Polyploidy is a prominent process in higher plants and is often described as a genomic shock that may induce stress and defense responses. The Brassica napus allotetraploid model was chosen to investigate the proteomic modifications that occur during allopolyploid formation. Large-scale analysis of the proteome from the leaves of B. napus was performed and compared with the homozygous diploid progenitors, Brassica rapa and Brassica oleracea, and among the proteomic changes in B. napus in the early generations (F1–F4). The abundance of all these differentially expressed proteins in the F1 generation differed from that of the corresponding proteins expressed in its progenitors, some of which relatively deviated from mid-parent predictions, exhibiting somewhat non-additive expression repatterning. Proteomic changes in the resynthesized B. napus from the first to the fourth generations were detected, which indicated that gene silencing was a permanent phenomenon and it could be reactivated at any moment. Although leaf proteins were extensively modified in synthetic B. napus, the distribution of the “housekeeping” proteins was not disturbed. Moreover, no evidence of chaos or large disorder was observed after the merging of the two genomes. Instead, a novel order quickly developed, which might evolve in further generations of synthetic B. napus.
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