Journal of Animal Science

Confirmation of quantitative trait loci using a low-density single nucleotide polymorphism 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

Abstarc :

Traditional genetic selection in cattle for traits with lowheritability, such as reproduction, has had very little success.With the addition of DNA technologies to the genetic selectiontoolbox for livestock, the opportunity may exist to improvereproductive efficiency more rapidly in cattle. The US MeatAnimal Research Center Production Efficiency Population has9,186 twinning and 29,571 ovulation rate records for multiplegenerations of animals, but a significant number of these animalsdo not have tissue samples available for DNA genotyping. Theobjectives of this study were to confirm QTL for twinning andovulation rate previously found on BTA5 and to evaluate theability of GenoProb to predict genotypic information in a pedigreecontaining 16,035 animals when using genotypes for 24 SNP from3 data sets containing 48, 724, or 2,900 animals. Marker datafor 21 microsatellites on BTA5 with 297 to 3,395 animals permarker were used in conjunction with each data set of genotypedanimals. Genotypic probabilities for females were used to calculateindependent variables for regressions of additive, dominance,and imprinting effects. Genotypic regressions were fitted asfixed effects in a 2-trait mixed model analysis by using multiple-traitderivative-free REML. Each SNP was analyzed individually, followedby backward selection fitting all individually significant SNPsimultaneously and then removing the least significant SNP untilonly significant SNP were left. Five significant SNP associationswere detected for twinning rate and 3 were detected for ovulationrate. Two of these SNP, 1 for each trait, were significant forimprinting. Additional modeling of paternal and maternal alleliceffects confirmed the initial results of imprinting done bycontrasting heterozygotes. These results are supported by comparativemapping of mouse and human imprinted genes to this region ofbovine chromosome 5.

Key Word :
GenoProb, multiple-trait derivative-free restricted maximum likelihood, single nucleotide polymorphism, twinning

Volume 87, Number 1, January 2009