A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance
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- 作者：Marco Moroldo (1)
Sophie Paillard (1) (2)
Raffaella Marconi (3)
Legeai Fabrice (4)
Aurelie Canaguier (1)
Corinne Cruaud (5)
Veronique De Berardinis (5)
Cecile Guichard (1)
Veronique Brunaud (1)
Isabelle Le Clainche (1)
Simone Scalabrin (6) (7)
Raffaele Testolin (3) (7)
Gabriele Di Gaspero (3) (7)
Michele Morgante (3) (7)
Anne-Francoise Adam-Blondon (1) - 刊名：BMC Plant Biology
- 出版年：2008
- 出版时间：December 2008
- 年：2008
- 卷：8
- 期：1
- 全文大小：2297KB
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Sophie Paillard (1) (2)
Raffaella Marconi (3)
Legeai Fabrice (4)
Aurelie Canaguier (1)
Corinne Cruaud (5)
Veronique De Berardinis (5)
Cecile Guichard (1)
Veronique Brunaud (1)
Isabelle Le Clainche (1)
Simone Scalabrin (6) (7)
Raffaele Testolin (3) (7)
Gabriele Di Gaspero (3) (7)
Michele Morgante (3) (7)
Anne-Francoise Adam-Blondon (1)
1. UMR de G茅nomique V茅g茅tale, INRA-CNRS-UEVE, 2, Rue Gaston, Cr茅mieux, CP5708, 91057, Evry Cedex, France
2. UMR118, INRA-Agrocampus, University of Rennes, Am茅lioration des Plantes et Biotechnologies, V茅g茅tales, F-35650, Le Rheu, France
3. Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100, Udine, Italy
4. Unit茅 de Recherche G茅nomique-Info, URGI, Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034, Evry, Cedex, France
5. Gnoscope, 2, rue Gaston Cr茅mieux, CP5706, 91057, Evry, Cedex, France
6. Dipartimento di Scienze Matematiche, University of Udine, via delle Scienze 208, 33100, Udine, Italy
7. Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
文摘
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. Conclusion 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.