Open Access Open Badges Research article

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

Patrick Ollitrault12*, Javier Terol3, Chunxian Chen4, Claire T Federici5, Samia Lotfy16, Isabelle Hippolyte1, Frédérique Ollitrault2, Aurélie Bérard7, Aurélie Chauveau7, Jose Cuenca2, Gilles Costantino8, Yildiz Kacar9, Lisa Mu5, Andres Garcia-Lor2, Yann Froelicher1, Pablo Aleza2, Anne Boland10, Claire Billot1, Luis Navarro2, François Luro8, Mikeal L Roose5, Frederick G Gmitter4, Manuel Talon3 and Dominique Brunel7

Author affiliations

1 CIRAD, UMR AGAP, F-34398 Montpellier, France

2 IVIA, Centro Proteccion Vegetal y Biotechnologia, Ctra. Moncada-Náquera Km 4.5, 46113 Moncada, Valencia, Spain

3 IVIA, Centro de Genomica, Apartado Oficial, 46113, Moncada, Valencia, Spain

4 Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA

5 Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA

6 Institut National de la Recherche Agronomique, BP, 293, 14 000, Kénitra, Morocco

7 INRA, UR EPGV, 2 rue Gaston Cremieux, 91057, Evry, France

8 INRA, UR GEQA, San Giuliano, 20230, San Nicolao, France

9 Department of Horticulture, Faculty of Agriculture, University of Çukurova, 01330, Adana, Turkey

10 CNG, CEA/DSV/Institut de Génomique, 2 rue Gaston Cremieux, 91057, Evry, France

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Citation and License

BMC Genomics 2012, 13:593  doi:10.1186/1471-2164-13-593

Published: 5 November 2012



Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine.


Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome.


A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the ‘Mediterranean’ mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents.

C. clementina; C. sinensis; C. maxima; SSRs; SNPs; Indels; Genetic maps