Variation structurelle d'une région génomique contrôlant la biosynthèse des tannins condensés chez la vigne sauvage et cultivée

Type de poste
Niveau d'étude minimal
Dates
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Localisation
Nom de la structure d'accueil
Adresse

UMR 1334 AGAP Amélioration génétique et adaptation de plantes. Equipe Diversité, Amélioration et Adaptation de la Vigne (DAAV)
INRAE – CIRAD – Univ. Montpellier – Institut Agro, 2 Place P. Viala
34060 Montpellier
France

Contacts
Charles Romieu (biochimie)
Roberto Bacilieri (génétique)
Dominique This (génomique)
Email du/des contacts
Charles.romieu@inrae.fr
Roberto.bacilieri@inrae.fr
dominique.this@supagro.fr
Description

By combining genotyping [1] and biochemical characterization of hundreds of cultivated grapes [2], we identified a genomic region controlling the hydroxylation of condensed tannins in the berry. This region, of about 0.6 Mbases, integrates 8 to 16 potentially functional copies of the candidate gene (hydrolase), framed by other genes and long sequences of repeated elements [3]. These hydrolases appear to be differentially expressed during berry development, impacting specifically the tannin composition, as compared to that of anthocyanins.

The aim of this internship is to understand the structural variations affecting this complex genomic region on a panel of cultivated and wild vines, and at the interspecific level in Asian and American Vitis [4], by taking advantage of the genomic assemblages available in international databases (NCBI, ENA, etc. examples in [5]).

Mission: Using available long-range genome sequences from a set of cultivated (n=7) and wild grapes (n=>8), the trainee will study the genome synteny at the intra- and inter-specific level, transpose the annotations from one genotype to another, detect repeated elements, and analyze the variations across botanical taxa and phenotypic categories. He/she will produce a comparative map of the region with the different annotated elements. This work will be conducted on the SouthGreen bioinformatics platform, using both existing softwares, and developing specific pipelines and scripts when needed. In a second phase, he/she will exploit short-range genomic data available on a much wider range of diversity to detect signals of selection. This work should make it possible to specify which events in the genome could have contributed to the specific extinction of tannin hydroxylation in certain Vitaceae, and the evolution of this trait under human-mediated selection during grape domestication.

Terms and Conditions:
- Knowledge in genomics and bioinformatics
- Duration: six months from January or February 2020
- Gratification: 600€/month
- Preliminary interview (telephone or skype)

Citations:
[1] Laucou L, Launay A, Bacilieri R, Lacombe T, Adam-Blondon AF, Bérard A, Chauveau A, de Andres MT, Hausmann L, Ibañez J, Le Paslier MC, Maghradze D, Martinez-Zapater JM, Maul E, Ponnaiah M, Töpfer R, Péros JP, Boursiquot JM, 2018. Extended Diversity Analysis of Cultivated Grapevine Vitis vinifera with 10K Genome-wide SNPs. PloS ONE 13(2): e0192540. https://doi.org/10.1371/journal.pone.0192540.
[2] Romieu C, Bacilieri R, Fulcrand H, Billerach G, Marchal C, Dentraygues C, Jiang J, Musayev M, Reynders M, Nick P, Maghradze D, Grisoni M and Brillouet JM. (2019). Condensed tannins in the pericarp of diverse Vitis species. Acta Hortic. 1248, 439-444.DOI: 10.17660/ActaHortic.2019.1248.61.
[3] Falginella L, Castellarin S, Testolin R, Gambetta GA, Morgante M, Di Gaspero. (2010). Expansion and subfunctionalisation of flavonoid 3’,5’-hydroxylases in the grapevine lineage. BMC Genomics 2010, 11:562, http://www.biomedcentral.com/1471-2164/11/562.
[4] Wan Y, Schwaninger H R, Baldo A M, Labate J A, Zhong G-Y, Simon C J. 2013. A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change. BMC Evol Biol. 13, 141-161. doi: 10.1186/1471-2148-13-141.
[5] http://www.grapegenomics.com/pages/all.php,
https://www.ebi.ac.uk/ena/browser/text-search?query=SAMEA6619703,
https://www.ncbi.nlm.nih.gov/Traces/wgs/QGNW01?display=contigs

Other related publications of the DAAV Team:
Badouin H, Bacilieri R, et al. 2020. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biology volume 21, Article number: 223 (2020). https://doi.org/10.1186/s13059-020-02131-y.
Ramos‐Madrigal J, Bacilieri R, et al. 2019. Palaeogenomic insights into the origins of French grapevine diversity. Nature Plants, 5: 595-603. DOI:10.1038/s41477-019-0437-5.
Laucou L, Bacilieri R, et al. 2018. Extended Diversity Analysis of Cultivated Grapevine Vitis vinifera with 10K Genome-wide SNPs. PloS ONE 13(2): e0192540. https://doi.org/10.1371/journal.pone.0192540.
Clément Y, Bacilieri R, et al. 2017. Evolutionary forces affecting synonymous variations in plant genomes. PLoS Genet 13(5): e1006799. https://doi.org/10.1371/journal.pgen.1006799.
Brillouet, J.-M., Romieu, C., et al. 2013. The tannosome is an organelle forming condensed tannins in the chlorophyllous organs of Tracheophyta. Ann. Bot. 112, 1003-1014. doi:10.1093/aob/mct168.

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