Open Access Highly Accessed Research article

A selective sweep of >8 Mb on chromosome 26 in the Boxer genome

Javier Quilez1*, Andrea D Short2, Verónica Martínez1, Lorna J Kennedy2, William Ollier2, Armand Sanchez1, Laura Altet1 and Olga Francino1

Author Affiliations

1 Molecular Genetics Veterinary Service (SVGM), Department of Animal and Food Science, Veterinary School, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain

2 Centre for Integrated Genomic Medical Research (CIGMR), Stopford Building, Oxford Road, Manchester, M13 9PT, UK

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BMC Genomics 2011, 12:339  doi:10.1186/1471-2164-12-339

Published: 1 July 2011

Additional files

Additional file 1:

Comparison of the ROHs on CFA 1, 10 and 26 common in sets A (Figure S1a-e) and B (Figure S1f-j). Red lines indicate ROH as defined in each set.

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Additional file 2:

Summary statistics of the 50-SNP sliding windows.

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Additional file 3:

Comparison of ROHs identified in Set B and Set B pruned for SNPs significantly deviating from HWE. Note that for the region setB_06 two different regions were detected and that the end of setB_07 overlaps with start of setB_08.

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Additional file 4:

Genotypes of samples from brachycephalic breeds for the segment of the ROH on CFA 26 shared between Boxer and English and French bulldogs. For the Boxer, a random sample of 20 dogs is displayed.

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Additional file 5:

Genotypes for the CNV on CFA 9 in samples from other breeds than Boxer and Iberian wolf genotyped with the Illumina's CanineSNP20. Chromosome positions corresponding to the described CNV are highlighted in green and genotypes grouped by breed. Homozygous genotypes are coded as '11' (grey) and '22' (orange), respectively, and heterozygous genotypes as '12' (blue); '00' represents missing values (white).

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Additional file 6:

Genotypes for the CNV on CFA 9 in samples from other breeds than Boxer and Iberian wolf genotyped with the Illumina's CanineHD. Chromosome positions corresponding to the described CNV are highlighted in green and genotypes grouped by breed. Homozygous genotypes are coded as '11' (grey) and '22' (orange), respectively, and heterozygous genotypes as '12' (blue); '00' represents missing values (white).

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Additional file 7:

FAA_long: functional annotation categories are classified either as biological processes (BP) or diseases (DIS). Function annotations that either involve genes laying in the region of homozygosity common in Boxer, English and French bulldogs (orange) or relate to inherited diseases overrepresented in the Boxer (blue) are highlighted. FAA_GenomicPosition: annotated elements in the selective sweep on chromosome 26 and in the syntenic region in the human genome. Whether annotated elements lay in the region of homozygosity in each breed (Boxer and English and French bulldogs) is indicated. Annotated elements significant in the functional annotation analysis are highlighted (orange). InheritedDiseases: inherited diseases reported in Boxer, English and French bulldogs [4]. Of these, those significant in the functional annotation analysis are highlighted (blue).

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Additional file 8:

File containing genetic content, Gene Ontology Biological Process (GO BP) annotation and synteny information for the CNV on CFA 9.

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Additional file 9:

Multidimensional scaling (MDS) plot of the two first dimensions C1 and C2. The excluded outlier samples are indicated by the arrows.

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