Genet. Sel. Evol. 32 (2000) 357-381

Detection and parameter estimation for quantitative trait loci using regression models and multiple markers

Yang Daa - Paul M. VanRadenb - Lawrence B. Schookc

aDepartment of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
bAnimal Improvement Programs Laboratory, ARS-USDA, Beltsville, Maryland 20705, USA
cDepartment of Veterinary Pathobiology, University of Minnesota, Saint Paul, MN 55108, USA

(Received 12 July 1999; accepted 12 April 2000)


A strategy of multi-step minimal conditional regression analysis has been developed to determine the existence of statistical testing and parameter estimation for a quantitative trait locus (QTL) that are unaffected by linked QTLs. The estimation of marker-QTL recombination frequency needs to consider only three cases: 1) the chromosome has only one QTL, 2) one side of the target QTL has one or more QTLs, and 3) either side of the target QTL has one or more QTLs. Analytical formula was derived to estimate marker-QTL recombination frequency for each of the three cases. The formula involves two flanking markers for case 1), two flanking markers plus a conditional marker for case 2), and two flanking markers plus two conditional markers for case 3). Each QTL variance and effect, and the total QTL variance were also estimated using analytical formulae. Simulation data show that the formulae for estimating marker-QTL recombination frequency could be a useful statistical tool for fine QTL mapping. With 1000 observations, a QTL could be mapped to a narrow chromosome region of 1.5 cM if no linked QTL is present, and to a 2.8 cM chromosome region if either side of the target QTL has at least one linked QTL.

Keywords: multiple markers / regression analysis / quantitative trait loci / QTL detection / QTL parameters

Correspondence and reprints: Yang Da

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