Abstract
The pearl oyster, Pinctada margaritifera var. cumingii (Linnaeus, 1758), is the second economic resource of French Polynesia. It is one of the only bivalves expressing such a varied range of internal shell coloring, and by correlation, pearl color. This phenotypic variability which is weakly characterized in the literature is partly under genetic control, but is also under environmental influence. In this context, this thesis is interested by identifying in three phenotypes of interest for pearl farming (red, yellow and green): i) a method to characterize these chromatic variations, ii) the key genes expressed during the formation of shells leading to contrasting color phenotypes; iii) the genetic variants responsible for the expression of these colors; iv) epigenetic mechanisms controlling the expression of chromatic plasticity in response to the environment. The combination of these different fields made it possible to understand processes explaining the plasticity and the diversity of the pigmentary coloration of these phenotypes. These results allowed to identify a battery of genomic and epigenomic markers that will grant the future genomic selection of highly colored individuals. This information coupled with the future results of genomic studies on other pearl quality criteria (luster, size, etc.) will make it possible to obtain reference populations selected by genomic markers for the production of high-quality graft donor pearl oyster lines. In addition to the importance of these results for pearl farming, this thesis considerably improves our knowledge of pigmentation processes in bivalve and could favor the emergence of a new biological model for the multidisciplinary study of pigmentation