Regulatory and non-coding patterns associated to genome diversification and early development in an allopolyploid crop

Abstract

Oilseed rape (Brassica napus) is the third-most widely grown crop globally for vegetable oil production after soybean and oil palm. The relevance of oilseed rape relies not only in its economic value but also in its allopolyploidy and close linkage to Arabidopsis thaliana, which make it a useful model crop for other allopolyploids like wheat, cotton and sugarcane. Part of the increase of B. napus yield is due to enhanced performance in F1 hybrids, through exploitation of heterosis during the last few decades in all major oilseed rape production areas in the world. Until now, heterosis and hybrid-specific patterns have been mostly examined under allelic interaction hypotheses. Therefore, this thesis focuses on assessing genomic, transcriptomic and epigenomic features in the context of heterosis in a hybrid cross between two highly homozygous, yet genetically divergent, inbred oilseed rape accessions. Spontaneous large-scale genomic rearrangements that differed between F1 sister plants generated early and rapid gene copy number variation in a single generation. The implications of such preliminary findings suggest possible scenarios of post-polyploidization mechanisms to survive the evolutionary dead end of allopolyploidization. Furthermore, gene expression, small RNA and genome-wide methylation during seed and seedling development in the F1-hybrid were evaluated. Parental dominance was observed in transcriptomic and epigenomic patterns and key differentially expressed genes involved in reproduction and development during seed formation were detected through gene expression and microRNA analyses. Candidate epigenetic alleles with diverse core biological functions were identified and linkages between epigenomic and transcriptomic features were assessed. The insight provided through this research aims at exploring molecular patterns with potential implications in hybrids and heterosis and establishing frameworks for future multi-omics and pangenomic research in polyploid crops.