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Additional file 3: Figure S3. Relationship between observed heterozygosity versus (left) ROH coverage or (right) within-population allele-sharing distances. Red and dark blue indicate insular and continental breeds, respectively, with high homozygosity. Pink and light blue indicate insular and continental breeds, respectively, with low or modest homozygosity.

Additional file 3: Table S1. Environmental variables considered for the landscape genomic analysis. Table S2. FLK and hapFLK windows for the sub-continental groups after filtering steps. Overlapping or partially overlapping regions across the different geographical subdivisions are reported with the same letter as used for the population group (from a to m). Table S3. Selective sweeps of early adaptation. The bold values indicate overlap or partial overlap between comparisons. Table S4 Common regions between ROH and XP-EHH and/or FST analyses for the group of “fiber-producing” goat breeds and genes within these regions. Table S5. Common regions between ROH and XP-EHH and/or FST analyses for the group of “meat-producing” goat breeds and genes within these regions. Table S6. Common regions between ROH and XP-EHH and/or FST analyses for the group of “milk-producing” goat breeds and genes within these regions. Table S7. Top four regions detected for the coat color groups (Black, White and Red), indicated comparisons between the groups and genes located nearby these regions. Table S8. Results of the most significant associations involving the 57 filtered SNPs. For each SNP: SNP probe, genotype, genomic coordinate, associated environmental variable (“Env”) and scores and statistical test output values (“Gscore”, “WaldScore”, “Efron”, “AIC”, “Beta_0” and “Beta_1”) are reported. Table S9. List of genes located nearby (± 100 kb) the 57 filtered SNPs obtained by the landscape genomics analysis. Table S10. GO term biological processes. Table S11. MAF (minor allele frequency) and major allele of the 13 SNPs shared by Dry and Temperate/Continental groups. Table S12. Samβada significant results for the SNPs of the FST analyses. For each SNP probe: chromosome and position are reported, as well as Environment, G score, Wald Score, AIC, Abs_Beta1 and the Köppen group in which the SNP was detected by the FST analyses. Table S13. List of genes located nearby (± 100 kb) of the 65 SNPs selected with the FST approach and confirmed by Samβada. The * symbol indicates the SNPs with the highest value (> 0.999) also in landscape genomic analysis

Additional file 1. Treemix plots. Each page shows the output of a continental/sub-continental group

Additional file 2: Figure S2. PCA plot of 25 insular and continental goats for coordinate PC1 against PC2, PC3 and PC4 averaged across individuals. Red and dark blue indicate insular and continental breeds, respectively, with high homozygosity. Pink and light blue indicate insular and continental breeds, respectively, with low or modest homozygosity.

Additional file 5. Genotype distribution of the SNPs detected in the landscape genomics analysis based on the GPS coordinates. Each page represent a SNP, with its coordinates reported on the upper right part of each sheet, with environmental variable associated and statistics (G score, Beta 1 and AIC). The three possible genotypes are labelled with three different colors: AA = red; AB = green; BB = blue

Additional file 4. Graphical representation of ROH and iHS results at the breed level of the signals FLK and hapFLK in the sub continental groups. Left panel: FLK (points) and hapFLK (line) signatures, with as header the chromosomal region investigated. Middle panels: ROH signatures. Right panels: iHS signatures [see Additional file 2]

Additional file 2: Figure S1. MDS plot of the breeds, grouped by production purpose: milk, meat and fiber groups. Group colors: milk = green, meat = red, fiber = blue; MDS and box plots of the first two components pre-filtering (upper) and MDS plots after filtering. Figure S2. Manhattan plot of the FLK results for the sub-continental group after filtering steps. Sub-geographical group names are given on top of each plot. Chromosomes are alternately red and black. Figure S3. Manhattan plot of the hapFLK results for the sub-continental group after filtering steps. Sub-geographical group names are given on top of each plot. Chromosomes are alternately red and black. Figure S4. Genomic distribution of FLK and hapFLK signals across population groups. For each chromosome and each sub-continental group, the chromosomal position detected with at least one of the two approaches is indicated. Figure S5. Signatures of selection on chromosome 5 for the North western Africa, South eastern Africa and South western Africa groups. North western Africa (NWA): red; South eastern Europe (SEE): green; South western Europe (SWE): blue. The table (bottom-right) reports the genes within the region in which a signature was detected. Figure S6. Signatures of selection on chromosome 6 for the Central Asia, East Africa and South east Europe groups. Central Asia (CA): red; East Africa (EA): green; South east Europe (SEE): blue. The table (upper-right) reports the genes within the region in which a signature was detected. Figure S7. Signatures of selection on chromosome 13 for the Alpines and Central Asia groups. Alpines (Alps): red; Central Asia (CA): blue. The table (right) reports the genes within the region in which a signature was detected. Figure S8. Signatures of selection on chromosome 1 for the Alpines and South Western Europe groups. Alpines (Alps); red; South Western Europe (SWE): blue. The table (bottom-right) reports the genes within the region in which a signature was detected. Figure S9. FLK signals on chromosome 6 around the casein gene cluster. The cluster of unannotated genes between YTHDC1 and SULT1B1 consists of genes coding for glucuronosyltransferase enzymes. Alps; red; East Arica (EA): blue. The table (right) reports the genes within the casein cluster region. Figure S10. Signatures of selection on chromosome 6 for the Egypt, South Eastern Europe and South Western Europe groups. Egypt (Egypt): red; South Eastern Europe (SEE): green; South Western Europe (SWE): blue. The table (bottom-right) reports the genes within the region in which a signature was detected. Figure S11. Signatures of selection on chromosome 12 for the Central Asia and South Western Europe groups. Central Asia (CA); red; South Western Europe (SWE): blue. The table (right) reports the genes within the region in which a signature was detected. Figure S12. ROH, FST and XP-EHH results for the group of “meat-producing” goat breeds. Types of analysis are indicated with different plot colors, within the most external squared-based circle, where each color represent a chromosome (chromosome number outside the squares): green (external) = ROH; blue (middle) = Fst; violet (internal): XP-EHH. For the three analyses, the regions above the threshold are marked in red. Figure S13. ROH, FST and XP-EHH results for the group of “milk-producing” goat breeds. Types of analysis are indicated with different plot colors, within the most external squared-based circle, where each color represent a chromosome (chromosome number outside the squares): green (external) = ROH; blue (middle) = Fst; violet (internal): XP-EHH. For the three analyses, the regions above the threshold are marked in red. Figure S14. CDA for the region on chromosome 25 detected for the group of “fiber-producing” goat breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S15. CDA for the region on chromosome 25 detected for the group of “meat-producing” goat breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S16. CDA for the region on chromosome 25 detected for the group of “milk-producing” goat breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S17. MDS plot of breeds considered for the panel of coat colors. Breed codes and subdivisions based on the coat color pattern are indicated in the right part of the plot. Figure S18. CDA for the region on chromosome 18 near the MC1R gene detected for the group of coat color breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S19. CDA for the region on chromosome 13 near the ASIP gene detected for the group of coat color breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S20. CDA for the region on chromosome 5 near the ADAMTS20 gene detected for the group of coat color breeds. (a): LONG and (b) SHORT: (b). Left: CDA plot. Right: Correlation value of the SNPs used for the analyses for CAN1 and CAN2. Figure S21. MDS plot of the filtered dataset considering components 1 and 2. Animals are color-coded based on the Köppen classification of groups: Tropical (green), Dry (red), Temperate (orange), Continental (blue). Figure S22. FST plot of the comparison of the Dry group vs. the other groups. The threshold line in red represents the 0.995 of the percentile distribution (FST = 0.398). Figure S23. FST plot of the comparison of the Temperate group vs. the other groups. The threshold line in red represents the 0.995 of the percentile distribution (FST = 0.320). Figure S24. FST plot of the comparison of the Continental group vs. the other groups. The threshold line in red represents the 0.995 of the percentile distribution (FST = 0.507).

Additional file 1: Figure S1. Geographic locations of the insular and continental breeds considered in our study. Red and dark blue indicate insular and continental breeds, respectively, with high homozygosity. Pink and light blue indicate insular and continental breeds, respectively, with low or modest homozygosity.

Additional file 3. Comparison of ROH across the breeds raised in different countries. The higher the value on the y axis, the bigger is the difference. The threshold of Hâ =â 5 is indicated with a red line.

Additional file 1: Table S1. Animals used for the analyses. Breed symbol, name and number (N). The country in which samples were collected (Country), the continental and subcontinental groups used for the analyses are reported. Table S2. Average fraction of the genome that contains ROH in each one of the breeds under analysis. Breed code (Breed) and average fraction of the genome that contains ROH (FROH). Breeds are reported based on FROH increasing values. Table S3. Summary statistics of number of ROH regions and genome coverage considering the sub-geographical and continental classification. min: minimum number of ROH regions or coverage detected; max: minimum number of ROH regions or coverage detected; mean: average number of ROH regions or coverage detected; sd: standard deviation from the mean value. Table S4. Comparison of pairwise least square means of the sub-geographical comparisons. Comparison: pairwise comparison considered; estimate: estimated difference in LSM; p.value: adjusted Bonferroni P value. Table S5. Summary statistics of number of ROH regions and genome coverage for comparison 1 and pairwise least square means comparison. min: minimum number of ROH regions or coverage detected; max: maximum number of ROH regions or coverage detected; mean: average number of ROH regions or coverage detected; sd: standard deviation from the mean value; estimate: estimated difference in LSM; p.value: adjusted Bonferroni P-value. Table S6. Chromosomal regions with a high level of homozygosity (the top 0.998 percentile of at least three consecutive SNPs) and overlaps (partial or complete) across continents and continental sub-divisions. NP = not present; “-“: no overlap detected; for the regions shared by most of the subgroups (All), the symbol of the genes detected within those regions are reported. See the bold number in the “overlap with other continental/sub-continental” column. (1) MIR217; MIR216B; CFAP36; PNPT1; PPP4R3B; EFEMP1. (2) GJB6; SAP18; MRPL57; ATP12A; CENPJ; MPHOSPH8; ZMYM5; GJA3; GJB2; CRYL1; IL17D; EEF1AKMT1; LATS2; SKA3; ZDHHC20; FGF9; RNF17; PSPC1; ZMYM2; IFT88; XPO4; MICU2; PARP4. (3) MAB21L1; DCLK1; NBEA. (4) TPPP3; AGRP; CARMIL2; PARD6A; ENKD1; C18H16orf86; TSNAXIP1; THAP11; NUTF2; EDC4; NRN1L; LCAT; DPEP3; DPEP2; DDX28; SLC7A6OS; LRRC36; ZDHHC1; ATP6V0D1; FAM65A; ACD; GFOD2; CENPT; PSKH1; PSMB10; DUS2; ESRP2; PLA2G15; SLC7A6; SMPD3; HSD11B2; CTCF; RANBP10; NFATC3; PRMT7; SLC12A4. Table S7. Chromosomal regions displaying a high divergence in homozygosity across countries for the same breeds. For each breed-based analysis, chromosome (chr), start and end of the regions with H ≥ 5 are reported.

Additional file 5: Table S3. List of markers and genes identified by both CDA and FST approaches. This table reports the markers and the genes in common between the two considered approaches for detection of selection signatures.

Additional file 4: Figure S2. Plot of the individual scores of the first three canonical variables (CVA1, CVA2, and CVA3) extracted from BTA13 in the five breeds. This plot represents the clear separation between Italian Holstein and Marchigiana obtained on BTA13; circles = Italian Brown Swiss; flowers = Italian Holstein; diamonds = Piemontese; cubes = Marchigiana; pyramids = Italian Simmental.

Additional file 1: Table S1. Matrices of Mahalanobis distances between the five breeds on the 29 autosomes. This table reports the Mahalanobis distance between the centroids of the five cattle populations calculated with the canonical discriminant analysis. The distances are reported for all the 29 autosomes. BRW = Italian Brown Swiss; HOL = Italian Holstein; MAR = Marchigiana; PIE = Piemontese; SIM = Italian Simmental.

Additional file 3: Table S2. List of putative candidate genes detected using CDA derived from Bos taurus UMD 3.1/bosTau6 assembly. This table reports the genes that have been identified considering an interval of 0.5Â Mb around SNPs that have the highest (top 1Â %) correlations with the canonical variables.

Additional file 2: Figure S1. Manhattan plot of FST values (light and dark grey dots) and canonical coefficients (red dots) for all ten pairwise comparisons. This plot reports the FST values and the canonical coefficient along the whole genome obtained in the ten pairwise comparisons between all the five breeds considered in this study, evidencing the concordance between the two approaches in the detection of selection signatures. BRW = Italian Brown Swiss; HOL = Italian Holstein; MAR = Marchigiana; PIE = Piemontese; ISIM = Italian Simmental.