Identification and Characterization of Rye Genes Silenced in Allohexaploid Triticale

High-throughput cDNA sequence comparisons between diploid rye, Secale cereale, and hexaploid triticale, an intergeneric allohexaploid plant generated from durum wheat, Triticum turgidum, and, Secale cereale, detected suppression of expression of approximately 2% of rye genes surveyed in triticale. The expression levels of 23,503 rye cDNA reference contigs were analyzed in 454-cDNA libraries obtained from anther, root and stem from both triticale and rye, as well as in five 454-cDNA data sets created from triticale ovary, pollen, seed, seedling shoot and stigma tissues. Among these, 112 rye cDNA contigs were undetected in all triticale tissues, although their expression was relatively high in rye tissues. Suppressed rye genes were found to be strikingly less similar to their closest BLASTN matches in the wheat genome when compared to a control set of 200 random rye genes. PCR assays showed that six out of ten candidate suppressed genes were deleted from the triticale genome. The strikingly low similarity between suppressed rye sequences and their closest matches in wheat genomes suggests the involvement of gene deletion or suppression in the recognition of non-similar sequences in the allopolyploid genome. There appears to be a bias for the suppression of rye genes that do not have a close homeolog in the other Triticum genomes.