The french-italian sequencing project of the grapevine genome A-F Adam-Blondon UMR INRA-CNRS-UEVE of Research in Plant Genomics Bruxelles 2007, December 19th
Challenges in viticulture Develop sustainable practices while maintaining : high quality wines reasonable farming cost/ ha Find solutions for uncontrolled diseases 45000 40000 Face 35000 climatic changes New 30000 25000 diseases Tons of activ compound 0 Fungicides (France) 20000 Other crops Changes 15000 in the equilibrium between sugar 10000 content 5000 and organoleptic maturity 1992 1993 1994 1995 1996 1997 1998 1999 Years Cereales Grapevine 2. FOOD, AGRICULTURE AND FISHERIES AND BIOTECHNOLOGY 2.1 Sustainable production and management of biological resources from land, forest, and aquatic environments (3)
2001 : creation of the International Grape Genome Program consortium Promote and coordinate the development of public genomic resources for grapevine Based on informal agreements between scientists www.vitaceae.org 2004-2008 : EU COST 858 action coordinated by S. Delrot
Set up of a strategy Whole genome shotgun 12X coverage Nearly homozygous line PN40024
The French-Italian public consortium for the sequencing of the grapevine nuclear genome The sequencing of the grapevine nuclear genome (475 Mbp) was launched in July 2005. This bilateral initiative collects 6 laboratories France Genoscope (7X) URGV URGI Italy ( 2.5X ) University of Padova ( 2.5X ) University of Udine University of Milano
A first 8X draft of the genome sequence released in august 2007 www.genoscope.cns.fr/vitis Grapevine genome: 4th plant genome completely sequenced Arabidopsis, 2000 Rice, 2005 Poplar, 2006
Sequence Assemblies French-Italian assembly :: 6X 6X Assembly total total size size :: 487 487 Mb Mb Contigs :: Nb= Nb= 57 57662 N50= N50= 23 23 Kb Kb 8X 8X Assembly total total size size :: 487 487 Mb Mb Contigs :: Nb= Nb= 19 19577 N50= N50= 65.9 65.9 Kb Kb IASMA-Myriad assembly :: 7X 7X Sanger + 4X 4X pyrosequencing Assembly total total size size :: 550 550 Mb Mb Contigs :: Nb= Nb= 66 66165 N50= N50= 10 10 Kb Kb =>As expected the low heterozygocity of PN40024 facilitate the assembly
69% of the draft sequence is anchored on the genetic map 61% is anchored and orientated http://urgi.versailles.inra.fr/cmap Under improvement for the final 12X version ( 2008 )
Tools for Annotation 290 000 Vitis ESTs developped by the international community A ressource of around 100 000 full length cdna (90 000 already available) in the frame of the french-italian sequencing project To be finished with the 12X version
Annotation 30 434 genes : ( genes 12 996 common with poplar (45 000 ( genes 11 404 common with Arabidopsis (25 498 ( genes 9 731 common with rice (37 544 41 % of repeats 12% of introns contain TE
11 4 9
Probably less than100 Myr 130-240 Myr The ancestor of grapevine, poplar and Arabidopsis had a triplicated genome The monocotyledons do not present this triplication The more recent supplementary duplications in poplar and Arabidopsis genomes can be better placed in the evolution
WEB SITES The consortium web site is accessible from France and Italy: hppt://www.genoscope.cns.fr & hppt://www.appliedgenomics.org Public policy in giving a free and complete access to all results. All sequence reads + 8X assembly are accessible in the Trace Repository database (NCBI & Ensembl).
Facilitate the integration of data and access to data URGI Plateform Sequences Mapping data Transcriptomic data Proteomic data SNP data SNP proteome transcriptome core mutants mapping sequence Reference database for the genome sequence and its annotations?
Functional genomic : studying the molecular mechanisms underlying traits
Terpenes synthase family Plant pathogen interactions isopentenyl diphosphate C5 Aromas, Plant pathogen interactions Gibberellic Acid, Plant pathogen interactions Manual expertise of the gene family : 89 genes and 27 pseudogenes in grapevine Arabidopsis, rice and poplar : around 40 genes Existence of heterodimeric GPPS like in menth and Clarkia Organisation in clusters of tandem repeats of genes (Ex: 33 genes on 672kb on chr ( 18
Understand the genetic basis of trait variation
PRIMARY AMERICAN GERMPLASM FOR TOLERANCE TO MAJOR DISEASES From Reisch, 2005 CROWN GALL (Agrobacterium) PIERCE'S DISEASE (Xylella) BOTRYTIS BUNCH ROT V. labrusca, V. riparia, V. rupestris V. rotundifolia, V. simpsoni, V. shuttleworthii, V. arizonica V. riparia, V. rupestris, V. rotundifolia (and more) BLACK ROT (Guignardia) V. riparia, V. candicans, V. cinerea, V. rupestris, V. vulpina, V. rotundifolia, V. berlandieri => Comparative genomics between V. vinifera and PHOMOPSIS resistant species and genomics of its pathogens V. rotundifolia, V. aestivalis, V. palmata, V. acerifolia DOWNY MILDEW (Plasmopara) POWDERY MILDEW (Uncinula) V. riparia, V. aestivalis, V. cinerea V. labrusca, V. candicans, V. berlandieri V. aestivalis, V. cinerea, V. riparia, V. berlandieri, V. rotundifolia, V. labrusca, V. rupestris D après BI Reisch, 2005
COREGRAPEGEN : Exploitation of natural diversity in grape functional genomics Coordinators: France : A-F Adam-Blondon, URGV, INRA-CNRS Germany : Eva Zyprian and Reinhard Töpfer, FCBR, Institute for Grapevine Breeding Geilweilerhof Spain : José M. Martínez-Zapater and Rosa Arroyo CNB-CSIC Other participants : URGI, Infobiogen, Contact : F. Legeai UMR DGPC, Génétique de la vigne, Contact : P. This IMIA, Banco de Germoplasma de El Encín, Contact : F. Cabello
92 accessions 326 alleles = 100% FRENCH-GERMAN- SPANISH TRILATERAL PROJECT 48 accessions 271 alleles = 83% 20 SSR on 4000 accessions of cultivated Vitis vinifera 2261 uniques genotypes 24 accessions 238 alleles = 73% Organisation in nested corecollections retaining the maximum of diversity 12 accessions 191 alleles = 59% SNPGrapeMap project (2007-2008): study the sequence diversity in 1500 gene fragments
Combination of QTL mapping and LD approaches Syrah x Grenache : full sib family, 192 ind Core collection QTL for fertility LOD-score QTL confidence interval : from 10 cm to 40kb cm
Sequencing project, french part Genoscope (Sequencing, Annotation) Francis Quetier Jean Weissenbach Patrick Wincker Teams Libraries, Sequencing, Bioinformatics ( databases INRA URGI (mapping Fabrice Legeai Michael Alaux ( DEA ) Eleonore Durand INRA SVQV (Homozygous line) Vincent Dumas INRA URGV (Mapping; Annotation) Anne-Françoise Adam-Blondon Christian Clepet Delphine Jublot ( doc Marco Moroldo (post Aurelie Canaguier Isabelle LeClainche Julie Jusseaumes Sébastien Aubourg Alain Lecharny Clémence Bruyère Sequencing Project, Italian part CRIBI, Padova Giorgio Valle Teams sequencing and bioinformatics IGA, Udine Michele Morgante Alberto Policriti Team Sequencing, physical mapping and bioinformatics University of Milano and CIB Trieste Enrico Pé Claudio Scheider Team Mapping, full length cdna, mirna University of Verona Mario Pezzotti Massimo Delledonne