In connection with the international Citrus genomics consortium, the SEAPAG team coordinated the construction of the reference genetic map (Ollitrault et al., 2012a), which involved 8 teams from 5 countries and was closely involved in the ANR ‘citruseq’ project coordinated by Génoscope, which was decisive for establishing the reference sequence of the genome of a doubled haploid clementine (Wu et al., 2014).  In partnership with IVIA, some large sets of nuclear markers, SSRs, InDels and SNPs have been developed (Terol et al.,2008; Froelicher et al., 2008, Luro et al., 2008; Garcia et al., 202, 2013a; Ollitrault et al., 2010, 2012b, c; Cuenca et al., 2013; Curk et al., 2015a) and the centromeres of each chromosome were positioned on the reference map by ”Half Tetrad Analysis” (Cuenca et al., 2011; Aleza et al., 2015). Some cytoplasmic markers have also been developed (Froelicher et al., 2011; Oueslati et al., 2016). Work on deciphering interspecific mosaic structures of the genomes of cultivated forms is under way. These studies have revealed the introgression of C. maxima in the genome of modern mandarin varieties (Wu .et al. 2014; Curk et al., 2014, 2015a; Garcia-Lor et al., 2015), helped to specify the phylogenomics of the main horticultural species (Garcia-Lor et al., 2012, 2013b ; Wu et al., 2014, 2018 ; Curk et al., 2015) and, in particular, analyse the origin and phylogenomic structure of lime trees (C. aurantifolia) and lemon trees (C. limon) (Curk, 2014 ; Curk et al., 2016). The team recently demonstrated the merits of genotyping by sequencing (GBS) to establish phylogenetic karyotypes on large populations (Oueslati et al., 2017).

References cited

• Aleza P., Cuenca J., Hernandez M., Juarez J., Navarro L., Ollitrault P. (2015) Genetic mapping of centromeres in the nine Citrus clementina chromosomes using half-tetrad analysis and recombination patterns in unreduced and haploid gametes. BMC Plant Biology, 15 (80) : 13 p.
• Cuenca J., Froelicher Y., Aleza P., Juarez J., Navarro L., Ollitrault P. (2011) Multilocus half-tetrad analysis and centromere mapping in citrus: evidence of SDR mechanism for 2n megagametophyte production and partial chiasma interference in mandarin cv "Fortune". Heredity, 107 (5) : p. 462-470.
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• Curk F. (2014) Organisation du complexe d'espèce et décryptage des structures des génomes en mosaïque interspécifiques chez les agrumes cultivés. PHD thesis. Ecole Doctoral SIBAGHE, Université de Montpellier 2. 260 p
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• 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
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