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

A strategy of multi-step minimal conditional regression analysis has been d eveloped to determine the existence of statistical testing and parameter es timation for a quantitative trait locus (QTL) that are unaffected by linked QTLs. The estimation of marker-QTL recombination frequency needs to consid er 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 rec ombination frequency for each of the three cases. The formula involves two flanking markers for case 1), two flanking markers plus a conditional marke r for case 2), and two flanking markers plus two conditional markers for ca se 3). Each QTL variance and effect, and the total QTL variance were also e stimated using analytical formulae. Simulation data show that the formulae for estimating marker-QTL recombination frequency could be a useful statist ical tool for fine QTL mapping. With 1000 observations, a QTL could be mapp ed 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 leas t one linked QTL.