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Title: Confirmation of quantitative trait loci using a low-density single nucleotide polymorphism map for twinning and ovulation rate on bovine chromosome 5

item Allan, Mark
item Kuehn, Larry
item Cushman, Robert - Bob
item Snelling, Warren
item Echternkamp, Sherrill
item Thallman, Richard - Mark

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/2/2008
Publication Date: 1/2/2009
Citation: Allan, M.F., Kuehn, L.A., Cushman, R.A., Snelling, W.M., Echternkamp, S.E., Thallman, R.M. 2009. Confirmation of quantitative trait loci using a low-density single nucleotide polymorphism map for twinning and ovulation rate on bovine chromosome 5. Journal of Animal Science. 87(1):46-56.

Interpretive Summary: Fine mapping and marker development for marker-assisted selection (MAS) in all species has had limited success. However with technological advances in genomics and the ongoing development of the bovine whole genome sequence, the rate of success in the discovery of DNA markers for MAS should accelerate. To date, successes in MAS have resulted from phenotypic traits with moderate to high heritability and commercialization of markers for MAS in beef cattle has been limited to traits related to meat tenderness and fat deposition. Discovery of DNA markers for reproductive traits will give the producer a tool to identify superior or inferior animals and improve selection response, further enhancing the economic gains for the cow-calf producer. Results of this study show efforts to develop DNA markers for twinning and ovulation rate discovered in the USMARC Production Efficiency population (twinning herd) by confirming a quantitative trait loci on bovine chromosome 5 from previous studies. These markers will need to be validated in other cattle populations where the twinning phenotype is segregating.

Technical Abstract: Traditional genetic selection, in cattle, for traits with low heritability, such as reproduction, has had very little success. With the addition of DNA technologies to the genetic selection toolbox in livestock, opportunity may exist to improve reproductive efficiency in cattle. The U.S. Meat Animal Research Center (USMARC) Production Efficiency Population has 9,186 twinning and 29,571 ovulation rate records for multiple generations of animals, but a significant number of these animals do not have tissue samples available for DNA genotyping. The objectives of this study were to confirm QTL for twinning and ovulation rate previously found on BTA5 and to evaluate the ability to use GenoProb to predict genotypic information in a pedigree containing 16,035 animals when using genotypes for 24 SNP from 3 data sets containing 48, 724, or 2,900 animals. Marker data for 20 microsatellites on BTA5 with 297 to 3,395 animals per marker were used in conjunction with each data set of genotyped animals. Genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fitted as fixed effects in a two trait mixed model analysis using MTDFREML. Each SNP was analyzed individually followed by backward selection fitting all individually significant SNP simultaneously and then removing the least significant SNP until only significant SNP were left. Five significant SNP associations were detected for twinning rate and three for ovulation rate. Two of these SNP, one for each trait, were significant for imprinting. Additional modeling of paternal and maternal allelic effects confirmed the initial results of imprinting done by contrasting heterozygotes. These results are supported by comparative mapping of mouse and human imprinted genes to this region of bovine chromosome 5.