J. Anim Sci.
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Published online first on September 12, 2008
J. Anim Sci. 1910. doi:10.2527/jas.2008-0959
© 2008 American Society of Animal Science
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Confirmation of QTL using a low density SNP map for twinning and ovulation rate on bovine chromosome 5

M. F. Allan, L. A. Kuehn, R. A. Cushman, W. M. Snelling, S. E. Echternkamp and R. M. Thallman

USDA, ARS, U. S. Meat Animal Research Center, Clay Center, NE 68933

Mark.Allan{at}ars.usda.gov

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 more rapidly 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 of 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 21 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 2-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 3 for ovulation rate. Two of these SNP, 1 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.

Key Words: GenoProb • MTDFREML • SNP • twinning




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E.-S. Kim, X. Shi, O. Cobanoglu, K. Weigel, P. J. Berger, and B. W. Kirkpatrick
Refined mapping of twinning-rate quantitative trait loci on bovine chromosome 5 and analysis of insulin-like growth factor-1 as a positional candidate gene
J Anim Sci, March 1, 2009; 87(3): 835 - 843.
[Abstract] [Full Text] [PDF]


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