| Polyploidy has played an important role in the evolution of plants, and numerous studies on resynthesized polyploids have contributed to our understanding of how polyploidization may lead to novel phenotypic variation. However, most studies on the effects of polyploidization have involved analysis of a small number of independently resynthesized lines, and few studies have integrated genetic, epigenetic, gene expression, and phenotypic data. Here we summarize data from an analysis of approximately fifty independently resynthesized Brassica napus allopolyploids. The lines were derived by hybridizing double haploid (DH) B. rapa and B. oleracea parents, followed by chromosome doubling and self fertilization for six generations. We tested the null hypothesis that the lines would show no changes and remain genetically, epigenetically, transcriptionally, and phenotypically identical at the S0:1 and S5:6 generations. We analyzed the lines using a combination of RFLP, SSR, cDNA-AFLP, and cDNA-SSCP markers, and measured phenotypes in a randomized complete block design (RCBD). Genetic changes occurred in all lines and were correlated with the qualitative loss of parent-specific transcript markers and phenotypic variation. Many genetic changes were homoeologous non-reciprocal transpositions (HNRTs) that most likely resulted from segregation of inter-genomic recombinations during selfing. Three lines with differing numbers of genetic changes were selected for an additional analysis of transcriptome-wide changes in gene expression using an Arabidopsis 70mer oligonucleotide microarray. We compared gene expression among the DH parents and tested non-midparent (NMP) expression in the allopolyploids by comparison to a 1:1 mix of parental RNA. The parents showed differential expression for 6--15% of 26,107 genes. Individual allopolyploid lines showed NMP expression for up to 32% of all genes; however ≤0.3% of all genes reproducibly demonstrated NMP expression in all lines at either generation. Genes that were differentially expressed in the allopolyploids were overrepresented by those showing differences in expression among the parents. |
