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Background  Studies in resynthesized  Brassica napus  allopolyploids indicate that homoeologous chromosome exchanges in advanced generations (S 5∶6 ) alter gene expression through the loss and doubling of homoeologous genes within the rearrangements. Rearrangements may also indirectly affect global gene expression if homoeologous copies of gene regulators within rearrangements have differential affects on the transcription of genes in networks.    Methodology/Principal Findings  We utilized  Arabidopsis  70mer oligonucleotide microarrays for exploring gene expression in three resynthesized  B. napus  lineages at the S 0∶1  and S 5∶6  generations as well as their diploid progenitors  B. rapa  and  B. oleracea . Differential gene expression between the progenitors and additive (midparent) expression in the allopolyploids were tested. The S 5∶6  lines differed in the number of genetic rearrangements, allowing us to test if the number of genes displaying nonadditive expression was related to the number of rearrangements. Estimates using per-gene and common variance ANOVA models indicated that 6–15% of 26,107 genes were differentially expressed between the progenitors. Individual allopolyploids showed nonadditive expression for 1.6–32% of all genes. Less than 0.3% of genes displayed nonadditive expression in all S 0∶1  lines and 0.1–0.2% were nonadditive among all S 5∶6  lines. Differentially expressed genes in the polyploids were over-represented by genes differential between the progenitors. The total number of differentially expressed genes was correlated with the number of genetic changes in S 5∶6  lines under the common variance model; however, there was no relationship using a per-gene variance model, and many genes showed nonadditive expression in S 0∶1  lines.    Conclusions/Significance  Few genes reproducibly demonstrated nonadditive expression among lineages, suggesting few changes resulted from a general response to polyploidization. Furthermore, our microarray analysis did not provide strong evidence that homoeologous rearrangements were a determinant of genome-wide nonadditive gene expression. In light of the inherent limitations of the  Arabidopsis  microarray to measure gene expression in polyploid  Brassicas , further studies are warranted.

Analysis of Gene Expression in Resynthesized Brassica napus Allopolyploids Using Arabidopsis 70mer Oligo Microarrays