MOESM3 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

Additional file 3. TLA results. The genomic region chr3:118,590,000–118,632,000 (bosTau8) is displayed. The arrows indicate the position of the primer sets used for TLA. For the belted animal (GLW54-2), an increased copy number (3 to 4.5 times) was detected in the region indicated by the red rectangle. The y-axis is limited to max. 1000X

MOESM2 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

Additional file 2. Alignment of CH240-104M22 and the reference sequence. Pairwise alignment of the BAC-clone CH240-104M22 with the bosTaurus6 reference sequence of the 6-kb candidate region showing almost complete identity

MOESM6 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

Additional file 6. Alignment of the repetitive elements at the beginning of the 6-kb candidate segment according to bosTaurus6 and bosTaurus8. The pairwise alignment of the reference sequence of the SINE element ART2A (bosTau6) and the LINE element BovB (bosTau8) at the beginning of the 6-kb candidate segment shows that ART2A is part of BovB

MOESM7 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

Additional file 7. Gene interaction network. This figure illustrates the interactions between KIT (causal for the belt in pigs), ADAMTS20 (causal for the belt in mice) and TWIST2 (most likely causal for the belt in cattle) in mice. Interaction line colors are as follows: orange: predicted functional relationship, red: physical interactions, purple: co-expression; grey: phenotype (based on mouse genome informatics) and blue: participation in the same reaction within a pathway

MOESM5 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

Additional file 5. Nanopore sequencing results. (a) Nanopore reads mapped (minimap2) to the belted candidate region are shown. The shaded parts of the reads highlight unmapped portions of the read that were mapped as a secondary alignment in a separate read. These secondary alignments are highlighted by blue borders. (b) Split-alignment of breakpoint-spanning read visualized by Ribbon [52]. The highlighted read (bold blue line) is shown as a zoom in the lower panel, showing that the beginning of the read is found at the end of the repeated region and the end is found at the beginning, thus illustrating the concatenation of the repeat units found in belted cattle. (c) Exact breakpoints were identified by inspection of the partially mapped reads. The right breakpoint at 118,614,132 bp shows that the unmapped portion of the split-aligned reads starts with a sequence that is located at 118,608,362 bp, which thus defines the left breakpoint

MOESM8 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

Additional file 8. Haplotypes of the Russian Yakutian animals checked by qPCR. This file shows 42-SNP haplotypes of the 10 Russian Yakutian animals that were checked by qPCR. As in Additional file 1, SNPs that were excluded from the mapping procedure (MAF < 0.025) are marked in grey color in the first line, and the first five haplotypes represent the most common and extended haplotypes of the European breeds Belted Galloway (BGAhap1 and BGAhap2), Dutch Belted (DBEhap) and Gurtenvieh (GUVhap1 and GUVhap2). Red boxes again indicate common parts of these five haplotypes and represent the four inner candidate haplotypes (IC-Hap1-4, Table 3). Below these common haplotypes, the haplotypes of the 10 Siberian Russian Yakutian animals are grouped as follows: the first seven animals were belted according to phenotype and qPCR, the next animal was belted according to phenotype but non-belted in the qPCR, and the last two animals were non-belted according to phenotype and qPCR. Interestingly, the belted Russian Yakutian (RUY) animals do not share a common haplotype within IC-Hap4, which carries the candidate mutation BeltMulti6kb

MOESM1 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

Additional file 1. Inner candidate haplotypes detected by manual analysis of the extended confidence interval. This file shows the 60-SNP haplotypes of the extended candidate interval for all 110 animals that were used for remapping of the belt locus. SNPs that were excluded from the mapping procedure (MAF < 0.025) are marked with grey color in the first line. The black box indicates the 336-kb interval identified by Drögemüller et al. [13]. The first five haplotypes represent the most common and extended haplotypes for Belted Galloway (BGAhap1 and BGAhap2, shown in bright and dark blue), Dutch Belted (DBEhap, shown in beige) and Gurtenvieh (GUVhap1 and GUVhap2, shown in dark and bright green). Red boxes indicate common parts of these five haplotypes and represent the four inner candidate haplotypes (IC-Hap1-4, Table 3). The haplotypes of the animals that were used for remapping are shown below in the following order: (i) Belted Galloway, (ii) Dutch Belted, (iii) Gurtenvieh, (iv) a belted cross between Gurtenvieh and Pinzgauer cattle and (v) non-belted control animals