The french-italian sequencing project of the grapevine genome

Transcription

1 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

2 Challenges in viticulture Develop sustainable practices while maintaining : high quality wines reasonable farming cost/ ha Find solutions for uncontrolled diseases Face climatic changes New diseases Tons of activ compound 0 Fungicides (France) Other crops Changes in the equilibrium between sugar content 5000 and organoleptic maturity 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)

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 : EU COST 858 action coordinated by S. Delrot

4 Set up of a strategy Whole genome shotgun 12X coverage Nearly homozygous line PN40024

5 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 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

6 A first 8X draft of the genome sequence released in august Grapevine genome: 4th plant genome completely sequenced Arabidopsis, 2000 Rice, 2005 Poplar, 2006

7 Sequence Assemblies French-Italian assembly :: 6X 6X Assembly total total size size :: Mb Mb Contigs :: Nb= Nb= N50= N50= Kb Kb 8X 8X Assembly total total size size :: Mb Mb Contigs :: Nb= Nb= N50= N50= Kb Kb IASMA-Myriad assembly :: 7X 7X Sanger + 4X 4X pyrosequencing Assembly total total size size :: Mb Mb Contigs :: Nb= Nb= N50= N50= Kb Kb =>As expected the low heterozygocity of PN40024 facilitate the assembly

8 69% of the draft sequence is anchored on the genetic map 61% is anchored and orientated Under improvement for the final 12X version ( 2008 )

9 Tools for Annotation Vitis ESTs developped by the international community A ressource of around full length cdna ( already available) in the frame of the french-italian sequencing project To be finished with the 12X version

10 Annotation genes : ( genes common with poplar ( ( genes common with Arabidopsis ( ( genes common with rice ( % of repeats 12% of introns contain TE

11 11 4 9

12 Probably less than100 Myr 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

13 WEB SITES The consortium web site is accessible from France and Italy: hppt:// & hppt:// 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).

14 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?

15 Functional genomic : studying the molecular mechanisms underlying traits

16 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

17 Understand the genetic basis of trait variation

18 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

19 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

20 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 ( ): study the sequence diversity in 1500 gene fragments

21 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

22 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