2009-Allan_et_al - Confirmation of quantitative trait loci...

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Thallman M. F. Allan, L. A. Kuehn, R. A. Cushman, W. M. Snelling, S. E. Echternkamp and R. M. polymorphism map for twinning and ovulation rate on bovine chromosome 5 Confirmation of quantitative trait loci using a low-density single nucleotide doi: 10.2527/jas.2008-0959 originally published online Sep 12, 2008; 2009.87:46-56. J Anim Sci http://jas.fass.org/cgi/content/full/87/1/46 the World Wide Web at: The online version of this article, along with updated information and services, is located on www.asas.org by on October 22, 2010. jas.fass.org Downloaded from
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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 for live- stock, the opportunity may exist to improve reproduc- tive efficiency more rapidly in cattle. The US Meat An- imal Research Center 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 geno- types 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 ani- mals. Genotypic probabilities for females were used to calculate independent variables for regressions of addi- tive, dominance, and imprinting effects. Genotypic re- gressions were fitted as fixed effects in a 2-trait mixed model analysis by using multiple-trait derivative-free REML. Each SNP was analyzed individually, followed by backward selection fitting all individually significant SNP simultaneously and then removing the least sig- nificant SNP until only significant SNP were left. Five significant SNP associations were detected for twinning rate and 3 were detected for ovulation rate. Two of these SNP, 1 for each trait, were significant for imprint- ing. Additional modeling of paternal and maternal al- lelic effects confirmed the initial results of imprinting done by contrasting heterozygotes. These results are supported by comparative mapping of mouse and hu- man imprinted genes to this region of bovine chromo- some 5. Key words: GenoProb, multiple-trait derivative-free restricted maximum likelihood, single nucleotide polymorphism, twinning ©2009 American Society of Animal Science. All rights reserved. J. Anim. Sci. 2009. 87:46–56 doi:10.2527/jas.2008-0959 INTRODUCTION Fine mapping and marker development for marker- assisted selection ( MAS ) in all species has had lim- ited success; however, with technological advances in genomics and the ongoing development of the bovine whole-genome sequence, the rate of success in the dis- covery of DNA markers for MAS should accelerate. To date, successes in MAS have resulted from phenotypic
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2009-Allan_et_al - Confirmation of quantitative trait loci...

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