Spain.
Tel: (34) 941299698
Fax: (34) 941299608
Email: zapater@[Link]
Christopher L. Owens
USDA-ARS Grape Genetics Research Unit, Cornell University, Geneva,
NY, USA.
Tel: (1) 315782437
Fax: (1) 315782339
Email: [Link]@[Link]
Frédérique Pelsy
INRA, UMR SVQV INRA-ULP Strasbourg, 28 rue de Herrlisheim, 68021
Colmar Cedex.
Tel: (33) 389224946
Fax: (33) 389224933
Email: pelsy@[Link]
Jean-Pierre Péros
UMR INRA1334 CIRAD Montpellier SupAgro AGAP 2, place P. Viala, 34060
Montpellier Cedex, France.
Tel: (33) 499612026
Fax: (33) 499612064
Email: peros@[Link]
Charles Romieu
UMR INRA1334 CIRAD Montpellier SupAgro AGAP 2, place P. Viala, 34060
Montpellier Cedex, France.
Tel: (33) 499612888
Fax: (33) 499612064
Email: romieu@[Link]
xx Genetics, Genomics and Breeding of Grapes

Johan Tassin
Centre National de Génotypage, CNG-IG CEA, 2 rue Gastron Crémieux
CP 5721, 91057 Evry Cedex, France.
Tel: (33) 160878344
Fax: (33) 160878485
Email: tassin@[Link]
Raffaele Testolin
Dipartiment di Scienze Agrarie e Ambientali, University of Udine, via delle
scienze 208, 33100 Udine, Italy.
Vincent Thareau
IBP, UMR CNRS Université Paris-Sud, bat 630, 91405 Orsay cedex,
France.
Tel: (33)169153330
Fax: (33) 1691153330
Email: [Link]@[Link]
Patrice This
UMR INRA1334 CIRAD Montpellier SupAgro AGAP 2, place P. Viala, 34060
Montpellier Cedex, France.
Tel: (33) 499612292
Fax: (33) 499612064
Email: this@[Link]
Richard L. Tillett
Department of Biochemistry and Molecular Biology, MS 200, University of
Nevada, Reno, Nevada 89557-0200, USA.
Tel: (1) 7757841918
Fax: (1) 7757841650
Reinhard Töpfer
JKI Institute for Grapevine Breeding, Geilweilerhof, D-76833 Siebeldingen,
Germany.
Tel: (49) 634541114
Fax: (49) 6345919050
Email: [Link]@[Link]
Laurent Torregrosa
UMR INRA1334 CIRAD Montpellier SupAgro AGAP 2, place P. Viala, 34060
Montpellier Cedex, France.
Tel: (33) 499612455
Fax: (33) 499612064
Email: [Link]@[Link]
 List of Contributors xxi

Michela Troggio
IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via
E. Mach 1, 38010, S. Michele all‘Adige, Trento, Italy.
Tel: (39) 0461615132
Fax: (39) 0461650956
Email: [Link]@[Link]
Riccardo Velasco
IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via
E. Mach 1, 38010, S. Michele all‘Adige, Trento, Italy.
Tel: (39) 0461615257
Fax: (39) 0461650956
Email: [Link]@[Link]
Silvia Vezzulli
IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via
E. Mach 1, 38010, S. Michele all‘Adige, Trento, Italy.
Tel: (39) 0461615536
Fax: (39) 0461650956
Email: [Link]@[Link]
Leocir Welter
Federal University of Pampa, Rua Luiz Joaquim de Sa Britto, 97650-000,
Itaqui, Rio Grande do Sul, Brazil.
Tel: (55) 34331669213
Fax: (55) 34331669
Email: leocirwelter@[Link]
Eva Zyprian
Julius Kühn Institut, Federal Centre for Cultivated Plants, Institute for
Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany.
Tel: (49) 63451126
Fax: (49) 634591050
Email: [Link]@[Link]
Andrey Zharkikh
Myriad Genetics Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA.
Tel: (1) 8015843600
Fax: (1) 8015843640
Email: zharkikh@[Link]
 Abbreviations

2DGE Two-dimensional gel electrophoresis (2DGE)

ABA Abscisic acid
AFLP Amplified fragment length polymorphism
AGI Arabidopsis Genome Initiative
ANR Anthocyanidin reductase
ArMV Arabis Mosaic Virus
AROS Array-Ready Oligo Set
BAC Bacterial artificial chromosome
BC Back-Cross or Before Christ depending on the context
BES BAC end sequences
bp base pair
BSA Bulked segregant analysis
CaOMT Caffeoyl methyl transferase
CAPS Cleaved amplified polymorphic sequence
cDNA Complementary DNA
cDNA-AFLP cDNA-amplified fragment length polymorphism
ChIP Chromatine immuno precipitation
CHS Chalcone synthase
CLS Carpel less
cM centi Morgan
cpDNA Chloroplastic DNA
cv Cultivar
DFCI Dana-Fraber Cancer Institute
DFR di hydroflavonol reductase
DNA Deoxyribonucleic acid
DXS 1-deoxy-D-xylulose 5-phosphate synthase
EB Ethidium bromide
EBI European Bioinformatics Institute
EMBL European Molecular Biology Laboratory
EMS Ethylmethane sulfonate
e-QTL Expression quantitative trait locus
ESI Electrospray ionization
EST Expressed Sequence Tag
EU European Union
xxiv Genetics, Genomics and Breeding of Grapes

F3’5’H Flavonoid 3’ 5’ hydroxylase

F3’H Flavonoid 3’ hydroxylase
F3H Flavanone 3 hydroxylase
FAME Fatty acid methyl ester
flb Fleshless berry
flcDNAs full length cDNA
FT-ICR Fourier transform ion cyclotron resonance
GAI1 Gibberellic Acid Insensitive1
GCB Grapevine Corky Bark
GC Gas chromatography
GEO Gene Expression Omnibus
GFkV Grapevine Fleck Virus
GFLV Grapevine Fanleaf Virus
GIS Geographical Information Systems
GLRaV Grapevine leafroll associated virus
GM/GMO Genetically modified (organism)
GO Gene Ontology
GPP Geranyl diphosphate
GPS Global Positioning System
GRIP Grape Ripening-Induced Protein
GS Genome Sequencer
GSS Genome Survey Sequences
GST Glutathione S-transferase
GVM Grapevine Vein Mosaic
GVN Grapevine Vein Necrosis
H0 Observed heterozygosity
HC Hydrogen Cyanamide
HMA/HTA Homozygous assembly/heterozygous assembly
HPLC High Performance Liquid Chromatography
IBD Identity-by-descent
ICAT Isotope-coded affinity tags
IGGP International Grapevine Genome Program
IGS Intergenic spacer
Indel Insertion/deletion
IPCC Intergovernmental Panel on Climatic Change
IPP Isopentenyl diphosphate
IRGSP International Rice Genome Sequencing Project
ITMS Ion trap mass spectrometry
iTRAQ Isobaric tagging for relative and absolute quantitation
ITS Internally transcribed spacer
kbp Kilobase pair
KSG Kober Stem Grooving
LAR Leucoanthocyanidin reductase
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