Analyzing Non-Synonymous SNPs in Cattle
Author Information
Author(s): Lee Michael A, Keane Orla M, Glass Belinda C, Manley Tim R, Cullen Neil G, Dodds Ken G, McCulloch Alan F, Morris Chris A, Schreiber Mark, Warren Jonathan, Zadissa Amonida, Wilson Theresa, McEwan John C
Primary Institution: AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
Hypothesis
We examined bovine expressed sequences for non-synonymous SNPs and validated selected SNPs for their association with measured traits.
Conclusion
We identified 15,353 putative SNPs in bovine genes, with 2,868 predicted to be non-synonymous, and found that approximately 29% of these were polymorphic.
Supporting Evidence
- 15,353 putative SNPs were detected in the transcribed sequences studied.
- 2,868 of the detected SNPs were predicted to result in a change in the amino acid encoded.
- 29% of the SNPs tested were found to be polymorphic with a minor allele frequency >10%.
- Three SNPs were nominally associated with resistance to facial eczema.
Takeaway
Scientists looked at the DNA of cows to find tiny changes that might affect their traits, and they found many new changes that could help in breeding better cows.
Methodology
The study involved mining public bovine expressed sequence tagged sequences to identify coding SNPs, followed by genotyping a subset of these SNPs through pooled cattle DNA.
Potential Biases
Some SNPs may be specific to breeds not tested, and the study relied on a limited number of animals for SNP detection.
Limitations
The SNPs were genotyped through a limited number of cattle breeds, which may not represent all possible polymorphisms.
Participant Demographics
The study involved various breeds of cattle, including Angus, Hereford, and Jersey.
Statistical Information
P-Value
p<0.01
Statistical Significance
p<0.01
Digital Object Identifier (DOI)
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