Joint Tests for Quantitative Trait Loci in Experimental Crosses

• Activity Number: 28
• Type: Contributed
• Date/Time: Sunday, August 3, 2003 : 2:00 PM to 3:50 PM
• Sponsor: Biometrics Section
• Author(s): T. Mark Beasley*+ and Dongyan Yang and David B. Allison and Christopher I. Amos
• Companies: University of Alabama, Birmingham and University of Alabama and University of Alabama, Birmingham and
• Keywords: joint tests ; genetics ; inbred strains ; QTL

Abstract

Selective genotyping is common because it can increase the expected correlation between QTL genotype and phenotype and thus increase the statistical power of linkage tests that assess whether the phenotype is dependent on the genotype (regression tests). A marginal test that assesses whether the marginal genotypic distribution conforms to its expectation can also be used to test linkage. We develop OLS-based and logistic-based joint tests that, by constraining intercepts in regression analyses, capitalize on the information available in both regression and marginal tests. We simulated data corresponding to the null hypothesis of no linkage and the alternative of a QTL effect at the locus for two study designs: a backcross and an F2 intercross between inbred strains. We studied the effects of random sampling, selection from a single tail of the phenotypic distribution, and selection from both tails of the phenotypic distribution. Joint tests were nearly as powerful as all competing alternatives for random sampling and two-tailed selection for both backcross and F2 intercross designs. Joint tests were generally more powerful for one-tailed selection for both backcross and F2 designs.