Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies

Bolormaa, Sunduimijid, Pryce, Jennie E., Kemper, Kathryn E., Hayes, Ben J., Zhang, Yuandan, Tier, Bruce, Barendse, William, Reverter, Antonio and Goddard, Mike E. (2013) Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies. Genetics Selection Evolution, 45 1: 43.1-43.12. doi:10.1186/1297-9686-45-43


Author Bolormaa, Sunduimijid
Pryce, Jennie E.
Kemper, Kathryn E.
Hayes, Ben J.
Zhang, Yuandan
Tier, Bruce
Barendse, William
Reverter, Antonio
Goddard, Mike E.
Title Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies
Formatted title
Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies
Journal name Genetics Selection Evolution   Check publisher's open access policy
ISSN 0999-193X
1297-9686
Publication date 2013
Sub-type Article (original research)
DOI 10.1186/1297-9686-45-43
Open Access Status DOI
Volume 45
Issue 1
Start page 43.1
End page 43.12
Total pages 12
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Subject 1103 Clinical Sciences
1105 Dentistry
1311 Genetics
2700 Medicine
Formatted abstract
Background: 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). 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.

Methods: Phenotype 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.

Results: Fitting 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.

Conclusions: The 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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