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Additional file 1

Additional file 1.

Table S1. Primer pairs used for PCR amplification and sequencing of the PRDM9 gene; and nucleotide sequences of PRDM9 exon10, partial coding sequences associated with the haplotype and individuals studied. (PDF 362 kb)

Figure S1. Characteristics of CNV distribution on each autosome. A. Distributions of CNV length per individual. B. Distributions of CNV count. Figure S2. Hierarchical clustering of 41 complex traits based on P values from association results between CNVRs and phenotypes. Pearson correlation was used to measure distances. Different colors represent various types of phenotype traits. (PDF 294 kb)

Correlation between recombination maps of four cattle breeds using the same sample size. The average correlations were calculated from 1000 repeatedly random samples. Each random sample has the same number of meioses across four cattle breeds. Correlations in males were presented in the top-right triangle and female correlations in the bottom-left. The Holstein data have been published previously [15] and are included for comparison purposes. (DOCX 14 kb)

Ingenuity pathway analysis of the MS data. Fig. S1A. Venn Diagrams showing the number of proteins with either no differential (ND) or differential expression between broilers (Br) and layers (La). n = 3 birds per strain, P ≤ 0.05, absolute fold change ≥1.5. B. Schematic presentation of the pathways highlighted by Ingenuity software (−log P value > 1.3). C. Schematic drawing of the intrinsic prothrombin activation pathway adapted from Ingenuity software. (DOCX 654 kb)

Example regions showing different recombination patterns between four cattle breeds. Top 2: males; Bottom 2: females. The Holstein data have been published previously [15] and are included for comparison purposes. (DOCX 183 kb)

Additional file 3: Table S3. Variable genomic regions (VGR) that differ between the Awassi and the Afec-Assaf according to PLINK and EMMAX analyses. SNPs were ranked according to their P-values, and the selected regions included the top 0.1% markers and their neighboring (1.5Â Mb upstream and 1.5Â Mb downstream) markers ranked in the top 1% of the markers. Two or more genomic regions were combined if they overlapped. Region position was determined using sheep genome assembly version 3.1. Regions identified by both analyses are marked in gray.

Additional file 5: Table S4. Association between presence of a 1.8-kb insertion at the 3â ˛-UTR of RXFP2 and horn phenotype in Awassi and Afec-Assaf sheep. A 428-bp PCR product indicates the presence of the insertion [19].

Characterization of NPHS1 and TNF. Figure S1. Predicted full length cDNA sequence of NPHS1 and its characterization. Figure S2. Predicted full length cDNA sequence of TNF and its characterization. Table S9. Coding sequence of chicken NPHS1 and TNF predicted transcripts. Table S10. List of NPHS1 and TNF exons in human, turtle, and chicken. Table S11. List of primers used for RT-PCR. Table S12. Probes used for expression profiling in the Sequence Read Archive (SRA) database. (PDF 1672 kb)

Additional file 1: Table S1. Genome-wide association studies in sheep reviewed in the current study [10â 14, 17, 18, 32â 39, 47, 48, 54, 65, 67â 95].

Additional file 4: Figure S1. Different horn phenotypes in Awassi (A to D) and Afec-Assaf (E to H) sheep. (A) Polled, female. (B) Knobs, female. (C) Horns, female. (D) Horns, male. (E) Polled, female. (F) Knobs, male. (G) Knobs, male. (H) Scurs, male.

Additional file 11: Table S8. Human genes associated with fat distribution [61, 63, 64, 98â 100].

Additional file 7. Candidate gene sequences. This file contains sequences of candidate genes in a FASTA-like format. Each sequence header consists of the gene symbol followed by its reference GenBank accession number and the breed name. Polymorphic nucleotide positions are indicated in blue and red font colors.

Additional file 8: Figure S2. Variability in fat-tail phenotypes in Assaf sheep. Awassi-like fat tail (A). Fat tails with different amounts of fat deposition and different lengths (B to H).

Additional file 10: Table S7. Genes known to affect coat pigmentation in humans, cattle and other mammals [55â 58].

Characterization of the high confidence novel genes. Table S13. Phylogenetic analysis of representative novel genes. Figure S3. Characterization of the novel transcripts. (PDF 232 kb)

Additional file 9: Table S6. Candidate genes and SNP markers associated with carrying fat tail in sheep [38, 39, 47, 49â 51].

Detailed materials and methods. Animals and tissue sampling. RNA-seq. Bioinformatic analysis. RT-PCR. Mass spectrometry analysis (MS). (PDF 283 kb)