2009-Hassen_et_al - The effect of heritability estimates on...

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A. Hassen, S. Avendano, W. G. Hill, R. L. Fernando, S. J. Lamont and J. C. M. Dekkers analyses with related animals The effect of heritability estimates on high-density single nucleotide polymorphism doi: 10.2527/jas.2008-0852 originally published online November 21, 2008 2009, 87:868-875. J ANIM SCI http://jas.fass.org/content/87/3/868 the World Wide Web at: The online version of this article, along with updated information and services, is located on www.asas.org by guest on October 11, 2011 jas.fass.org Downloaded from
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ABSTRACT: Analysis of high-density SNP data in outbred populations to identify SNP that are associ- ated with a quantitative trait requires efficient ways to handle large volumes of data and analyses. When using mixed animal models to account for polygenic effects and relationships, genetic parameters are not known with certainty, but must be chosen to ensure proper evaluation of SNP across chromosomes and lines or breeds. The objectives of this study were to evalu- ate the influence of heritability on the estimates and significance of SNP effects, to develop efficient com- putational strategies for analysis of high-density SNP data with uncertain heritability estimates, and to de- velop strategies to combine SNP test results across lines or breeds. Data included sire SNP genotypes and mean progeny performance from 2 commercial broiler breeding lines. Association analyses were done by fit- ting each SNP separately as a fixed effect in an animal model, using a range of heritabilities. The heritability used had a limited impact on SNP effect estimates, but affected the SE of estimates and levels of significance. The shape of the frequency distribution of P -values for the test of SNP effects changed from a highly skewed L-shaped curve at low heritability to a right-skewed distribution at high heritability. The P -values for al- ternative heritabilities could, however, be derived with- out reanalysis based on a strong linear relationship (R 2 = 0.99) between differences in log-likelihood values of models with and without the SNP at different levels of heritabilities. With uncertain estimates of heritability, line-specific heritabilities that ensure proper evaluation of SNP effects across lines were determined by analysis of simulated sire genotypes and by permutation tests. Resulting heritability estimates were between those ob- tained from the entire breeding populations and those obtained from the data included in the sample data set. In conclusion, the uncertainty of heritability estimates has a limited impact on SNP effect estimates in as- sociation analyses, but a large impact on significance tests. The impact of heritability on tests can, however, be dealt with in a computationally efficient manner by using the strong linear relationship between model statistics under alternate levels of heritability. These approaches allow efficient analysis of large numbers of SNP for multiple traits and populations and pooling of results across populations.
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This note was uploaded on 01/26/2012 for the course ECON 2272 taught by Professor Gay during the Spring '08 term at Birmingham-Southern College.

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2009-Hassen_et_al - The effect of heritability estimates on...

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