Natural variation in nutrient homeostasis mechanisms of Chlamydomonas reinhardtii

Natural variation in living organisms is essential in stress responses and adaptation to new environments. Many of the traits presenting natural variation are regulated by a complex genetic architecture of genes with small to moderate effects. Consequently, understanding which variants impact traits of medical, industrial or agronomical interest is fundamental. In photosynthetic organisms, the production of biomass is a complex process which results from interactions among mineral nutrition, photosynthesis and the environments. Mineral nutrients in particular, have wide range of functions in the cell, hence cells have evolved an intricate network to maintain intracellular nutrient concentrations within physiological range and avoid nutrient deficiency or excess.
Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic haploid microalga used as a model organism for the study of for instance photosynthesis, nutrient homeostasis, or flagella characterisation. Previous work within the Chlamydomonas community highlighted the extent of genetic and phenotypic variation among strains, making it a suitable species to study natural variation in nutrient homeostasis. This thesis focusses on the study of intraspecific variation in Chlamydomonas nutrient homeostasis, in both field and laboratory isolates, then on creating and leveraging a Multiparent Advanced Generation Inter-Crossing (MAGIC) population to dissect the genetic architecture of traits related to nutrient homeostasis.
First, a 24-strain Chlamydomonas panel was grown under mixotrophy (control), autotrophy, macronutrient (-Ca, -Mg, -N, -P, -S) or micronutrient (-Cu, -Fe, -Mn, -Zn) deficiency, and differences in growth and ionome were quantified. Globally, variation at the growth level was minor compared to that observed at the ionome level, and greater variation could also be found among the field isolates than among the laboratory strains. The comparison of diverging pairs of field strains revealed different strategies to manage nutrient deficiency, as underscored by the differential expression of key marker genes and impact on photosynthesis.
Secondly, taking advantage of the genetic and phenotypic variation observed previously, 8 strains were selected as founder lines of a MAGIC design. Biallelic crosses were performed during 8 generations, during which the contribution of each founder in each progeny was reduced by means of sexual recombination, creating 768 F8 progeny strains which are mosaics of the founders. Progeny lines were then sequenced and phenotyped under mixotrophy and nutrient deficiency (-Ca, -S, -Cu, -Fe, -Mn) to map Quantitative Trait Loci (QTL) related to mineral nutrition. The majority of the mapped QTLs was linked to the ionome (41) or photosynthesis (21) under nutrient deficiency. Many of the mapped QTLs contained a small number of genes or genes known to be involved in nutrient homeostasis, worth investigating in further studies.
Altogether the work developed in this thesis allowed a deeper understanding of the different strategies applied by field and laboratory strains in the management of nutrient deficiency, as well as the establishment of a MAGIC design using Chlamydomonas, and the mapping of QTLs related to mineral nutrition.