**Abbreviations**


#### **Appendix A**

**Figure A1.** Wheat nuclei with a pair of homologous rye chromosome arms after 3D-FISH. A nucleus of 2BS.2RL (**A**) and 5RS.5BL (**B**) translocation lines. Total genomic DNA of rye was labelled with TRITC using Nick translation (magenta) and the centromere-specific sequence was PCR-labelled with FITC (green). Nuclear DNA was counterstained with DAPI (blue). Scale bar 3 μm.

**Figure A2.** Rye nuclei with a pair of homologous wheat chromosomes. A nucleus carrying chromosome 3B (**A**) and chromosome 5B (**B**). Total genomic DNA of wheat was labelled with TRITC using Nick translation (yellow), centromeres of both wheat and rye chromosomes were visualized using oligonucleotide probe (magenta), and telomere-specific sequence was PCR-labelled with FITC (green). Nuclear DNA was counterstained with DAPI (blue). Nucleoli are indicated by white dashed lines. Scale bar 2 μm.

**Figure A3.** Wheat nuclei with a pair of homologous barley chromosomes. A nucleus carrying chromosome 3H (**A**) and chromosome 6H (**B**). Total genomic DNA of barley was labelled with TRITC using Nick translation (yellow), centromeres of wheat chromosomes were visualized using oligonucleotide probe (magenta), and telomere-specific sequence was PCR-labelled with FITC (green). Nuclear DNA was counterstained with DAPI (blue). Nucleoli are outlined by white dashed lines. Scale bar 3 μm.

**Figure A4.** Wheat nuclei with a pair of homologous rye chromosomes del1RS.1RL in wheat background. (**A**) Complete separation (**A**), parttaTial association (**B**) and complete association (**C**) of rye homologues. Total genomic DNA of rye was labelled with TRITC using Nick translation (yellow), centromeres of both rye and wheat chromosomes were visualized using oligonucleotide probe (magenta), and telomere-specific sequence was PCR-labelled with FITC (green). Nuclear DNA was counterstained with DAPI (blue). Nucleoli are indicated by white dashed lines. Scale bar 3 μm.
