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

Published: 5 November 2012

Additional files

Additional file 1:

Origin and information for all markers. This file contains a table showing detailed information for all markers: type of marker (Indels, SSRs or SNPs); the type of sequence data from which the markers were developed (genomic library, BAC end sequences, ESTs); GenBank accession number; the laboratory in which the markers were developed; the laboratory in which the different progenies were genotyped, the occurrence and configuration of null allele for the parents of analyzed progenies and the references for the papers in which the markers were published, with an indication of the modifications (if any) in the marker names.

Format: XLSX Size: 119KB Download file

Open Data

Additional file 2:

Detailed results of genetic mapping. This file contains the detailed information (marker locations, X2 for Mendelian segregation, and level of significance) on the genetic maps for male Clementine, female Clementine, reference Clementine, sweet orange, ‘Chandler’ pummelo and ‘Pink’ pummelo. The estimated location of all markers in the reference Clementine map is also provided (synthesis columns).

Format: XLSX Size: 324KB Download file

Open Data

Additional file 3:

Conserved linear order between male and female Clementine genetic maps. This file contains a figure showing the relative positions of the markers in the female Clementine map (y axis) and in the male Clementine map (x axis) for each linkage group.

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Open Data

Additional file 4:

Reference Clementine genetic map. This file contains a figure showing the nine linkage groups of the reference Clementine genetic map and the position of each marker (blue: SNPs; green: SSRs; red: Indels).

Format: PDF Size: 164KB Download file

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Open Data

Additional file 5:

‘Chandler’ pummelo genetic map. This file contains a figure showing the nine linkage groups from the ‘Chandler’ pummelo genetic map and the position of each marker (blue: SNPs; green: SSRs; red: Indels).

Format: PDF Size: 130KB Download file

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Open Data

Additional file 6:

‘Pink’ pummelo genetic map. This file contains a figure showing the nine linkage groups of the ‘Pink’ pummelo genetic map and the position of each marker (blue: SNPs; green: SSRs; red: Indels).

Format: PDF Size: 127KB Download file

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Open Data

Additional file 7:

Sweet orange genetic map. This file contains a figure showing the nine linkage groups of the sweet orange genetic map and the position of each marker (blue: SNPs).

Format: PDF Size: 146KB Download file

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Open Data

Additional file 8:

Variation of map length between male Clementine, female Clementine, and sweet orange based only on common SNP markers. This file contains a figure for each linkage group showing the relative position of the markers in the female Clementine map, the male Clementine map, and the sweet orange map in a new mapping analysis performed using only the common markers for the three parents. The x axis represent the location on the reference Clementine map established from all Clementine gametes (male + female). The relative locations in the other maps (the ratio between the locations in the other map relative to the location in the Clementine reference map) are shown on the y axis.

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Open Data

Additional file 9:

Comparative distribution of the skewed markers in the nine linkage groups for five parents. This file contains a figure for each linkage group showing the distortion magnitude (X2 of conformity with Mendelian segregation) for each marker and each mapped parent. Furthermore, 9b shows an example illustrating the method used to estimate the location in the reference Clementine map of markers mapped in the other parents.

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Open Data

Additional file 10:

Information on the new SNP markers included in the GoldenGate array. This file contains information regarding the new SNP markers included in the GoldenGate array. It includes the GenBank accession number, the sequence surrounding the SNPs, SNP position, the GoldenGate primers and designability rank.

Format: XLSX Size: 16KB Download file

Open Data

Additional file 11:

Characteristics and primers for the new SSR markers developed from ‘Cleopatra’ mandarin genomic library at CIRAD. This file contains information on the primers used for the new SSRs developed from a Cleopatra mandarin (C. reshni) genomic library (GenBank accession number, primer sequences, annealing temperature and microsatellite motif).

Format: PDF Size: 107KB Download file

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Open Data