Developing early selection methods, especially marker-assisted selection (MAS) are strong challenges for optimizing Citrus breeding, given the length of the juvenile phase (from 4 to 6 years) and the large areas needed to assess the progenies in orchards. It has been possible to distinguish between plants of zygotic origin (hybrids) and nucellar plants (identical to the mother-tree) in facultative apomictic varieties since the end of the 1980s, using isozyme markers, and this is routinely done today with SSR markers (Luro et al., 2008; Froelicher et al., 2008; Ollitrault et al., 2010) or SNPs using the Kaspar method (Garcia Lor et al., 2013; Cuenca et al., 2013a; Curk et al., 2015; Bruyère et al., 2016). Working with IVIA, the team has localized the major gene of resistance (recessive) to Alternaria (locus ABSr ; Alternaria brown spot resistance) near the centromeric region of chromosome III in clementine (Cuenca et al., 2013b, 2016); numerous homologues of resistance genes have been identified in the determined region. Some SSR and SNP markers flanking each side of the ABSr locus have been developed and now enable very efficient routine selection. Some markers of the Ruby gene, responsible for anthocyanin accumulation in blood oranges, have also been developed and are used to introgress that trait in mandarins. For rootstocks, immunity to the Tristeza virus provided by the species Poncirus trifoliata is also effectively selected using some SSR markers flanking a linkage group of resistance genes. Recent developments in Citrus genomics mean that genomic selection approaches will ultimately be a possibility.

References cited

• Bruyère S., Luro F., Froelicher Y., Morillon R., Ollitrault P. (2016) Poncirus phylogenetic diagnostic SNPs markers are useful to analyse zygotic rates in diploid and tetraploid Citrus x Poncirus rootstock seedlings. In : Mattos Dirceu (ed.), Fermino Carlos Eduardo (ed.), Moreira Novelli Valdenice (ed.), Alves de Azevedo Fernando (ed.), Della Coletta Filho Helvécio (ed.), Vicente Contador Zaccheo Paulo (ed.). Abstract book Sustainable citriculture: the role of applied knowledge. Londrina : IAPAR, p. 125-125 International Citrus Congress, 2016-09-18/2016-09-23, Foz do Iguaçu (Brésil).
• Cuenca J., Aleza P., Navarro L., Ollitrault P. (2013a) Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: Application to citrus triploid progeny. Annals of Botany, 111 (4) : p. 731-742.
• Cuenca J., Aleza P., Vicent A., Brunel D., Ollitrault P., Navarro L. (2013b) Genetically based location from triploid populations and gene ontology of a 3.3-Mb genome region linked to alternaria brown spot resistance in citrus reveal clusters of resistance genes. PloS One, 8 (10) : e76755 (18 p.).
• Cuenca J., Aleza P., Garcia-Lor A., Ollitrault P., Navarro L. (2016) Fine mapping for identification of citrus alternaria brown spot candidate resistance genes and development of new SNP markers for marker-assisted selection. Frontiers in Plant Science, 7 (1948), 13p.
• 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
• Froelicher Y., Dambier D., Bassene J.B., Costantino G., Lotfy S., Didout C., Beaumont V., Brottier P., Risterucci A.M., Luro F., Ollitrault P. (2008) Characterization of microsatellite markers in mandarin orange (C. reticulata Blanco). Molecular Ecology Resources, 8 (1) : p. 119-122.
• Garcia-Lor A, Ancillo G, Navarro L and Ollitrault P. (2013) Citrus (Rutaceae) SNP Markers Based on Competitive Allele-Specific PCR; Transferability Across the Aurantioideae SubfamilyApplications in Plant Sciences 1(4):1200406. 2013. doi: http://dx.doi.org/10.3732/apps.1200406
• Luro F., Costantino G., Terol J.F., Argout X., Allario T., Wincker P., Talon M., Ollitrault P., Morillon R. (2008) Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics, 9 (287) : p. 1-13.
• Ollitrault, F., Terol, J.F., Pina, J.A., Navarro, L., Talon, M., Ollitrault, P. (2010) Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus. American Journal of Botany, 97 (11): e124-e129e