Open Access Research article

An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis

Philippe Cubry16*, Fabien de Bellis1, Komlan Avia2, Sophie Bouchet3, David Pot1, Magali Dufour4, Hyacinthe Legnate5 and Thierry Leroy1

Author Affiliations

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

2 Department of Biology, University of Oulu, PO Box 3000, Oulu, FI-90014, Finland

3 INRA, UMR de Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParistech, Ferme du Moulon, Gif sur Yvette, F-91190, France

4 CIRAD, UMR CMAEE, Montpellier, F-34398, France

5 CNRA, Divo, BP 808, Côte d’Ivoire

6 Current address: DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Dublin, Glasnevin, Dublin 9, Ireland

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BMC Genomics 2013, 14:10  doi:10.1186/1471-2164-14-10

Published: 16 January 2013

Additional files

Additional file 1: Table S1:

Detailed information on the 108 SSR markers used.

Format: XLSX Size: 30KB Download file

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Additional file 2: Table S2:

Number of alleles, expected heterozigosity(He), observed heterozigosity and Hardy-Weinberg equilibrium exact test associated p-values (P-value )and standard deviation (s.d.) for each locus and for the whole population and the Diversity Groups SG2, SG1, C, G and GP. NA stands for not available due to monomorphic locus.

Format: XLSX Size: 35KB Download file

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Additional file 3: Table S3:

Number of alelles and Hardy-Weinberg equilibrium statistics for the Diversity Groups G, GP, Gsub1, Gsub2 and Gsub3. NA stands for not available due to monomorphic locus.

Format: XLSX Size: 30KB Download file

Open Data

Additional file 4: Table S4:

Amova and F-statistics computation over the 7 DG (SG1, SG2, C, GP, Gsub1, Gsub2 and Gsub3). * : significant value at 5%, ns: non significant value.

Format: XLSX Size: 11KB Download file

Open Data