Open Access Research article

SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

Patrick Ollitrault12*, Javier Terol3, Andres Garcia-Lor2, Aurélie Bérard4, Aurélie Chauveau4, Yann Froelicher1, Caroline Belzile2, Raphaël Morillon13, Luis Navarro2, Dominique Brunel4 and Manuel Talon3

Author Affiliations

1 CIRAD, UMR AGAP, Avenue Agropolis, TA A-108/02, 34398 Montpellier, Cedex 5, France

2 Centro de Proteccion Vegetal y Biotechnologia, IVIA, Apartado Oficial,46113 Moncada (Valencia), Spain

3 Centro de genomica, IVIA, Apartado Oficial, 46113 Moncada (Valencia), Spain

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

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

Published: 10 January 2012

Additional files

Additional file 1:

Information on SNP markers included in the GoldenGate array. This file contains the main information on the SNP markers included in the GoldenGate array. It includes GenBank accession number, sequence surrounding the SNPs, SNP position, GoldenGate primers and designability rank, genotyping code, identification of the loci used for the diversity study.

Format: XLSX Size: 302KB Download file

Open Data

Additional file 2:

Primers for SNP mining in candidate genes and polymorphism results for 7 genotypes representative of 4 basic Citrus taxa. This file contains the main information on the primers used for SNP mining in candidate gene sequences (GenBank accession number, primer sequences, annealing temperature and theoretical amplicon size from EST data) and result data (size of exploitable sequence, number and frequency of SNPs).

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Additional file 3:

Detailed diversity results for loci without null allele (WONA). This file contains main data on the results obtained with WONA loci. It includes heterozygosity in Clementine, observed and theoretical heterozygosity in the whole population and each species, Fstat parameters in the whole population and between and within the three main species (C. reticulata, C. medica, C. maxima) and structuration level between C. reticulata and C. maxima.

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Additional file 4:

Additional figures. This file contains two figures. Figure S1: Correlation between the contribution of SNPs loci to the first axis of PCA analysis (C. maxima and C. reticulata as active individuals) and the Fst values for C. maxima/C. reticulata differentiation. Figure S2: Co-distribution of LD between loci without null allele (WONA) pairs for Chandler × Clementine progeny and germplasm population

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Additional file 5:

Detailed diversity results for loci with null allele (WNA). This file contains main data on the results obtained with WNA loci. It includes (i) SNP heterozygosity and heterozygosity for null allele in Clementine, (ii) number of individual in heterozygosity (SNPs), homozygous for one SNP allele and homozygous for null allele in the whole population and within the different species, (iii) genotypic diversity in the whole population (PIC).

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Additional file 6:

List of germplasm analyzed. This file contains the list of citrus germplasm accession analyzed. It includes the gerplasm bank, the accession number, the varietal group, the common name, the Latin name according Swingle and Reece and Tanaka classifications and the use for SNP genotyping validation by sequencing.

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Additional file 7:

Primers for analyzing the origin of unexpected genotyping in the GoldenGate array. this file contains the main information on the primers used for analyzing the origin of unexpected genotyping in the GoldenGate array. It includes the locus name, the abnormality type, the primer sequences, annealing temperature and amplicon size.

Format: PDF Size: 69KB Download file

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Open Data