To test the hypothesis that interspecific genomic and chromosome interactions leading to nucleolar dominance could be reprogrammed in meiosis, we compared the expression of distinct nucleolar organizing region (NOR) loci in hexaploid triticale root tip meristematic cells, pollen mother cells and young pollen grains. Interphase and metaphase cells were silver stained to quantify nucleoli and active NOR loci respectively. A marked difference in the ribosomal RNA gene activity of each locus was observed when different types of cells were compared: in somatic and pollen mother cells, rRNA gene activity was mainly restricted to major wheat NORs (1B and 6B) with only a small contribution from rye NORs (1R). In contrast, in young pollen grains, all NORs present, including the 1R NORs, were consistently active. The expression of all NORs just after meiosis is considered to be a consequence of meiotic reprogramming of rye origin rDNA. Gene reprogramming mediated by the resetting of methylation patterns established early in embryogenesis is suggested to be responsible for the differential expression of the NORs of rye origin in distinct developmental stages of triticale.