The team’s work has shown that an essential share of the phenotypic variability of cultivated forms resulted from the initial differentiation of the four ancestral taxa having undergone allopatric evolution (Ollitrault et al. 2003; Fanciullino et al. 2006; Dugrand-Judek et al., 2015). Our phylogenomics work (Wu et al., 2014; Curk et al., 2014; 2015) revealed that different combinations of the genome of two of these taxa (C. reticulata and C. maxima) are the source of major horticultural groups, be it for rootstocks (C. aurantium the bitter oranges, derived from direct interspecific hybridization) or for varieties (C. sinensis, oranges and C. paradisi, grapefruits). It has also shown that introgressions of C. maxima have played a major role in the domestication of the mandarins, from a primarily C. reticulate gene pool. We recently demonstrated (Oueslati et al., 2017) the potential of genotyping by sequencing (GBS) to decipher the phylogenomic structures of varieties from breeding programmes involving hybridizations between mandarins, between mandarins and oranges (tangors), mandarins and grapefruits (tangelos), and oranges and grapefruits (orangelos). Reconstruction of these secondary species to introgress resistance/tolerance traits present in the genetic resources of the two ancestral taxa can now be envisaged. The study of the phylogenetic origins of lemons and limes recently revealed some very complex structures involving three or even four ancestral taxa for certain lime trees (Curk et al., 2016). Thus, the ‘Tahiti’ lime with large seedless fruits results from the fertilization of a Mediterranean lemon ovule with diploid pollen from a ‘Mexican’ type lime tree (Curk et al., 2016). The preferentially disomic heredity of the tetraploid (doubled diploid) ‘Mexican’ lime is, moreover, compatible with an origin of the ‘Tahiti’ lime, by interploid crossing (2x x 4x; Rouiss et al., 2017). These results form the basis for a triploid lime-breeding project for the Mediterranean and tropical regions. Fine deciphering of the interspecific mosaic structures of the major Citrus ideotypes, using massive resequencing data, will soon make it possible to combine genomic selection with ideotype reconstruction strategies.

References cited

• Curk F., Ancillo G., Garcia-Lor A., Luro F., Perrier X., Jacquemoud-Collet J.P., Navarro L., Ollitrault P. (2014) Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: Analysis of chromosome 2. BMC Genetics, 15 (152) : 19 p.
• Curk Franck, Gema Ancillo, Frédérique Ollitrault, Xavier Perrier, Jean-Pierre Jacquemoud-Collet, Andres Garcia-Lor, Luis Navarro, Patrick Ollitrault. (2015) Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties.  Plos ONE, 10(5): e0125628
• Curk F., Ollitrault F., Garcia-Lor A., Luro F, Navarro L and P. Ollitrault. (2016) Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. Annals of Botany. 117(4):565-83.
• Dugrand-Judek A., Olry A., Hehn A., Costantino G., Ollitrault P., Froelicher Y., Bourgaud F. (2015) The distribution of coumarins and furanocoumarins in Citrus species closely matches Citrus phylogeny and reflects the organization of biosynthetic pathways. PloS One, 10 (11) : e0142757 (25 p.).
• Fanciullino A.L., Dhuique-Mayer C.,, Luro F., Casanova J., Morillon R. and Ollitrault P. (2006) Carotenoid diversity in cultivated Citrus is highly influenced by genetic factors. J. Agric. Food. Chem. 54 (12), 4397 -4406.
• Oueslati A, Salhi Hannachi A, Luro F, Vignes H, Mournet P and P. Ollitrault. (2017) Genotyping By Sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits. PlosOne. In press.'
• Ollitrault P., Jacquemond C., Dubois C., Luro F.. (2003) Citrus In : Genetic diversity of cultivated tropical plants. Hamon Perla (ed.), Seguin Marc (ed.)
• Rouiss H., Bakry F., Froelicher Y., Navarro L., Aleza P. and Ollitrault P. (2017) Origin of C. latifolia and C. aurantiifolia triploid limes; the preferential disomic inheritance of doubled-diploid ‘Mexican’ lime is in line with an interploid hybridization hypothesis. Annals of Botany. In press.
• Wu G.A., Prochnik S., Jenkins J., Salse J., Hellsten U., Murat F., Perrier X., Ruiz M., Scalabrin S., Terol J.F., Takita M.A., Labadie K., Poulain J., Couloux A., Jabbari K., Cattonaro F., Del Fabbro C., Pinosio S., Zuccolo A., Chapman J., Grimwood J., Tadeo F., Estornell L.H., Muñoz-Sanz J.V., Ibáñez V., Herrero-Ortega A., Aleza P., Pérez-Pérez J., Ramón D., Brunel D., Luro F., Chen C., Farmerie W.G., Desany B., Kodira C., Mohiuddin M., Harkins T., Fredrikson K., Burns P., Lomsadze A., Borodovsky M., Reforgiato G., Freitas-Astúa J., Quetier F., Navarro L., Roose M.L., Wincker P., Schmutz J., Morgante M., Machado M.A., Talon M., Ollitrault P., Gmitter F.G.J., Rokhsar D.S. (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology, 32 : p. 656-662.