Background: Allopolyploidization is one of the major evolutionary modes of plant speciation. Recent interest in studying allopolyploids has provided significant novel insights into the mechanisms of allopolyploid formation. Compelling evidence indicates that genetic and/or epigenetic changes have played significant roles in shaping allopolyploids, but rates and modes of the changes can be very different among various species. Triticale (x Triticosecale) is an artificial species that has been used to study the evolutionary course of complex allopolyploids due to its recent origin and availability of a highly diversified germplasm pool. Scope This review summarizes recent genomics studies implemented in hexaploid and octoploid triticales and discusses the mechanisms of the changes and compares the major differences between genomic changes in triticale and other allopolyploid species.
Conclusions: Molecular studies have indicated extensive non-additive sequence changes or modifications in triticale, and the degree of variation appears to be higher than in other allopolyploid species. The data indicate that at least some sequence changes are non-random, and appear to be a function of genome relations, ploidy levels and sequence types. Specifically, the rye parental genome demonstrated a higher level of changes than the wheat genome. The frequency of lost parental bands was much higher than the frequency of gained novel bands, suggesting that sequence modification and/or elimination might be a major force causing genome variation in triticale. It was also shown that 68 % of the total changes occurred immediately following wide hybridization, but before chromosome doubling. Genome evolution following chromosome doubling occurred more slowly at a very low rate and the changes were mainly observed in the first five or so generations. The data suggest that cytoplasm and relationships between parental genomes are key factors in determining the direction, amount, timing and rate of genomic sequence variation that occurred during inter-generic allopolyploidization in this system.