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We conducted the comprehensive study on the genome instability of rye chromosomes or chromosome arms in wheat background. We found that the transmission of rye chromosomes to subsequent generations is lower than their wheat counterparts, which is a consequence of reduced pairing of rye chromosomes in meiosis. This lower frequency of pairing seems to be associated with the improper positioning of the telomeres of rye chromosomes at the onset of meiotic division and also in somatic nuclei. Our study indicates that improper positioning of alien chromosomes that leads to reduced pairing is not a strictly meiotic event but rather a consequence of a more systemic problem.
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