Figure 1.
Comparison of linkage disequilibrium (LD) measures for the genes in the study.
A. D′ and r2 plotted against distance between SNPs. D′ values are filled black circles, r2 values are open black circles. Least squares fitted regression lines of LD on length of haplotype (D′ solid line, r2 dashed line) are not statistically significant and the slopes are b<−1×10−5. This is evidence that the length differences between haplotypes are not important in accounting for LD between SNPs in this sample of genes. Values are means of LD estimates for each breed, not calculated from a sample of mixed breed individuals. B. Plot of D′ against r2 for the genes in this study. Most of the comparisons between pairs of SNPs show high D′and low r2 values, a typical result for cattle at this distance between SNPs. High D′values can indicate a reduced number of haplotypes or classes of haplotypes that are missing. r2 values are useful in describing how well the genotypes at one SNP predict the genotypes at the other SNP.
Table 1.
SNPs of the calpain-calpastatin gene haplotypes associated as single point associations to LLPF in the GWAS.
Table 2.
Calpain-calpastatin gene haplotypes associated to LLPF.
Table 3.
Single point SNP associations of candidate genes for IMF in the GWAS.
Figure 2.
Plot of –logP values for SNPs compared to haplotypes for candidate genes for IMF.
The SNPs are numbered 1, 2, and 3 in order along the chromosome and in the haplotypes, 1 = A and 2 = B alleles at each SNP. Haplotypes were fitted simultaneously. Note that for the gene CXCR4, this gene is the closest gene to the significant SNPs, but these are not located within the gene itself.
Table 4.
Haplotype associations of candidate genes for IMF in the GWAS.
Table 5.
Percent of phenotypic variance for IMF explained by haplotypes compared to SNPs.