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Additional file 6: Figure S3. Graph of Principal Component Analysis (PCA) performed with SNP alleles of goat breeds from the Euro2Step dataset, where admixed and related animals were excluded. Besides first and second principal components (A), the third principal component was also analyzed (B).

Additional file 5: Figure S2. Phylogenetic neighbor net of global goat breeds from the two-step (excluding admixed and related animals) optimized dataset constructed with Nei’s DA distances (scale in the upper left corner) calculated with the 4-SNP blocks.

Additional file 4: Figure S1. Phylogenetic neighbor net of European goat breeds from the two-step (excluding admixed and related animals) optimized dataset constructed with Nei’s DA distances (scale in the upper left corner) calculated with the 4-SNP blocks.

Additional file 7: Figure S4. Phylogenetic tree. Neighbor-joining tree based on Nei’s genetic distance DA using multi-allelic SNP blocks. Mongolian yak (YAK) was used as a root. Dotted lines indicate the reduced length of YAK and GIR to improve visibility. Special square marks represent the influence of East-Podolian (grey), Alpine (green) and North-West (olive green) group.

Additional file 2: Table S1. Phenotypic variance explained by all SNPs for all phenotype codings. Table S2. Genome-wide significance thresholds for LRT values of cLDLA for different phenotype codings detected by permutation testing. Table S3. Power to detect a QTL for the four different codings (Table 1) of 232 high-density genotyped animals. Table S4. Gene content of the respective intervals used for the gene set enrichment analysis.

Additional file 6: Figure S3. Tessellated projection. Spatial geographic presentation of the estimated allele sharing distance matrix (DPS) among breeds using multi-allelic SNP-blocks.

Additional file 6: Figure S3. Tessellated projection. Spatial geographic presentation of the estimated allele sharing distance matrix (DPS) among breeds using multi-allelic SNP-blocks.

Additional file 2. Detailed description of the indigenous Greek and Cypriot cattle. Compilation of information on Greek indigenous cattle breeds from diverse sources [16, 33, 71–87]. This includes also information from records in Greek, which were formerly not accessible to the international scientific community due to language barriers.

Additional file 3: Figure S2. Results of the cLDLA for scurs of BC1 phenotype coding with sw40. LRT-values are shown on the y-axis, bovine chromosomes on the x-axis. The red horizontal line marks the genome-wide significance threshold (α = 0.00005) derived from permutation testing.

Additional file 7: Figure S4. Phylogenetic tree. Neighbor-joining tree based on Nei’s genetic distance DA using multi-allelic SNP blocks. Mongolian yak (YAK) was used as a root. Dotted lines indicate the reduced length of YAK and GIR to improve visibility. Special square marks represent the influence of East-Podolian (grey), Alpine (green) and North-West (olive green) group.

Additional file 4: Figure S2. Tessellated projection. Spatial geographic presentation of the estimated effective population number (Ne5, Ne50, Ne2000).

Additional file 3: Figure S1. Tessellated projection. Spatial geographic presentation of the herein estimated diversity parameters (mA, AR, HE, HE(SNP), npA, nspA).

Additional file 8: Figure S5. Admixture analysis. Population structure of the 114 studied breeds/populations presented for each of K inferred ancestral population value, using a genome‐wide set of bi-allelic SNPs. All the analyzed individuals are presented as colored vertical bars, divided at most K segments and with proportional heights, according to their genotype membership. In the depicted plots (K = 2 to K = 26), a different color is presented for each cluster. From left to right within each group the presented breeds are as follows: Minor Asia: ATER, ATBC, ATSR, ATSY, TRG; Greece and Cyprus: CYP, AGT, CRT, NSY, GRB, KAS, KEA, PRG, ROG, SYK, KTR; South East Europe: RHS, MKB, SRB, PRE, RMB, SHB, DGB, DBB, MAB, LKB, SKB, MNB, BHB, HRB; East Podolian: HRI, HRP, UKP; Tyrrhenian: PODO, CINI, MOSI, RSIC, MOSA, SARD, SBRU, CORS, AGER, MARE, CHI, MPIS, CALV, MCH, RMG, GARF, PONT, MODE, CABA, REGG, PMT, BURL; Alpine: PRDO, OVAR, REND, BPUS, PUST, SIC, PIN, TGV, MWF, OBV, BBV, DFV, FGV, VOG, ABO, MON, TAR; France: RDBI, SAL, AUB, LIM, CHR, PAR, BAQ, GAS; Iberian: MNRQ, MALL, NGAN, CANA, MARI, ALEN, BAR, MARO, SYG; North West Europe: BPN, NOR, MAN, BBB, LKF, HF, GNS, JSY, HER, SHR, KRY, DXT, GLW, AAN, HGL, NRC, SERC, FJL, FIAY, FINE, FINW, FINN, YARO.

Additional file 1: Table S1. Sample description, group allocation, RGB (color) code assigned to the pre-defined groups within this paper, breed names, breed code, number of sampled and genotyped individuals (N), number of genotyped and unrelated individuals used to estimate the diversity parameters (Nd), current breeding purposes as well as sporadic or recent past breeding purposes in parenthesis, breed origin, and source of the samples or genotypes used in this study or from previous studies [17, 25, 28, 30, 34, 35, 67–70]. Table S2. Phenotypic, productive and reproductive traits. Description of phenotype, productive and reproductive traits of the 11 Greek and Cypriot analyzed breeds. Table S3. Evolution of bovine population sizes on the islands during the last 60 years. Statistical information regarding the evolution of cattle population on the Greek island based on [62].

Additional file 4. Alignment of the repetitive elements at the beginning and end of the 6-kb candidate segment. Pairwise alignment of the reference sequences (BosTaurus8) of LINE BovB at the beginning of the 6-kb candidate segment and LINE BovB at the end of the segment. This file shows the huge level of similarity between the start and end of the candidate segment as is also obvious in Fig. 2d.

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.

Additional file 2: Table S2 The joint dataset used in the study. Description: This table provides information on the joint dataset, which includes the Russian sheep breeds and sheep breeds from across the world. The breeds are grouped according to their ancestral geographic origin (Russia, the British Isles, Northern Europe, Central Europe, Southwestern Europe, Asia, Southwestern Asia, Africa and the Americas). The table presents the information concerning the breedsâ abbreviation and color representation for the geographical group of breeds, the sample size, country (region) of sample collection, and the references where the genotyping data were previously published.

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 118,614,132Â bp shows that the unmapped portion of the split-aligned reads starts with a sequence that is located at 118,608,362Â bp, which thus defines the left breakpoint.

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.

Additional file 3. TLA results. The genomic region chr3:118,590,000â 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.

Additional file 3: Table S3 Genetic differentiation of 25 Russian sheep breeds based on Weir and Cockerhamâ s fixation index (FST). This table provides information about FST values between the Russian breeds under study. The breedsâ groups of the same wool type are framed in blue (for coarse wool breeds), red (for semi-fine wool breeds) and green (for fine wool breeds). For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2).

Additional file 1: Table S1 Short description of the Russian sheep breeds under study.

Additional file 1: Fig. S1. Pedigree of the albino calves. As the red highlighted paths show, both albinos and all carriers of the SNPs g.39829806G>A and g.39864148C>T can be traced back to a single natural service sire (B1). Symbols are as follows: squares = males, circles = females, filled symbols = albinos (homozygous for both SNPs), symbols with dot inside = heterozygous individuals, symbols with question mark inside = genotype unknown, crossed out symbols = no material available. For bull S2, 50K genotype data was available from previous studies; however, no material for targeted genotyping was available.

Additional file 2: Figure S2. Identification of a common haplotype on BTA4. Description: Genotypes of a subset of 32 Weaver carriers and 13 Weaver-affected offspring were scanned for regions of homozygosity surrounding the main and secondary peaks. The segment of interest consisted of 197 SNPs between positions 44,387,787 and 47,598,264Â bp. Carets (^) indicate the position of the secondary peak (47,598,264Â bp), asterisks (*) indicate the position of the main peak (49,812,384Â bp). Red bars indicate shared haplotype segments, green bars indicate the common haplotype shared by both Weaver-affected and carrier animals.

Additional file 1: Figure S1. Comparison of the results of cLDLA mapping with the results of case–control homozygosity mapping. The blue line with blue dots represents the results of the cLDLA mapping approach using data on 43 Weaver-affected, 31 Weaver carriers and 86 Weaver-free animals which resulted in a maximum LRT value (LRT = 73.9) at position 49,812,384 bp. The corresponding 0.853-Mb confidence interval between SNPs at 49,514,652 and 50,367,484 bp, represented by the grey bar, is assumed to harbor the causative mutation. The black line with black squares represents the results of a case–control homozygosity mapping approach [37] based on all Weaver-affected (case group) and Weaver-free animals (control group) from the cLDLA mapping population. In a second run, all Weaver cases which had been identified as phenocopies in the course of our further analyses were removed from the case group. The results of this run are displayed by the red line with red squares. Only run 2 of the homozygosity mapping approach, i.e. after removal of the phenocopies which were identified later, displayed a significant association with a 1.913-Mb block of adjacent SNPs (between 48,408,626 and 50,412,884 bp). However, the cLDLA approach was able to map the Weaver locus to the same chromosomal region even if the phenocopies were still included in the mapping population. Furthermore, the 0.853-Mb confidence interval identified by the cLDLA method allows for more precise analyses than the 1.913-Mb block of SNPs identified by homozygosity mapping, accounting for the higher mapping resolution obtained by the cLDLA method.

Additional file 1: Table S1. Primers used for Sanger sequencing and genotyping the insertion in the 3’-UTR of RXFP2.

Additional file 3: Table S2. Genotypes at the insertion polymorphism in the 3’-UTR of RXFP2, at SNP rs421908034 in the 3’-UTR and SNP rs414104606 in exon 14 of RXFP2 for 61 sheep from three breeds with variable and sex-dependent horn status.