Open Access Research

Intraspecific variation of recombination rate in maize

Eva Bauer1*, Matthieu Falque2, Hildrun Walter1, Cyril Bauland2, Christian Camisan3, Laura Campo4, Nina Meyer5, Nicolas Ranc6, Renaud Rincent2357, Wolfgang Schipprack8, Thomas Altmann9, Pascal Flament3, Albrecht E Melchinger8, Monica Menz6, Jesús Moreno-González4, Milena Ouzunova5, Pedro Revilla10, Alain Charcosset2, Olivier C Martin2 and Chris-Carolin Schön1

  • * Corresponding author: Eva Bauer e.bauer@tum.de

  • † Equal contributors

Author Affiliations

1 Plant Breeding, Technische Universität München, 85354 Freising, Germany

2 INRA, UMR de Génétique Végétale/Université Paris-Sud - CNRS, 91190 Gif-sur-Yvette, France

3 Limagrain Europe, 63720 Chappes, France

4 Centro Investigacións Agrarias Mabegondo (CIAM), 15080 La Coruña, Spain

5 KWS SAAT AG, 37574 Einbeck, Germany

6 Syngenta SAS, 31790 Saint-Sauveur, France

7 BIOGEMMA, Genetics and Genomics in Cereals, 63720 Chappes, France

8 Plant Breeding, Universität Hohenheim, 70599 Stuttgart, Germany

9 Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany

10 Misión Biológica de Galicia (CSIC), 36080 Pontevedra, Spain

For all author emails, please log on.

Genome Biology 2013, 14:R103  doi:10.1186/gb-2013-14-9-r103

Published: 19 September 2013

Additional files

Additional file 1: Table S1:

Maize lines used in this study, assignment to gene pools and origin of the lines.

Format: XLSX Size: 10KB Download file

Open Data

Additional file 2: Text S1:

Supplementary results.

Format: PDF Size: 1.9MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3: Table S2:

Chromosome-wide genetic lengths and recombination rates for all genetic maps.

Format: XLS Size: 38KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4: Table S3:

Details of all genetic maps, including raw segregation data.

Format: XLSX Size: 14.4MB Download file

Open Data

Additional file 5: Figure S1:

Allele frequency of the central parent allele for all polymorphic markers (A) in all Dent populations and (B) in all Flint populations. The 10 chromosomes are represented along the same horizontal axis. The expected frequency of 0.5 is indicated by a dotted line, and surrounded by solid lines representing its 99% confidence intervals. The x-axis indicates physical coordinates in megabase pairs along the B73 genome. In the bottom of the figure, the heat map represents gene density (low for cold colors and high for hot colors). Gray horizontal line below the heat-map: sketch of the chromosome organization showing centromeres (cen), knobs, nucleolar organizer region (NOR), and known gametophytic factors (gax) (from [30]). Color filling of chromosome features is solid when the estimated boundaries of the region are known, and hatched when the box indicates only the extremities of the bin containing the region.

Format: PDF Size: 1.5MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6: Figure S2:

Statistical comparison of chromsome-wide recombination rates between the 23 populations of the experiment. Chromosome 'All' (first page) corresponds to the genome-wide analysis. 'DentAll', 'FlintAll', and 'All' correspond, respectively, to pooled analyses of all Dent × Dent populations, all Flint × Flint populations, and all 23 populations together. Dark blue, light blue, green, yellow, and red correspond respectively to P ≥ 5.10-2, 10-3P < 10-2, 10-4 ≤ P < 10-3, 10-5P < 10-4, P < 10-5 where P is the P value of the pairwise comparison test, corrected for multiple testing (Bonferroni). Arrows pointing to the right (respectively to the bottom) indicate that the cross listed in the vertical axis (respectively the horizontal axis) has a higher recombination rate than the cross listed in the horizontal axis (respectively the vertical axis). Dendrograms indicate hierarchical clustering of -log10(P value) based on Euclidian distances, and were used to order the populations.

Format: PDF Size: 69KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7: Figure S3:

Marey maps and recombination landscapes along the chromosomes for three examples illustrating the imputation of regions with missing or unreliable data: CFD01 chromosome 1, CFF07 chromosome 1, and CFF01 chromosome 3. The x-axis indicates physical position of the SNPs on the B73 physical map in megabase pairs. The left y-axis indicates genetic map position in centiMorgans. The right y-axis indicates recombination rate in cM/Mbp. Each black empty circle corresponds to a SNP. Red dots indicate the outlier markers removed from the smoothing analysis. Dark blue dotted line: smoothed Marey map. Red dotted line: first derivative of the smoothed Marey map. Hatched rectangles: regions masked when going from bare to masked Marey maps (see Materials and methods). Light blue solid line: imputed smoothed Marey map obtained after imputation in the excluded regions, using data from all maps pooled. Pink solid curve: recombination rate computed as the first derivative of the imputed smoothed Marey map.

Format: PDF Size: 72KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8: Text S2:

Detailed methods.

Format: PDF Size: 53KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9: Figure S4:

Recombination rates along maize chromosomes 1 to 10. The x-axis indicates physical position (Mbp) along chromosomes. The y-axis indicates genetic position (cM; top panel), recombination rate (cM/Mbp; middle panel), and pairwise parental similarity (frequency of identical SNP alleles in 10 Mbp sliding windows with a step size of 2 Mbp; bottom panel) for 6 of the 23 populations, after smoothing and imputation (see Materials and methods). Blue lines: Flint × Flint crosses. Red lines: Dent × Dent crosses. In both groups, the solid, dashed and dotted lines correspond to the population with the highest, median or lowest genome-wide recombination rate within its group, respectively. Gray parts of the lines correspond to regions where the information was missing or not reliable (IBD segments, non-colinearity with B73), and thus imputed from the other maps (see Materials and methods). Heat-maps below the curves of recombination rates indicate gene density (low for cold colors and high for hot colors). Gray horizontal line below the heat-map: sketch of the chromosome organization (from [30]) showing centromeres (cen), knobs, and nucleolar organizer region (NOR). Color filling of chromosome features is solid when the estimated boundaries of the region are known, and hatched when the box indicates only the extremities of the bin containing the region.

Format: PDF Size: 684KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 10: Figure S5:

Statistical comparison of genome-wide recombination landscapes between the 23 populations for all chromosomes pooled as well as for each chromosome. For each pairwise comparison test, both genetic map lengths were normalized to their average value, so the test is not affected by differences in the global recombination rate but only by differences in the shape of the recombination landscape. 'DentAll', 'FlintAll', and 'All' correspond, respectively, to pooled analyses of all Dent × Dent populations, all Flint × Flint populations, and all 23 populations together. Dark blue, light blue, green, yellow, and red correspond respectively to P ≥ 5.10-2, 10-3P < 10-2, 10-4 ≤ P < 10-3, 10-5 ≤ P < 10-4, P < 10-5 where P is the P value of the pairwise comparison test, corrected for multiple testing (Bonferroni). Dendrograms indicate hierarchical clustering of -log10(P value) based on Euclidian distances, and were used to order the populations.

Format: PDF Size: 55KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 11: Figure S6:

Illustration of the statistical test used to compare recombination landscapes between the pooled data of all Dent × Dent (red) and Flint × Flint (blue) populations. Within regions excluded from the analysis for one population, the data were imputed from the other pool for conservativeness of the test (Additional file 8). Solid curves: Marey maps normalized to the average genetic length, so the comparison focuses on differences in the shape of the recombination landscapes and is not affected by differences in the values of chromosome genetic lengths. Dotted curves: first derivative of the normalized Marey maps, indicating the recombination landscape along the chromosome. The black rectangles show the 10 bins used for the analysis (from left to right: bins 1 to 10). Bin boundaries were chosen so each bin contained regions of the same genetic length. On top of each bar, a black vertical arrow indicates the difference between both populations in average recombination rates over the bin considered, and the error bars indicate the 95% confidence intervals of these average recombination rates.

Format: PDF Size: 248KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 12: Figure S7:

Statistical comparisons of interference intensity in pathway P1 (nu) between individual populations, for all chromosomes pooled together. 'DentAll', 'FlintAll', and 'All' correspond, respectively, to pooled analyses of all Dent × Dent populations, all Flint × Flint populations, and all 23 populations together. Dark blue, light blue, green, yellow, and red correspond respectively to P ≥ 5.10-2, 10-3 ≤ P < 10-2, 10-4 ≤ P < 10-3, 10-5P < 10-4, P < 10-5 where P is the P value of the pairwise comparison test, corrected for multiple testing (Bonferroni). Arrows pointing to the right (respectively to the bottom) indicate that the cross listed in the vertical axis (respectively the horizontal axis) has a higher value of nu than the cross listed in the horizontal axis (respectively the vertical axis). Dendrograms indicate hierarchical clustering of -log10(P value) based on Euclidian distances, and were used to order the populations.

Format: PDF Size: 9KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 13: Figure S8:

Statistical comparisons between individual populations, of the fraction (p) of crossovers formed via the non-interfering pathway P2, for all chromosomes pooled together. 'DentAll', 'FlintAll', and 'All' correspond, respectively, to pooled analyses of all Dent × Dent populations, all Flint × Flint populations, and all 23 populations together. Dark blue, light blue, green, yellow, and red correspond respectively to P ≥ 5.10-2, 10-3 ≤ P < 10-2, 10-4 ≤ P < 10-3, 10-5 ≤ P < 10-4, P < 10-5 where P is the P value of the pairwise comparison test, corrected for multiple testing (Bonferroni). Arrows pointing to the right (respectively to the bottom) indicate that the cross listed in the vertical axis (respectively the horizontal axis) has a higher value of p than the cross listed in the horizontal axis (respectively the vertical axis). Dendrograms indicate hierarchical clustering of -log10(P value) based on Euclidian distances, and were used to order the populations.

Format: PDF Size: 10KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 14: Figure S9:

Correlation between interference intensity in pathway P1 (nu) and genome-wide recombination rate for the 10 chromosomes pooled together over all populations.

Format: PDF Size: 5KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 15: Figure S10:

Crossing scheme of the two Dent and Flint half-sib panels. In each panel, a central line was crossed to diverse founder lines and DH lines were developed from the resulting F1 plants using the in vivo haploid induction method. Dent lines are shown in red, Flint lines in blue. Red lines: Dent × Dent crosses. Blue lines: Flint × Flint crosses. Gray lines: Dent × Flint/Flint × Dent crosses. Two reciprocal crosses (CFD01, CFF01) connect the panels via the central lines F353 and UH007. Both panels are also connected by crossing the central parent to B73 (CFD02, CFF02). The panels consist of 11 CFD and 13 CFF full-sib families, respectively.

Format: PDF Size: 13KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data