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Additional file 1: Figure S1. Patterns of coancestry ( $$f$$ f ) in all chromosomes (except 1, 2, 7 and 12) for the CC, NEAC, CC × NEAC and $$ f_{{{\text{CC}}\;{\&}\;NEAC}} $$ f CC & N E A C populations. The data provided represent values of coancestry smoothed by using a sliding window approach. Figure S2. Genetic differentiation coefficients ( $$F$$ F ST) between populations CC and NEAC in all chromosomes (except 1, 2, 7 and 12). The showed values are genetic differentiation coefficients smoothed by using a sliding window approach. Figure S3. Private allele frequency in populations CC (left column) and NEAC (right column) in all chromosomes (except 1, 2, 7 and 12). A sliding window approach was used to smooth the private allele frequency. Figure S4. Principal components analysis in populations CC and NEAC in all chromosomes (except 1, 2, 7 and 12). First two principal components on the SNP data available.

Long distance LD pr. Mb separated by the chromosome for each population LD for each SNP pair with a distance between 10Â kb and 1Â Mb taken into account. Figure S2. Accuracy and yield of imputation between each location of SNPs. Figure S3. Comparing minor allele frequencies of SNPs between imputed and actual genotypes before quality control of imputed results separately plot by each SNP location. Figure S4. Comparing allele frequencies of SNPs between imputed and actual genotypes after quality control of imputed results separately plotted by each SNP location. Figure S5. Proportion of SNPs with lower AF after imputation vs initial AF. Figure S6. Comparing p-values between cases and controls of SNPs between imputed and actual genotypes before quality control of imputed results separately plotted by each SNP location. Figure S7. Comparing p-values between cases and controls of SNPs between imputed and actual genotypes after quality control of imputed results separately plotted according to each SNP location. Figure S8. Average linkage disequilibrium as r-squared for each region. SNPs were assigned to gene locations. Figure S9. LD, measured as r2, plotted against physical distance. (PDF 1286Â kb)

Supplementary figures and tables. (PDF 647 kb)

Additional file 2: Table S2. Primer sequences used for the reverse transcription qPCR (RT-qPCR).

Additional file 3: Figure S1. Further description of the procedure for estimating DBP protein levels. Detailed description of the protocol for estimating the DBP levels in serum from 50 NR cows. Figure S1 gives a schematic explanation of vitamin D3 metabolism.