Adaptation breeding is one of the key factors of minimizing possible negative impacts of climate change on plant production. Modern breeding approaches use genetic information to optimize the outcome of respective breeding programs. However, many crops are polyploid and therefore have complex and highly redundant genomes. The high degree of redundancy also increases the likelihood of structural genome variation. Moreover, duplicated genes may over time undergo sub-or neofunctionalisation, which complicates knowledge transfer from model systems and requires thoughtful approaches to dissect the underlying genetic regulation for adaptation traits. Brassica napus is the polyploid crop with the closest relationship to the model plant Arabidopsis thaliana and has a well-known evolutionary ancestry. In the presented works, B. napus was used as a model to study the influence of genomic redundancy, structural genome variation and subfunctionalisation on adaptation traits like flowering time and drought stress response. It could be shown that structural genome variation was extremely abundant in flowering time genes in B. napus, but also within its progenitor species B. rapa and B. oleracea. Some genomic exchange events obviously played an important role in formation of a subspecies, demonstrating the high adaptive value of structural variants. Moreover, it was found that important flowering time regulators underwent strong subfunctionalisation linked to either promoter variation or protein structure variation, indicating not all copies have the same adaptive value for breeding. When studying gene expression networks together with small RNA expression networks in reaction to drought stress at flowering, it was found that subfunctionalisation obviously also affects small RNA regulation patterns, adding a further dimension to the complexity of polyploid genomes. Obviously, different miRNA variants are upregulated under stress than under control conditions, indicating subfunctionalisation of small RNA expression assists in the fine-tuning of abiotic stress response in newly formed polyploids. In summary, it was found that understanding subfunctionalisation is key to judge the possible outcomes of both classical sequence variants and structural variants. In that respect, the variation of regulatory elements like promoters and small RNAs should attain more attention.
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