Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus.
BACKGROUND
Single nucleotide polymorphisms (SNPs) are an abundant form of genetic variation in the genome of every species and are useful for gene mapping and association studies. Of particular interest are non-synonymous SNPs, which may alter protein function and phenotype. We therefore examined bovine expressed sequences for non-synonymous SNPs and validated and tested selected SNPs for their association with measured traits.


RESULTS
Over 500,000 public bovine expressed sequence tagged (EST) sequences were used to search for coding SNPs (cSNPs). A total of 15,353 SNPs were detected in the transcribed sequences studied, of which 6,325 were predicted to be coding SNPs with the remaining 9,028 SNPs presumed to be in untranslated regions. Of the cSNPs detected, 2,868 were predicted to result in a change in the amino acid encoded. In order to determine the actual number of non-synonymous polymorphic SNPs we designed assays for 920 of the putative SNPs. These SNPs were then genotyped through a panel of cattle DNA pools using chip-based MALDI-TOF mass spectrometry. Of the SNPs tested, 29% were found to be polymorphic with a minor allele frequency >10%. A subset of the SNPs was genotyped through animal resources in order to look for association with age of puberty, facial eczema resistance or meat yield. Three SNPs were nominally associated with resistance to the disease facial eczema (P < 0.01).


CONCLUSIONS
We have identified 15,353 putative SNPs in or close to bovine genes and 2,868 of these SNPs were predicted to be non-synonymous. Approximately 29% of the non-synonymous SNPs were polymorphic and common with a minor allele frequency >10%. Of the SNPs detected in this study, 99% have not been previously reported. These novel SNPs will be useful for association studies or gene mapping.
Lee
Michael A
MA
AgResearch, Invermay Agricultural Centre, Mosgiel, Private Bag 50034, New Zealand. michael.lee@herongroup.co.uk <michael.lee@herongroup.co.uk>
Keane
Orla M
OM
Glass
Belinda C
BC
Manley
Tim R
TR
Cullen
Neil G
NG
Dodds
Ken G
KG
McCulloch
Alan F
AF
Morris
Chris A
CA
Schreiber
Mark
M
Warren
Jonathan
J
Zadissa
Amonida
A
Wilson
Theresa
T
McEwan
John C
JC
D019943:Amino Acid Substitution; D000818:Animals; D002417:Cattle / Q000235:genetics*; D002418:Cattle Diseases / Q000235:genetics; D002874:Chromosome Mapping; D003062:Codon; D030541:Databases, Genetic; D004485:Eczema / Q000235:genetics / Q000662:veterinary; D020224:Expressed Sequence Tags; D005260:Female; D005787:Gene Frequency; D016678:Genome; D007113:Immunity, Innate / Q000235:genetics; D008297:Male; D008460:Meat; D020641:Polymorphism, Single Nucleotide
D003062:Codon