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Background  In  Vitis vinifera  L., domestication induced a dramatic change in flower morphology: the wild  sylvestris  subspecies is dioecious while hermaphroditism is largely predominant in the domesticated subsp.  V. v. vinifera . The characterisation of polymorphisms in genes underlying the sex-determining chromosomal region may help clarify the history of domestication in grapevine and the evolution of sex chromosomes in plants. In the genus  Vitis,  sex determination is putatively controlled by one major locus with three alleles, male  M , hermaphrodite  H  and female  F,  with an allelic dominance  M  >  H  >  F.  Previous genetic studies located the sex locus on chromosome 2. We used DNA polymorphisms of geographically diverse  V. vinifera  genotypes to confirm the position of this locus, to characterise the genetic diversity and traces of selection in candidate genes, and to explore the origin of hermaphroditism.    Results  In  V. v. sylvestris , a sex-determining region of 154.8 kb, also present in other  Vitis  species, spans less than 1% of chromosome 2. It displays haplotype diversity, linkage disequilibrium and differentiation that typically correspond to a small XY sex-determining region with XY males and XX females. In male alleles, traces of purifying selection were found for a  trehalose phosphatase , an  exostosin  and a  WRKY transcription factor , with strikingly low polymorphism levels between distant geographic regions. Both diversity and network analysis revealed that  H  alleles are more closely related to  M  than to  F  alleles.    Conclusions  Hermaphrodite alleles appear to derive from male alleles of wild grapevines, with successive recombination events allowing import of diversity from the X into the Y chromosomal region and slowing down the expansion of the region into a full heteromorphic chromosome. Our data are consistent with multiple domestication events and show traces of introgression from other Asian  Vitis  species into the cultivated grapevine gene pool.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0229-z) contains supplementary material, which is available to authorized users.

A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines