such as "Introduction", "Conclusion"..etc
Marco Moroldo* 1 , Sophie Paillard* 1,2 , Raffaella Marconi3 , Legeai Fabrice4 , Aurelie Canaguier1 , Corinne Cruaud5 , Veronique De Berardinis5 , Cecile Guichard1 , Veronique Brunaud1 , Isabelle Le Clainche1 , Simone Scalabrin6,7 , Raffaele Testolin3,7 , Gabriele Di Gaspero3,7 , Michele Morgante3,7 and Anne-Francoise Adam-Blondon1
1UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
2UMR118, INRA-Agrocampus, University of Rennes, Amélioration des Plantes et Biotechnologies Végétales, F-35650 Le Rheu, France
3Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
4Unité de Recherche Génomique-Info, URGI, Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France
5Gnoscope, 2, rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
6Dipartimento di Scienze Matematiche, University of Udine, via delle Scienze 208, 33100 Udine, Italy
7Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
BMC Plant Biology 2008,
8:66doi:10.1186/1471-2229-8-66. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.
Whole-genome physical maps facilitate genome sequencing, sequence
assembly, mapping of candidate genes, and the design of targeted
genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet
Sauvignon' physical map. The quality of the result was addressed with
regard to the effect of high heterozygosity on the accuracy of contig
assembly. Its usefulness for the genome-wide mapping of genes for
disease resistance, which is an important trait for grapevine, was then
The physical map included 29,727 BAC clones assembled into 1,770
contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome
size. Map inflation was due to high heterozygosity, which caused either
the separation of allelic BACs in two different contigs, or local
mis-assembly in contigs containing BACs from the two haplotypes.
Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The
fully automated assembly and anchorage procedures were validated by
BAC-by-BAC blast of the end sequences against the grape genome
sequence, unveiling 7.3% of chimerical contigs. The distribution across
the physical map of candidate genes for non-host and host resistance,
and for defence signalling pathways was then studied. NBS-LRR and RLK
genes for host resistance were found in 424 contigs, 133 of them (32%)
were assigned to chromosomes, on which they are mostly organised in
clusters. Non-host and defence signalling genes were found in 99
contigs dispersed without a discernable pattern across the genome.
Despite some limitations that interfere with the correct assembly of
heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map
is a useful and reliable intermediary step between a genetic map and
the genome sequence. This tool was successfully exploited for a quick
mapping of complex families of genes, and it strengthened previous
clues of co-localisation of major NBS-LRR clusters and disease
resistance loci in grapevine.
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