A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance.
BACKGROUND
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 assessed.


RESULTS
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.


CONCLUSIONS
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.
UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France. moroldo@evry.inra.fr
Marco
M
Moroldo
Sophie
S
Paillard
Raffaella
R
Marconi
Legeai
L
Fabrice
Aurelie
A
Canaguier
Corinne
C
Cruaud
Veronique
V
De Berardinis
Cecile
C
Guichard
Veronique
V
Brunaud
Isabelle
I
Le Clainche
Simone
S
Scalabrin
Raffaele
R
Testolin
Gabriele
G
Di Gaspero
Michele
M
Morgante
Anne-Francoise
AF
Adam-Blondon
D032461:Chromosomes, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D006579:Heterozygote; D007113:Immunity, Innate / Q000235:genetics; D020161:Physical Chromosome Mapping / Q000379:methods*; D010935:Plant Diseases / Q000235:genetics*; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics; D027843:Vitis / Q000235:genetics*