Paris, France
October 2, 2008
Source: INRA
Une équipe internationale menée
par des chercheurs de l'INRA de
Clermont-Ferrand, Toulouse et Versailles, vient de réaliser la
première carte physique d'un chromosome du blé. Ceci constitue
un exploit sans précédent : en effet, le blé est une espèce dont
le séquençage et l'exploration moléculaire à large échelle
étaient considérés jusqu’à présent comme impossibles à cause de
la taille et la complexité de son génome. Ces travaux, qui
ouvrent la voie au séquençage total du génome du blé, ont été
publiés dans la revue « SCIENCE » du 3 octobre 2008.
Le blé (Triticum aestivum L.), aliment de base pour 35%
de la population mondiale, a une importance économique majeure.
Cependant, les outils d'exploration de son génome sont très en
retard par rapport à d'autres céréales comme le maïs, le riz ou
le sorgho. De ce fait, l'amélioration du blé reste aujourd'hui
trop lente au regard des défis que l’agriculture doit affronter.
Ce retard est dû à la difficulté d'accès à un génome très
particulier: d'une très grande taille (17 milliards de paires de
bases, soit 5 fois le génome humain et 40 fois le génome du riz)
et composé à 80% de séquences répétées.
Les cartes physiques sont le premier pas indispensable au
séquençage des génomes. Les chercheurs de l’INRA et leurs
collègues se sont focalisés sur le plus grand des chromosomes du
blé, le chromosome 3B, qui compte près d'un milliard de paires
de bases. La carte physique qu'ils ont réalisée de ce chromosome
est composée d'une série de 1036 groupes de séquences d'ADN
appelées contigs. Ces contigs, dont l'ordre a été établi grâce à
1443 marqueurs génétiques, permettent de reconstruire
l'essentiel du chromosome 3B. Avant de venir à bout de cette
tâche, les chercheurs ont dû faire face à de nombreuses
difficultés, inhérentes au génome du blé. En effet, celui-ci est
hexaploïde (6 jeux de chromosomes, 42 au total), contient un
nombre élevé de séquences répétées et présente une faible
variabilité génétique au sein des variétés cultivées.
Les cartes physiques constituent un outil précieux pour
localiser rapidement des gènes d'intérêt agronomique et pour
mettre au point de nouveaux marqueurs génétiques. Elles
permettent l'exploration des régions du génome responsables de
caractères d’intérêt agronomique comme le rendement, la qualité
et la résistance aux stress. Comme première application de leurs
travaux, les chercheurs ont localisé sur la carte physique du
chromosome 3B certains gènes importants comme un gène de
résistance à la rouille noire, maladie provoquée par un
champignon.
Ces travaux ont été réalisés dans le cadre d’un projet pilote du
consortium international pour le séquençage du génome de blé
(1). Ils démontrent qu'il est possible de construire des cartes
physiques pour des génomes complexes et de très grande taille.
Ils serviront, dans un premier temps, comme modèle pour
l'élaboration des cartes des autres chromosomes du blé et de
support au séquençage prochain du chromosome 3B. D'un point de
vue plus général, ces travaux constituent un jalon important
dans l'analyse du génome d'autres espèces végétales réputées «
impossibles ».
(1) IWGSC,
www.wheatgenome.org
Références:
"A physical map of the 1Gb bread wheat chromosome 3B "
Etienne Paux 1, Pierre Sourdille 1, Jérôme Salse 1, Cyrille
Saintenac 1, Frédéric Choulet 1, Philippe Leroy 1, Abraham Korol
2, Monika Michalak 3, Shahryar Kianian 3, Wolfgang Spielmeyer 4,
Evans Lagudah 4, Daryl Somers 5, Andrzej Kilian 6, Michael Alaux
7, Sonia Vautrin 8, Hélène Bergès 8, Kellye Eversole 9, Rudi
Appels 10, Jan Safar 11, Hana Simkova 11, Jaroslav Dolezel 11,
Michel Bernard 1 and Catherine Feuillet 1
SCIENCE, 3 Octobre 2008
1 INRA-UBP, UMR1095, Genetics Diversity and Ecophysiology of
Cereals, Clermont- Ferrand, France.
2 Institute of Evolution, University of Haifa, Israel.
3 Department of Plant Sciences, North Dakota State University,
USA
4 CSIRO Plant Industry, Canberra, Australia.
5 Agriculture and Agri-Food Canada, Cereal Research Centre,
Winnipeg, Canada.
6 Diversity Arrays Technology Pty Ltd, Yarralumla, Australia.
7 INRA-Unité de Recherches en Génomique-Info, Versailles,
France.
8 INRA-Centre National de Ressources Génomiques Végétales,
Toulouse, France.
9 International Wheat Genome Sequencing Consortium, Eversole
Associates, Bethesda,
USA.
10 Centre for Comparative Genomics, Murdoch University,
Australia.
11 Laboratory of Molecular Cytogenetics and Cytometry, IEB,
Olomouc, Czech Republic.
The first step towards sequencing the wheat genome: the physical
map of its largest chromosome
In an unprecedented achievement, an international team led by
INRA researchers from Clermont-Ferrand, Toulouse and Versailles
has completed the first physical map of the largest bread wheat
chromosome. Until now, the bread wheat genome has been
considered impossible to physically map and sequence because of
its size and complexity. This work, published in the prestigious
journal SCIENCE on 3 October 2008, opens the path towards
sequencing the wheat genome.
Wheat (Triticum aestivum L.) is the staple food for 35% of the
world’s population. Despite its socio-economic importance and
the need for accelerated wheat genetic improvement to meet the
challenges of agriculture, the tools for exploring the wheat
genome are far less advanced than those developed for other
cereals, such as corn, rice or sorghum. Both the size (17
billion base pairs - 5 times larger than the human genome and 40
times larger than the rice genome) and complexity (polyploid
structure of 3 genomes with more than 80% of the genome composed
of repetitive sequences) of the wheat genome have been stumbling
blocks to traditional sequencing approaches until now.
The construction of a physical map is the first essential step
towards sequencing a large genome. To reduce the complexity of
mapping the entire hexaploid bread wheat genome, the INRA
researchers and their colleagues have developed a strategy based
on the isolation and analysis of each of the individual wheat
chromosomes. They have focused first on the largest chromosome,
3B, which has nearly one billion base pairs (almost 3 times as
many as the entire rice genome) to establish their proof of
concept and the first physical map of a bread wheat chromosome.
The 3B physical map is composed of a series of 1036 groups of
DNA sequences called “contigs” that were anchored with 1443
molecular markers and ordered using a combination of different
mapping approaches to reconstruct a large part of chromosome 3B.
While completing this task, the researchers were faced with many
difficulties inherent to the bread wheat genome, such as the
lack of recombination in half of the chromosome and the reduced
genetic variability found within cultivated varieties.
Physical maps constitute a precious tool for locating rapidly
genes of agronomic interest and for identifying new molecular
markers. They make it possible to explore regions of the genome
responsible for agronomically important traits, such as yield,
quality and stress resistance. As the first application of their
work, the researchers located on the physical map of chromosome
3B some important genes, including a resistance gene to stem
rust, a major fungal disease of wheat.
This research was conducted as a pilot project within the
framework of the International Wheat Genome Sequencing
Consortium (1). It shows that it is possible to construct
physical maps for genomes with a chromosome-based approach
regardless of the size and complexity. The work serves now as a
model for other international groups to assemble the physical
maps of the 20 other wheat chromosomes within the IWGSC and
provides the basis for sequencing chromosome 3B in the near
future. From a more general point of view, this work opens new
perspectives for the analysis of genomes of other reputedly
“impossible” plant species.
(1) IWGSC,
www.wheatgenome.org
References:
"A physical map of the 1Gb bread wheat chromosome 3B "
SCIENCE, 3 October 2008
Etienne Paux1, Pierre Sourdille1, Jérôme Salse1, Cyrille
Saintenac1, Frédéric Choulet1,
Philippe Leroy1, Abraham Korol2, Monika Michalak3, Shahryar
Kianian3, Wolfgang Spielmeyer4, Evans Lagudah4, Daryl Somers5,
Andrzej Kilian6, Michael Alaux7, Sonia Vautrin8, Hélène Bergès8,
Kellye Eversole9, Rudi Appels10, Jan Safar11, Hana Simkova11,
Jaroslav Dolezel11, Michel Bernard1 and Catherine Feuillet1
1INRA-UBP, UMR1095, Genetics Diversity and Ecophysiology of
Cereals, Clermont- Ferrand, France.
2Institute of Evolution, University of Haifa, Israel.
3Department of Plant Sciences, North Dakota State University,
USA
4CSIRO Plant Industry, Canberra, Australia.
5Agriculture and Agri-Food Canada, Cereal Research Centre,
Winnipeg, Canada.
6Diversity Arrays Technology Pty Ltd, Yarralumla, Australia.
7INRA-Unité de Recherches en Génomique-Info, Versailles, France.
8INRA-Centre National de Ressources Génomiques Végétales,
Toulouse, France.
9International Wheat Genome Sequencing Consortium, Eversole
Associates, Bethesda, USA.
10Centre for Comparative Genomics, Murdoch University,
Australia.
11Laboratory of Molecular Cytogenetics and Cytometry, IEB,
Olomouc, Czech Republic.
A giant leap for wheat
genome
By Elizabeth Pennisi
Source:
ScienceNOW Daily News
2 October 2008
"Divide and conquer" has been a winning military strategy since
Roman times. Now an international team has applied this approach
to tackle the wheat genome, which is five times the size of the
human genome and much more complicated. Plant geneticist
Catherine Feuillet of INRA-UBP in Clermont-Ferrand, France, and
her colleagues have isolated one of wheat's 42 chromosomes and
made a physical map of it, placing more than 1400 molecular
landmarks along its 995 million bases.
"For wheat researchers languishing in genomic poverty, this is
the beginning of genomic empowerment," says Bikram Gill, a plant
geneticist at Kansas State University in Manhattan. The map will
not only assist in sequencing but also help researchers more
easily find genes important to increasing yields and dealing
with drought and disease.
Like computer memory, genome sequencing capacity has been rising
exponentially and decreasing in cost, making possible the
deciphering of ever-larger genomes. Nonetheless, the wheat
genome has seemed too daunting, and not just because it's 17
gigabases long. Triticum aestivum contains three sets of
chromosomes rolled into one nucleus. This so-called hexaploid
arrangement arose in two steps. First, two wild grasses combined
genomes to make what was the ancestor to durum (pasta) wheat.
Later, this hybrid hybridized with another wild wheat species.
The resulting genome has three sets of DNA--known as the A, B,
and D genomes--which are quite similar but not identical.
Another complication is the fact that, like corn and the human
genome, the bread wheat genome is rife with repetitive
sequences. Repetitive DNA and similar sequences are a
sequencer's nightmare because the sequence is generated in
pieces that must be matched up correctly to figure out the order
of the bases along each chromosome. The wheat genome "was
thought to be intractable," says Gill.
To overcome these obstacles, Feuillet and her colleagues are
attacking the bread wheat genome chromosome by chromosome--an
early strategy used for sequencing the yeast genome and,
initially, the human genome. She picked the largest, 3B
(chromosome 3 of the B genome), which by itself is double the
size of the entire rice genome, containing about 6000 genes. Her
group teamed up with Jaroslav Dolezel of the Institute of
Experimental Botany in Olomouc, Czech Republic, whose team has
developed a way to sort similar chromosomes by size so as to be
able to sequence each chromosome independently. In all, the
researchers were able to position more than 1000 markers on the
chromosome that will help them and others hunt for useful genes.
The map is reported in tomorrow's issue of Science.
The divide-and-conquer tactic also puts financing--and
sequencing--the entire wheat genome more in reach. "Chromosomes
can be 'divided up' into manageable packages amongst the wheat
groups in different countries," explains Graham Moore of the
John Innes Centre in Norwich, U.K. For example, the French
government is supporting Feuillet's completion of 3B, and the
U.S. government is supporting Gill's mapping of several other
chromosomes. Given that wheat feeds more than one-third of
Earth's population, says Gill, "this is good news for world food
security."
A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B
Etienne Paux, Pierre Sourdille, Jérôme Salse, Cyrille Saintenac,
Frédéric Choulet, Philippe Leroy, Abraham Korol, Monika
Michalak, Shahryar Kianian, Wolfgang Spielmeyer, Evans Lagudah,
Daryl Somers, Andrzej Kilian, Michael Alaux, Sonia Vautrin,
Hélène Bergès, Kellye Eversole, Rudi Appels, Jan Safar, Hana
Simkova, Jaroslav Dolezel, Michel Bernard, and Catherine
Feuillet (3 October 2008)
Science 322 (5898), 101. [DOI: 10.1126/science.1161847]
Abstract:
http://www.sciencemag.org/cgi/content/abstract/sci;322/5898/101
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French scientists reported this
week that they have mapped the
largest chromosome in the wheat
genome, chromosome 3B, a feat
reported in more detail in the
current edition of the journal
Science |
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