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Analysis of multiple Brassica transcriptomes reveals subgenome dominance in the response of Brassica napus to Sclerotinia sclerotiorum de Jong, Grant


Whole-genome duplication (WGD; polyploidy) events have played an extensive role in the evolution of flowering plants. The sudden doubling of genetic material can expedite rapid novel changes to polyploid transcriptomes. For example, polyploids formed via an interspecific hybridization of closely related species, known as allopolyploids, can exhibit inconsistent expression patterns between their parental genome. These incipient disparities in parental gene dosage can have profound effects on the transcriptome of newly formed polyploids, which in turn can influence their response to environmental stressors. In particular, the extent to which the transcriptomic shock of polyploidization modulates the biotic stress response of plant species remains a nascent topic in polyploidy research. To elicit such a response, I subjected both natural and newly formed lines of Brassica napus to pathogen infection with the fungal necrotroph Sclerotinia sclerotiorum. To understand the origin of subgenome divergence in the newly formed polyploid, I also performed infections on the diploid parents of the resynthesized B. napus, Brassica rapa and Brassica oleracea. RNA-seq analyses of these pathosystems revealed wide-spread divergence between polyploid subgenomes in terms of both constitutive gene expression and alternative splicing patterns. This manifested in a global expression bias towards the B. oleracea-derived (C) subgenome among both polyploid hosts, enhanced by widespread non-parental down-regulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus specifically, this resulted a disproportionate C subgenome contribution to plant innate immunity and pathogen defense response, characterized by biases in both transcript expression level and the proportion of induced genes. Supplementary material available at: http://hdl.handle.net/2429/73521.

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