[en] The complex regulation of cell metabolism challenges the development of novel biotechnologies driving a more efficient use of natural resources. For instance, microalgae are considered sustainable sources of proteins, biomaterials, nutraceuticals, and biofuels, but their large-scale adoption is limited by their low cost-efficiency. The deeper understanding of algal metabolism and investigation of its natural variants occupy a central role in the development of algal biotechnologies. In this thesis, I explored and exploited the natural diversity present among divergent strains of Chlamydomonas reinhardtii, providing new insights about the multilevel regulation of the photosynthetic metabolism and its response to photo-oxidative stress. This study includes a comprehensive fluorescence-based phenotypic description of 25 wild-type strains partitioned into 14 laboratory isolates and 11 field-isolates. The presence of phenotypic divergence between the two groups with respect to their photosynthetic and photoprotective efficiency, particularly under mixotrophic condition is discussed. An in-depth multimethodological comparison between the laboratory-isolate CC-1010 and the field-isolate CC-2936 revealed the presence of wide intraspecific diversity in proton-motive force regulation and accumulation of low-CO2-inducible transcripts and proteins. Shotgun proteomics was used to provide a thorough overview of the two strains’ physiological response to photo-oxidative stress, showcasing the extent of intraspecific diversity in C. reinhardtii. Mating efficiency, genomics, and phenotypic data were used to select a subset of 8 strains to use as parental lines for the construction of a Multiparent Advanced Generation Inter-Cross (MAGIC) design. A detailed genomic analysis of the resulting 768 F8-lines was performed to track recombination events and unravel the population’s structure. The optimization of the fluorescence-based mass-phenotyping method used to characterise the MAGIC population is also described. Several parameters describing the photochemical and non-photochemical chloroplastic activity were measured under photo-autotrophic and mixotrophic growth. The large size of the phenotypic dataset was exploited to investigate covariance among photosynthetic traits. The complex relationship between photochemistry and photoprotection in presence/absence of acetate is discussed. Heritability and genetic correlation were computed for each trait, providing a fresh view on the link between genetics and fluorescence-derived parameters. Finally, the genomic and phenotypic datasets were used to develop a quantitative genetics study, mapping genomic loci associated to the different photosynthetic traits. A total of 26 quantitative-trait loci (QTLs) were found to be associated to Photosystem II’s quantum yield and non-photochemical quenching-related parameters. Our fine-mapping analysis found the presence of several major candidate-genes among some of the confidence intervals, providing strong bases for the development of future scientific studies targeting to the identification and exploitation of natural genetic variants. Overall, this thesis describes why the MAGIC population represents a landmark resource in the scientific history of C. reinhardtii’s community, and how the use of fluorescence-based high-throughput phenotyping is a powerful tool to help us understand and master photosynthetic cells’ physiology.
