Manhattan plot with GWAS for AVPCV, AVLWT, and AVFEC.

<p>QQ plots of observed −log10 p-values against expected values (top) and histogram of SNP effects (bottom) on the right hand side. Dashed red line for AVPCV corresponds to the lowest −log10 p-value amongst relevant SNPs (3.936).Dashed red line for AVLWT corresponds to the lowest −log10 p-value amongst relevant SNPs (3.898).Dashed red line for AVFEC corresponds to the lowest −log10 p-value amongst relevant SNPs (3.794).</p

Genotype effects of AVFEC top SNP markers on packed cell volume and live weight.

<p>Genotype effects of AVFEC top SNP markers on packed cell volume and live weight.</p

Top SNP markers and cluster positions on sheep chromosomes (OAR) 01, 02, 03, and 06 (a-d).

<p>Dashed red line corresponds to the SNP with the highest −log10 p-value.</p

Manhattan plot for AVPCV, AVLWT, and AVFEC using EMMAX (permutation results in grey) and BLUPf90/PostGSf90 (permutation results in grey).

<p>Horizontal dashed lines in orange represent significant SNP markers in the BLUPf90/PostGSf90 analysis. Dashed red line for AVPCV corresponds to the lowest −log10 p-value amongst relevant SNPs (3.936).Dashed red line for AVLWT corresponds to the lowest −log10 p-value amongst relevant SNPs (3.898).Dashed red line for AVFEC corresponds to the lowest −log10 p-value amongst relevant SNPs (3.794).</p

Descriptive statistics of Red Maasai x Dorper backcrossed sheep selected phenotypes.

<p>Traits: Packed cell volume (AVPCV), starting packed cell volume (PCV_ST), decline in packed cell volume (%) (PCVD), liveweight (AVLWT), non-transformed faecal egg counts (FEC), log-transformed FEC (LFEC), Box-Cox transformed FEC (AVFEC)</p><p>Letters correspond to Tukey HSD test significance using α = 0.05.</p><p>Descriptive statistics of Red Maasai x Dorper backcrossed sheep selected phenotypes.</p

AVPCV, AVLWT, and AVFEC relevant SNP markers: top −log₁₀ p-value and cluster markers.

<p>AVPCV, AVLWT, and AVFEC relevant SNP markers: top −log₁₀ p-value and cluster markers.</p

Additional file 1: Table S1. of Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression

Tissue samples used in the RRBS analysis. Table S2. RRBS validation results. Table S3. Different methylated cytosine information. Table S4. Significantly correlated DMCs and gene information. Table S5. Different methylated CpG island information. Table S6. Significantly correlated DMIs and gene information. Table S7. Tissue-specific different methylated cytosine information. Table S8. Tissue-specific different methylated CpG island information. Table S9. Primers used for validation of RRBS results. (XLS 2962 kb

Additional file 1: Table S1. of Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus

Detail information of the CNVs detected with high confidence. Table S2. CNV validation by qPCR. Table S3. Number of animals used in the association analysis for each traits. Table S4. Primers for qPCR and rtPCR validations. (XLSX 37 kb

Additional file 2: Figure S1. of Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus

Alignment of the protein sequences of KCNJ12 in different species. Figure S2. Boxplot of reliability of the nine body traits. Figure S3. Expression levels of KCNJ12 in 45 tissues. Figure S4. The effect of the CNV100’s copy number on the gene expression of KCNJ12 in muscle tissues. (PDF 678 kb