, The Genetics of Cattle (CAB International, 1999.
, Mason's World Dictionary of Livestock Breeds, Types, and Varieties (CAB International, 2002.
, Highly effective SNP-based association mapping and management of recessive defects in livestock, Nature Genet, vol.40, pp.449-454, 2008.
, Microsatellite mapping of the bovine roan locus: a major determinant of white heifer disease, Mamm. Genome, vol.7, pp.138-142, 1996.
, PennCNV: an integrated hidden Markov model designed for highresolution copy number variation detection in whole-genome SNP genotyping data, Genome Res, vol.17, pp.1665-1674, 2007.
, Melanocyte migration and survival controlled by SCF/c-kit expression, J. Investig. Dermatol. Symp. Proc, vol.6, pp.1-5, 2001.
, A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses, Cytogenet. Genome Res, vol.119, pp.225-230, 2007.
, Molecular basis for the dominant white phenotype in the domestic pig, Genome Res, vol.8, pp.826-833, 1998.
, Mechansisms of change in gene copy number, Nature Rev. Genet, vol.10, pp.551-564, 2009.
, Survey of allelic expression using EST mining, Genome Res, vol.15, pp.1584-1591, 2005.
, Origins and functional impact of copy number variation in the human genome, Nature, vol.464, pp.704-712, 2010.
, Analysis of copy number variations among diverse cattle breeds, Genome Res, vol.20, pp.693-703, 2010.
, Analysis of recent segmental duplications in the bovine genome, BMC Genomics, vol.10, p.571, 2009.
, Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae, PLoS Genet, vol.7, p.1001287, 2011.
, Heterogeneous patterns of amplification of the NUP214-ABL1 fusion gene in T-cell acute lymphoblastic, Leukemia, vol.23, pp.125-133, 2009.
, Merlin-rapid analysis of dense genetic maps using sparse gene flow trees, Nature Genet, vol.30, pp.97-101, 2002.
, The 300 ml sample was placed in a 1.5 ml Eppendorf tube and sonicated for 8 min with the instrument set to high and a cycle of 30 s on and 30 s off. A 5-kb insert library was generated for a Cs/Cs Belgian blue animal and a 2-kb and 5-kb for a Cs/Cs brown Swiss animal. A paired-end library with a 400 bp insert size was also generated for a Cs/1 Belgian blue animal using the Illumina paired-end kit, following the instructions of the manufacturer, The resulting libraries were quantified using Pico-Green (Quant-it, Invitrogen) and the Agilent 2100 Bioanalyzer High Sensitivity DNA kit
, Breakpoints were identified by visually inspecting the mate pairs using the integrative genomics viewer 22 in the ,2-Mb region surrounding the Cs-specific duplications in Belgian blue and brown Swiss animals and looking for discordant mate pairs. PCR amplification of translocation breakpoints. PCR primers were designed to span each of the breakpoints identified by mate-pair sequencing. The primers were tested on genomic DNA from colour-sided and wild-type animals. PCR products were visualized on a 2% agarose gel. Primers with amplification confined to colour-sided animals were purified using the QIAquick PCR purification kit (Qiagen), where multiple bands were observed the relevant band was excised and purified using the QIAquick gel extraction kit (Qiagen). The fragments were then sequenced using Big Dye terminator cycle-sequencing kit v.3.1 (Applied Biosystems) with the purified reaction run on a ABI PRISM 3730 DNA analyser (Applied Biosystems). Primers used are listed in Supplementary Table 2. Analysis of Cs 29 -derived KIT transcripts. To ensure that no mutations were present in the coding sequence of the Cs 29 -specific KIT gene, primers were designed to amplify all the exons and the 39 UTR from genomic DNA (Supplementary Table 2). The resulting PCR products were sequenced as outlined above, which did not reveal any protein altering DNA sequence variant. To examine expression of KIT from the Cs 29 allele, a small biopsy of skin was removed from the back (white skin) and side (pigmented skin) of a colour-sided Belgian blue animal (the relevant ethical procedures were adhered to). The samples were immediately frozen in liquid nitrogen and stored at 280 uC until RNA extraction. The tissue was homogenized using a Tissue Lyser (Qiagen), total RNA was extracted using the, Sequencing was carried out on an Illumina GAIIx instrument. Mapping of the 36 bp from each end of the mate-pair libraries and the 110 bp from the ends of the paired-end library was performed using the BWA tool 21
, To determine if the Cs 29 allele was expressed, the cDNA from the skin biopsies was amplified using primers spanning both SNPs and sequenced as outlined above. Moreover, and to ensure the integrity of Cs 29 -derived KIT transcripts, primers located in the first exon and the 39 UTR (Supplementary Table 2) were used with the Expand Long Template PCR System (Roche) to amplify the near full-length KIT cDNA. The product was run on 1% gel and examined for evidence of alternative splicing. Genotyping the duplicated B and C segments of the Cs 6 allele. Long-range PCR was carried out using the Expand Long Template PCR System (Roche). The genomic DNA used as template was extracted using QIAamp DNA Mini columns (Qiagen) following the manufacturer's instructions to produce high molecular weight DNA. For each reaction the following mix was prepared: 2 ml Buffer 1, 140 mM dNTP, 120 nM upstream and downstream primer, 0.3 ml enzyme mix and 100 ng genomic DNA, final volume was 20 ml. Extension time and the thermal profile recommended by the manufacturer was followed, Genomic DNA was extracted from whole blood from the same animal using standard phenol-chloroform extraction. The intronic regions of the KIT gene were searched for SNPs using the mate-pair sequences produced from the Cs/Cs Belgian blue animal
, Analysis of chromosome breakpoints in neuroblastoma at subkilobase resolution using fine-tiling oligonucleotide array CGH, Genes Chromosom. Cancer, vol.44, pp.305-319, 2005.
, A new non-linear normalization method for reducing variability in DNA microarray experiments, Genome Biol, vol.3, p.48, 2002.
, Circular binary segmentation for the analysis of array-based DNA copy number data, Biostatistics, vol.5, pp.557-572, 2004.
, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.
, Integrative genomics viewer, Nature Biotechnol, vol.29, pp.24-26, 2011.