Abstract
BackgroundThe apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL). However, the phase of LD between a SNP and a QTL may differ between Bos indicus and Bos taurus because they diverged at least one hundred thousand years ago. Here, we test the hypothesis that the apparent effect of a SNP on a quantitative trait depends on whether the SNP allele is inherited from a Bos taurus or Bos indicus ancestor.MethodsPhenotype data on one or more traits and SNP genotype data for 10 181 cattle from Bos taurus, Bos indicus and composite breeds were used. All animals had genotypes for 729 068 SNPs (real or imputed). Chromosome segments were classified as originating from B. indicus or B. taurus on the basis of the haplotype of SNP alleles they contained. Consequently, SNP alleles were classified according to their sub-species origin. Three models were used for the association study: (1) conventional GWAS (genome-wide association study), fitting a single SNP effect regardless of subspecies origin, (2) interaction GWAS, fitting an interaction between SNP and subspecies-origin, and (3) best variable GWAS, fitting the most significant combination of SNP and sub-species origin.ResultsFitting an interaction between SNP and subspecies origin resulted in more significant SNPs (i.e. more power) than a conventional GWAS. Thus, the effect of a SNP depends on the subspecies that the allele originates from. Also, most QTL segregated in only one subspecies, suggesting that many mutations that affect the traits studied occurred after divergence of the subspecies or the mutation became fixed or was lost in one of the subspecies.ConclusionsThe results imply that GWAS and genomic selection could gain power by distinguishing SNP alleles based on their subspecies origin, and that only few QTL segregate in both B. indicus and B. taurus cattle. Thus, the QTL that segregate in current populations likely resulted from mutations that occurred in one of the subspecies and can have both positive and negative effects on the traits. There was no evidence that selection has increased the frequency of alleles that increase body weight.
Highlights
The apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL)
Since the extent and phase of LD can vary between breeds, combining data from different breeds can reduce the association between a SNP and trait phenotype. de Roos et al [7,8] reported that the phase of LD between adjacent markers on the 50 K Bovine SNP chip frequently differed among B. taurus cattle breeds, which means that the power of association studies based on the 50 K chip will be reduced when using multiple breeds because the LD between SNPs and QTL is unlikely to be conserved across breeds
For B. taurus animals, ‘b’ values were low but only 7.1% of the ‘b’ values were found in the range of 0.1 < b < 0.2 and 1.5% in the range of 0.2 < =b < 0.32, indicating some uncertainty, probably because many B. taurus breeds were included in the dataset
Summary
The apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL). Genomic selection and GWAS depend on the presence of linkage disequilibrium (LD) between markers (usually single nucleotide polymorphisms or SNPs) and quantitative trait loci (QTL). De Roos et al [7,8] reported that the phase of LD between adjacent markers on the 50 K Bovine SNP chip frequently differed among B. taurus cattle breeds, which means that the power of association studies based on the 50 K chip will be reduced when using multiple breeds because the LD between SNPs and QTL is unlikely to be conserved across breeds Since the extent and phase of LD can vary between breeds, combining data from different breeds can reduce the association between a SNP and trait phenotype. de Roos et al [7,8] reported that the phase of LD between adjacent markers on the 50 K Bovine SNP chip frequently differed among B. taurus cattle breeds, which means that the power of association studies based on the 50 K chip will be reduced when using multiple breeds because the LD between SNPs and QTL is unlikely to be conserved across breeds
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
