Open Access Research article

High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination

Emilie Chancerel12, Jean-Baptiste Lamy12, Isabelle Lesur13, Céline Noirot4, Christophe Klopp4, François Ehrenmann12, Christophe Boury12, Grégoire Le Provost12, Philippe Label56, Céline Lalanne12, Valérie Léger12, Franck Salin12, Jean-Marc Gion17 and Christophe Plomion12*

Author Affiliations

1 INRA, UMR1202 BIOGECO, F-33610 Cestas, France

2 Université de Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France

3 HelixVenture, F-33700, Mérignac, France

4 Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326 Auzeville Castanet-Tolosan, France

5 INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075 Orléans, France

6 INRA, UMR547 PIAF, Les Cézeaux, 24 Avenue des Landais, F-63177 Aubière cedex, France

7 CIRAD, UMR AGAP, Campus de Baillarguet TA 10C, F-34398 Montpellier Cedex 5, France

For all author emails, please log on.

BMC Biology 2013, 11:50  doi:10.1186/1741-7007-11-50

Published: 18 April 2013

Additional files

Additional file 1:

Occurrence of loci displaying inconsistent failure in the two mapping populations studied (F2 and G2): A, B, C, D, polymorphic vs. failed; E, F, G, H monomorphic vs. failed (see illustration in Figure 1).

Format: DOC Size: 32KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

List of SNP markers with dbSNP accessions, corresponding contig ID in PineContig_v2, and linkage group assignment on the G2F, G2M and F2 linkage maps.

Format: XLS Size: 5.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Genetic linkage maps obtained from segregation data for the G2 and F2 mapping populations. Markers common to the female (G2F), male (G2M) and F2 maps are linked by green dashed lines. Framework markers (segregating in a 1:1 ratio) are indicated in black, whereas accessory markers (segregating in a 1:2:1 ratio) are indicated in blue, followed, in brackets, by the distance (in cM) to the nearest framework marker and the corresponding LOD score. Markers displaying segregation distortion in the initial dataset are indicated with an asterisk (*).

Format: PPT Size: 5.2MB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 4:

Segregation pattern in the F2 progeny before and after validation on a larger sample size. Only SNPs from the 12 k array were genotyped by the iPLEX Sequenom assay.

Format: DOC Size: 54KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

Analysis of allele transmission and segregation distortion in the F2 pedigree. Alleles inherited from the Corsican grandparent are highlighted in green.

Format: DOCX Size: 13KB Download file

Open Data

Additional file 6:

Summary of polymorphic and mapped markers on map 1 and map 3 for the G2F, G2M and F2 linkage maps.

Format: DOC Size: 54KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 7:

Map length and number of markers for the three maps: G2F, G2M and F2.

Format: DOC Size: 71KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 8:

Result of the Wilcoxon signed rank test (P-values) of pair-wise recombination for markers common to F2 and G2F and to F2 and G2M.

Format: DOC Size: 43KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 9:

Distribution of the observed number of markers relative to the expected number of markers, assuming a Poisson distribution for the F2, G2F and G2M parental trees. Blocks with the same marker counts were summed and the resulting frequencies compared with the expected frequencies generated from the Poisson distribution function (indeed, if recombination on each chromosome were completely random, a Poisson distribution with a variance equal to the mean would be expected, as suggest by Haldane (1931). Haldane, J. B. S. (1931) The cytological basis of genetical interference. Cytologia 3:54–65). Black squares indicate the lower and upper thresholds (in terms of the number of markers per block) defining hotspots and coldspots of recombination, respectively.

Format: DOC Size: 74KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 10:

This supplementary data file contains three items. *A representation of marker density in the linkage groups of the G2F, G2M and F2 maps, highlighting coldspots and hotspots of recombination. Marker density was determined by shifting an interval along the map in 1 cM increments. The horizontal lines indicate the lower and upper thresholds defining gene clusters and gaps, respectively. x-axis: map distance for the whole linkage group (marker position as in Additional file 3, common markers are highlighted in green (between G2F and F2) and in pink (between G2M and F2), and markers common to G2F, G2M and F2 are enclosed in a box. y-axis: number of genes in the interval. Clusters common to the F2 map and at least one G2 map are indicated by orange circles connected by dotted orange lines. Clusters common to the G2F and G2M maps are indicated by black circles connected by dotted black lines. Clusters observed on only one map are indicated by black circles. *A table indicating the number of recombination hot- and coldspots on the G2F, G2M and F2 linkage maps. *A Venn diagram based on the table, to visualize the number of cold- (in black) and hotspots (in red) specific to a given map or common to different maps.

Format: DOC Size: 2.2MB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 11:

Distribution of the map distance between two adjacent mapped markers for the three maps (G2F, G2M, F2). x-axis: distance between the markers, y-axis: number of intervals.

Format: DOC Size: 32KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 12:

Polymorphism rate (last column) estimated from in silico screening of aligned 454 reads for the three mapped genotypes (10.159.3, G2M map; 9.106.3, G2F map; and H12, F2 map).

Format: DOC Size: 30KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 13:

Pinus pinaster pedigrees used for linkage mapping.

Format: DOC Size: 262KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 14:

Overview of the EST datasets used to construct PineContig_v2. The accession ID of 454 data is as for the Sequence Read Archive of the NCBI database [82].

Format: DOC Size: 63KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 15:

PineContig_v2 libraries produced with Aquitaine genotypes of maritime pine.

Format: DOC Size: 36KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 16:

Distribution of the 584,089 cleaned reads obtained from Aquitaine genotypes.

Format: DOC Size: 40KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 17:

Summary of SNPs included in the 12 k bead type Infinium assay.

Format: DOC Size: 29KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 18:

Information obtained with MassArray assay design 4.1 software (Sequenom). Two multiplexes (W1 with 22 SNPs and W2 with 12 SNPs) were developed.

Format: XLS Size: 40KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 19:

Summary of the various types of markers combined with the 12 k-SNP markers for the construction of the G2 (A) and F2 (B) linkage maps.

Format: DOC Size: 32KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 20:

Bandwidth values obtained from Kernel density analysis for the F2, G2F and G2M linkage maps.

Format: DOC Size: 34KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data