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The environmental conditions under which plants grow affect the quality of seeds produced in a genotype-dependent manner. In nature, genotype-by-environment interactions are often observed however little is known about the underlying mechanisms. The combined use of genetic tools and omics data can help to explore the influence of the environment on the genetic control of seed performance. The research presented in this thesis explores genotype-by-environment interaction at the phenotypic with an effort to connect phenotypic changes to changes observed at the metabolome and transcriptome in a systems genetics approach. For this purpose, an Arabidopsis thaliana recombinant inbred lines population derived from the cross between the parental lines Bay-0 and Sha was grown under different conditions, namely standard, high light, high temperature and low phosphate conditions from flowering until seed harvest. The germination properties of the seeds produced under the different environments were investigated and the seed germination QTLs identified displayed large QTL-by-environment interaction. Quantitative changes in primary metabolites in response to the maternal environment were investigated by GC-TOF-MS. Further, mQTLs under the different environments were identified. RNA-seq of the same lines enabled to explore changes in gene expression across genotypes and environments as well as differences in the eQTL landscape under the different maternal environment. The findings of this research show that seed quality is largely influenced by genotype-by-environment interactions which result in large changes at the molecular level. The data generated provide many opportunities to further study.

Environmental tuning of the genetic control of seed performance : a systems genetics approach