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Dissecting the molecular basis of deleterious genetic interactions involving naturally occurring alleles in Arabidopsis

Final Report Summary - NATSYNTHLETHALARA (Dissecting the molecular basis of deleterious genetic interactions involving naturally occurring alleles in Arabidopsis)

The NATSYNTHLETHALARA project set out to decipher the genetic basis of an observed, supposedly synthetic lethal genetic interaction in the model plant, Arabidopsis thaliana. Analysis of this phenomenon is important in adding to our understanding of genetic incompatibility processes and how they arise.

Setting out from a highly complex genetic material, i.e. an Arabidopsis line derived from several natural and mutant backgrounds, the cause for aberrant phenotypes only observed in this line, but initially not the parents, was targeted by genetic mapping. To this end, state of the art high throughput technologies, such as multiplex genotyping or whole genome sequencing, were applied. The genetic riddle posed by the genotyping and sequence data acquired was eventually resolved through careful analysis of the hybrid and parental lines in different growth conditions. This analysis split the phenotype into two components:

i. a naturally occurring small deletion in the VIP3 gene, a determinant of mRNA stability, which was contributed by the Sav-0 parental line. This loss of function mutation results in a dwarf phenotype, which is, however, only tractable in high humidity conditions, since otherwise the mutation is seedling lethal;
ii. a spontaneous mutation in the COP1 developmental regulator that occurred during the production of the hybrid line. This mutation proves for the first time an essential role of the RIG finger domain of COP1, a universal ubiquitin ligase that is not only found in plants but also mammals including humans. The fact that this spontaneous mutation mimicked a synthetic lethal interaction is due to the incomplete penetrance of the mutant phenotype and the linkage disequilibrium between the mutant locus on chromosome 2 and the upper arm of chromosome 5. The latter appears to be due to transposon-driven structural re-arrangements on chromosome 5, including transposition of sequences around the COP1 locus. Follow up analyses will be conducted to find out whether this re-arrangement might have a role in the phenotype or its penetrance.

In summary, the objectives of the project have been largely achieved by solving the genetic puzzle that formed the basis of the project proposal. Various useful resources have been created by the project, such as whole genome sequences of natural Arabidopsis strains. The project required a high intellectual and technical level, which contributed strongly to the training of the fellow. Thus, the project contributed to the formation of highly qualified personnel, who is able to transfer the technical advances and conceptual progress made into other systems, including application, thereby contributing to the build up of a knowledge-based economy.