During early meiosis, chromosomes pair via their telomeres and centromeres. This pairing induces a conformational change which propagates from these regions along each chromosome, making the chromatin of the partners accessible for intimate pairing. In the present study, we show by exploiting wheat-rye hybrids that the signal is initiated in both the presence and absence of either the Ph1 or Ph2 locus. However, the chromatin change only continues to propagate through rye telomeric heterochromatin when Ph1 is absent. This failure to propagate the chromatin change through the rye heterochromatin in the absence of Ph2 correlates with a subsequent lack of wheat-rye chromosome association at metaphase I.