0000000000895657
AUTHOR
Maria Sardina
Additional file 2: of Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability
Table S5. Goat haplogroup frequencies based on modern and ancient control-region mtDNA data from this study and downloaded from GenBanka. Table S6. Diagnostic mutational motifs of goat mtDNA haplogroups and sub-haplogroups. Table S7. A comparison of the phylogeographic features of goat, taurine and horse mtDNA haplogroups identified by analyzing domestic breeds from Eurasia. Table S8. Oligonucleotides used to amplify and to sequence (Sanger method) the goat mitochondrial genome. (PDF 652Â kb)
MOESM2 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
Additional file 2: Figure S2. Total number of runs of homozygosity (ROH) longer than 1Â Mb and total length of genome (Mb) covered by ROH segments per individual. Observed (black) vs simulated (red) data.
MOESM3 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
Additional file 3: Figures S3, S4, S5, S6. Plot of SNP occurrences (%) in ROH against the genomic regions of QTL for OAR chromosomes with the highest inbreeding coefficient (OAR 2, 4, 11, 23).
MOESM1 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
Additional file 1: Figure S1. Mean sum of runs of homozygosity (ROH) per animal estimated within four different generation categories. ROH were mapped according to their genetic positions (i.e. linkage map positions). ROH length (l cM) within each category was determined using 100/2 g, replacing g with the number of generations of interest.
MOESM4 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
Additional file 4: Figure S7. Plot of SNP occurrences in ROH against recombination rate. Recombination rate is the solid red line and the occurrence of a SNP in a ROH is represented by blue dots. (A) OAR2, (B) OAR4, (C) OAR11, and (D) OAR23. Recombination rate (cM/Mb) was estimated every 500Â kb.
MOESM5 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
Additional file 5: Table S1. List of 239 SNPs considered as candidate markers under directional selection in the Valle del Belice sheep breed.
Additional file 1: of Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability
Table S1. Sources for the 758 goat control-region sequences. Table S2. Control-region haplotypes and haplogroup classification of the 758 mtDNA sequences from Capra aegagrus (n = 19) and Capra hircus (n = 739). Table S3. Partial coding-region haplotypes and haplogroup classification of two bezoar mtDNAs. Table S4. Source and haplogroup affiliation of the goat complete mtDNA sequences. Figure S1. Nucleotide diversity and total number of substitutions along the entire mtDNA. Figure S2. A putative most parsimonious tree of 84 complete mtDNA sequences from goats. (XLSX 1268 kb)
MOESM6 of Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
Additional file 6: Table S2. List of 107 potential candidate genes under directional selection in the Valle del Belice sheep breed.