Supplementary Material for: High Penetrance of a Pan-<b><i>Canina</i></b> Type rDNA Family in Intersection <b><i>Rosa</i></b> Hybrids Suggests Strong Selection of Bivalent Chromosomes in the Section <b><i>Caninae</i></b>

All dogroses <i>(Rosa</i> sect. <i>Caninae)</i> are characterized by the peculiar <i>canina</i> meiosis in which genetic material is unevenly distributed between female and male gametes. The pan-<i>canina</i> rDNA family (termed beta) appears to be conserved in all dogroses analyzed so far. Here, we have studied rDNAs in experimental hybrids obtained from open pollination of F1 plants derived from 2 independent intersectional crosses between the pentaploid dogrose species (2n = 5x = 35) <i>Rosa rubiginosa</i> as female parent (producing 4x egg cells due to the unique asymmetrical <i>canina</i> meiosis) and the tetraploid (2n = 4x = 28) garden rose <i>R. hybrida</i> ‘André Brichet' as male parent (producing 2x pollen after normal meiosis). We analyzed the structure of rDNA units by molecular methods [CAPS and extensive sequencing of internal transcribed spacers (ITS)] and determined the number of loci on chromosomes by FISH. FISH showed that <i>R. rubiginosa</i> and ‘André Brichet' harbored 5 and 4 highly heteromorphic rDNA loci, respectively. In the second generation of hybrid lines, we observed a reduced number of loci (4 and 5 instead of the expected 6). In <i>R. rubiginosa</i> and ‘André Brichet', 2-3 major ITS types were found which is consistent with a weak homogenization pressure maintaining high diversity of ITS types in this genus. In contrast to expectation (the null hypothesis of Mendelian inheritance of ITS families), we observed reduced ITS diversity in some individuals of the second generation which might derive from self-fertilization or from a backcross to <i>R. rubiginosa</i>. In these individuals, the pan-<i>canina</i> beta family appeared to be markedly enriched, while the paternal families were lost or diminished in copies. Although the mechanism of biased meiotic transmission of certain rDNA types is currently unknown, we speculate that the bivalent-forming chromosomes carrying the beta rDNA family exhibit extraordinary pairing efficiency and/or are subjected to strong selection in <i>Caninae</i> polyploids