The influence of polyploidy on mutation rates in the oil crop Brassica napus
Final Report Abstract
The central hypothesis of the project was the assumption that mutation rates in Brassica species increase through polyploidisation and then decrease again over evolutionary time in the course of diploidisation. The mutation rate is a central parameter in evolutionary and breeding research. For example, common genetic mapping approaches assume that the mutation rate is negligible compared to the recombination rate and that deviations in the sequence are always due to recombination, but not to mutation. To investigate this hypothesis, 16 genotypes of the species Brassica napus (neoallopolyploid, genome AACC), Brassica rapa (mesopolyploid/diploidised, genome AA) and Brassica oleracea (mesopolyploid/diploidised, genome CC) were selected. These genotypes were cultivated over four generations and sampled in the first and last generation. Due to the large diversity in the selected set, cultivation proved to be more time-consuming than expected, as some genotypes had a very high vernalisation requirement. Furthermore, the fertility of the resyntheses was challenging. Nevertheless, 4 out of 5 resynthesis families could finally be sampled over 4 generations, the fifth over 3 generations. The original plan of exome sequencing was dropped in favour of PacBio HiFi sequencing due to the great technical progress and the favourable price development. This not only enables better detection of structural variants and variants in non-genic regions, but also the detection of methylation patterns, which also allows conclusions to be drawn about the mechanisms of potential changes. However, the extraction of high-molecular DNA from leaf samples stored for several years was a practical challenge, which is why the desired pairing could not be achieved for all generation pairs. Due to the known relationship, it should nevertheless be possible to estimate the mutation rate. For this purpose, as-semblies from the Pac-Bio HiFi reads were created for all samples of the first generation, to which the reads of the fourth generation can then be mapped back in order to determine the mutation rate independently of a reference genome. These analyses are still ongoing.
Publications
-
Ancient and Recent Polyploid Evolution in Brassica. Brassica Improvement, 49-66. Springer International Publishing.
Schiessl, Sarah V. & Mason, Annaliese S.
-
Regulation and Subfunctionalization of Flowering Time Genes in the Allotetraploid Oil Crop Brassica napus. Frontiers in Plant Science, 11.
Schiessl, Sarah
-
Using wild relatives and related species to build climate resilience in Brassica crops. Theoretical and Applied Genetics, 134(6), 1711-1728.
Quezada-Martinez, Daniela; Addo, Nyarko Charles P.; Schiessl, Sarah V. & Mason, Annaliese S.
-
Redundante Genome als evolutionäre Ressource. Fachtagung Transformation der Pflanzenproduktion, Berlin.
Schiessl-Weidenweber, S.
