Estimation of Candidate Gene Effects in Dairy Cattle Populations

¹ Hebrew University of Jerusalem, Jerusalem 91904, Israel
² Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel

Standard programs for animal models can be modified to include the effect of a candidate gene, even if only a fraction of the population is genotyped. The elements of the incidence matrix for this effect is 0 or 1 for genotyped individuals and for the probabilities of the candidate gene genotypes for individuals that were not genotyped. The effects of a diallelic candidate gene that were estimated by this method were compared on simulated populations with three alternative estimation methods: analysis of genetic evaluations, yield deviations, and daughter yield deviations, all of which were derived from a standard animal model. The bases of comparison were mean squared error and bias. Four types of experimental designs were considered: genotyping sires only, genotyping cows only, genotyping half of the cows but no sires, and genotyping half of the sires and half of the cows. The estimates that were derived from the three alternative methods all underestimated the simulated effects. The genetic evaluations were more biased than were the yield deviations and the daughter yield deviations. The proposed method was significantly biased only for the design in which half of the daughters, but no sires, were genotyped. Bias and mean squared errors were always lowest by the proposed method.

Key Words: candidate genes • animal model • genetic markers • marker-assisted selection

Submitted on November 11, 1996
Accepted on February 19, 1998

This article has been cited by other articles:

				E. Baruch and J. I. Weller Incorporation of Discrete Genotype Effects for Multiple Genes into Animal Model Evaluations when only a Small Fraction of the Population Has Been Genotyped J Dairy Sci, November 1, 2008; 91(11): 4365 - 4371. [Abstract] [Full Text] [PDF]

				H. D. Daetwyler, F. S. Schenkel, M. Sargolzaei, and J. A. B. Robinson A Genome Scan to Detect Quantitative Trait Loci for Economically Important Traits in Holstein Cattle Using Two Methods and a Dense Single Nucleotide Polymorphism Map J Dairy Sci, August 1, 2008; 91(8): 3225 - 3236. [Abstract] [Full Text] [PDF]

				J. I. Weller, M. Golik, E. Seroussi, M. Ron, and E. Ezra Detection of Quantitative Trait Loci Affecting Twinning Rate in Israeli Holsteins by the Daughter Design J Dairy Sci, June 1, 2008; 91(6): 2469 - 2474. [Abstract] [Full Text] [PDF]

				N. Gengler, S. Abras, C. Verkenne, S. Vanderick, M. Szydlowski, and R. Renaville Accuracy of Prediction of Gene Content in Large Animal Populations and its Use for Candidate Gene Detection and Genetic Evaluation J Dairy Sci, April 1, 2008; 91(4): 1652 - 1659. [Abstract] [Full Text] [PDF]

				J. I. Weller, M. Golik, S. Reikhav, R. Domochovsky, E. Seroussi, and M. Ron Detection and Analysis of Quantitative Trait Loci Affecting Production and Secondary Traits on Chromosome 7 in Israeli Holsteins J Dairy Sci, February 1, 2008; 91(2): 802 - 813. [Abstract] [Full Text] [PDF]

				M. Soller, S. Weigend, M. N. Romanov, J. C. M. Dekkers, and S. J. Lamont Strategies to Assess Structural Variation in the Chicken Genome and its Associations with Biodiversity and Biological Performance Poult. Sci., December 1, 2006; 85(12): 2061 - 2078. [Abstract] [Full Text] [PDF]

				H. Khatib, S. D. Leonard, V. Schutzkus, W. Luo, and Y. M. Chang Association of the OLR1 Gene with Milk Composition in Holstein Dairy Cattle J Dairy Sci, May 1, 2006; 89(5): 1753 - 1760. [Abstract] [Full Text] [PDF]

				M. Cohen-Zinder, E. Seroussi, D. M. Larkin, J. J. Loor, A. E.-v. d. Wind, J.-H. Lee, J. K. Drackley, M. R. Band, A.G. Hernandez, M. Shani, et al. Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle Genome Res., July 1, 2005; 15(7): 936 - 944. [Abstract] [Full Text] [PDF]

				H. Khatib, E. Heifetz, and J. C. M. Dekkers Association of the Protease Inhibitor Gene with Production Traits in Holstein Dairy Cattle J Dairy Sci, March 1, 2005; 88(3): 1208 - 1213. [Abstract] [Full Text] [PDF]

				M. Ron, E. Feldmesser, M. Golik, I. Tager-Cohen, D. Kliger, V. Reiss, R. Domochovsky, O. Alus, E. Seroussi, E. Ezra, et al. A Complete Genome Scan of the Israeli Holstein Population for Quantitative Trait Loci by a Daughter Design J Dairy Sci, February 1, 2004; 87(2): 476 - 490. [Abstract] [Full Text] [PDF]

				G. Thaller, W. Kramer, A. Winter, B. Kaupe, G. Erhardt, and R. Fries Effects of DGAT1 variants on milk production traits in German cattle breeds J Anim Sci, August 1, 2003; 81(8): 1911 - 1918. [Abstract] [Full Text] [PDF]

				J. I. Weller, M. Golik, E. Seroussi, E. Ezra, and M. Ron Population-Wide Analysis of a QTL Affecting Milk-Fat Production in the Israeli Holstein Population J Dairy Sci, June 1, 2003; 86(6): 2219 - 2227. [Abstract] [Full Text] [PDF]

				J. I. Weller, H. Weller, D. Kliger, and M. Ron Estimation of Quantitative Trait Locus Allele Frequency via a Modified Granddaughter Design Genetics, October 1, 2002; 162(2): 841 - 849. [Abstract] [Full Text] [PDF]

				M. Ron, D. Kliger, E. Feldmesser, E. Seroussi, E. Ezra, and J. I. Weller Multiple Quantitative Trait Locus Analysis of Bovine Chromosome 6 in the Israeli Holstein Population by a Daughter Design Genetics, October 1, 2001; 159(2): 727 - 735. [Abstract] [Full Text] [PDF]

				M. O. Mosig, E. Lipkin, G. Khutoreskaya, E. Tchourzyna, M. Soller, and A. Friedmann A Whole Genome Scan for Quantitative Trait Loci Affecting Milk Protein Percentage in Israeli-Holstein Cattle, by Means of Selective Milk DNA Pooling in a Daughter Design, Using an Adjusted False Discovery Rate Criterion Genetics, April 1, 2001; 157(4): 1683 - 1698. [Abstract] [Full Text]