Somatic hybridization by protoplast fusion is an important tool of citrus improvement programs around the world and particularly those developed by CIRAD in Corsica. These strategies of ploidy manipulation raise new research questions regarding the phenotypic and genomic expression of polyploid citrus. The objective of this thesis is (i) to determine the impact of nucleo-cytoplasmic interactions on the phenotype of diploid somatic hybrids (cybrids), particularly on criteria of fruit quality, and (ii) to analyze the inheritance of phenotypic characters under allotetraploidization in relation with possible neoregulation of genomic expression. The approach is (i) molecular (nuclear and chloroplast SSR and mitochondrial PCR markers) and pomological description of two parents with very contrasting phenotypic characters (mandarin Willow leaf (WLM) and Eureka lemon (EUR)) and their somatic hybrids diploid and tetraploid; (ii) qualitative and quantitative analysis of compounds involved in fruit quality (sugars, organic acids, aromas and carotenoids) by HPLC; (iii) an analysis of expression of genes involved in the biosynthetic pathway of carotenoids by real-time PCR. This work is complemented by a global analysis of the transcriptome with a 20K cDNA microarray developed by the Citrus Functional Genomic Project in Spain. Analysis of nuclear and cytoplasmic genomes permitted to characterize a cybrid with nucleus and chloroplasts of lemon plus mitochondria of mandarin, and a tetraploid somatic hybrid resulting from the addition of the nuclear genomes of both parents combined with cytoplasmic organelles of mandarin. Morphological and biochemical characterization of the cybrid WLM + EUR 2x has shown that the interaction between lemon-nucleus and mandarin-mitochondria affects very slightly the phenotype. However, leaf transcriptome analysis of the cybrid shows an alteration of expression profile of nuclear genes involved in a wide range of metabolic process. For the somatic allot