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The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Hélène Badouin 1, * Amandine Velt 2 François Gindraud 1 Timothée Flutre 3 Vincent Dumas 2 Sonia Vautrin 4 William Marande 4 Jonathan Corbi 1 Erika Sallet 5 Jérémy Ganofsky 1 Sylvain Santoni 6 Dominique Guyot 7 Eugenia Ricciardelli 8 Kristen Jepsen 8 Jos Käfer 1 Hélène Berges 4 Eric Duchene 2 Franck Picard 1 Philippe Hugueney 2 Raquel Tavares 1 Roberto Bacilieri 6 Camille Rustenholz 2 Gabriel Marais 1
* Corresponding author
1 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
2 SVQV - Santé de la vigne et qualité du vin
3 GQE-Le Moulon - Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale)
4 CNRGV - Centre National de Ressources Génomiques Végétales
5 LIPME - Laboratoire des Interactions Plantes Microbes Environnement
6 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
7 PRABI - Pôle Rhône-Alpin de BioInformatique [Lyon]
8 University of California
Abstract : Background: A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditismin cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results: We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions: We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.
Keywords : Grapevine Dioecy Sex chromosomes Sex-determining genes
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Hélène Badouin, Amandine Velt, François Gindraud, Timothée Flutre, Vincent Dumas, et al.. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biology, BioMed Central, 2020, 21 (1), pp.223. ⟨10.1186/s13059-020-02131-y⟩. ⟨hal-02946414⟩

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