Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/14397
Title: Detection of quantitative trait loci in 'Bos indicus' and 'Bos taurus' cattle using genome-wide association studies
Contributor(s): Bolormaa, Sunduimijid (author); Pryce, Jennie E (author); Kemper, Kathryn E (author); Hayes, Ben J (author); Zhang, Yuandan  (author); Tier, Bruce  (author); Barendse, William (author); Reverter, Antonio (author); Goddard, Mike E (author)
Publication Date: 2013
Open Access: Yes
DOI: 10.1186/1297-9686-45-43Open Access Link
Handle Link: https://hdl.handle.net/1959.11/14397
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.
Publication Type: Journal Article
Source of Publication: Genetics Selection Evolution, v.45, p. 1-12
Publisher: BioMed Central Ltd
Place of Publication: United Kingdom
ISSN: 0999-193X
1297-9686
Field of Research (FOR): 070201 Animal Breeding
060408 Genomics
Socio-Economic Outcome Codes: 830301 Beef Cattle
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Other Links: http://www.gsejournal.org/content/45/1/43
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Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
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