Joint tests for quantitative trait loci in experimental crosses

  • T Mark Beasley1Email author,

    Affiliated with

    • Dongyan Yang1,

      Affiliated with

      • Nengjun Yi1,

        Affiliated with

        • Daniel C Bullard2,

          Affiliated with

          • Elizabeth L Travis3,

            Affiliated with

            • Christopher I Amos4,

              Affiliated with

              • Shizhong Xu5 and

                Affiliated with

                • David B Allison1, 6

                  Affiliated with

                  Genetics Selection Evolution200436:601

                  DOI: 10.1186/1297-9686-36-6-601

                  Received: 16 February 2004

                  Accepted: 24 May 2004

                  Published: 15 November 2004


                  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 (i.e., regression-based tests). Linkage can also be tested by assessing whether the marginal genotypic distribution conforms to its expectation, a marginal-based test. We developed a class of joint tests that, by constraining intercepts in regression-based analyses, capitalize on the information available in both regression-based and marginal-based tests. We simulated data corresponding to the null hypothesis of no QTL effect and the alternative of some QTL effect at the locus for a backcross and an F2 intercross between inbred strains. Regression-based and marginal-based tests were compared to corresponding joint tests. We studied the effects of random sampling, selective sampling from a single tail of the phenotypic distribution, and selective sampling from both tails of the phenotypic distribution. Joint tests were nearly as powerful as all competing alternatives for random sampling and two-tailed selection under both backcross and F2 intercross situations. Joint tests were generally more powerful for one-tailed selection under both backcross and F2 intercross situations. However, joint tests cannot be recommended for one-tailed selective genotyping if segregation distortion is suspected.

                  joint tests quantitative trait loci linkage F2 cross backcross

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                  Authors’ Affiliations

                  Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham
                  Department of Genomics and Pathobiology, University of Alabama at Birmingham
                  Department of Experimental Radiation Oncology, University of Texas, M.D. Anderson Cancer Center
                  Department of Epidemiology, University of Texas, M.D. Anderson Cancer Center
                  University of California
                  Clinical Nutrition Research Center, University of Alabama at Birmingham


                  © INRA, EDP Sciences 2004