A whole-genome scan was conducted to map quantitative trait loci (QTL) for BSEresistance or susceptibility. Cows from four half-sib families were included and173 microsatellite markers were used to construct a 2835-cM (Kosambi) linkagemap covering 29 autosomes and the pseudoautosomal region of the sex chromosome.Interval mapping by linear regression was applied and extended to a multiple-QTLanalysis approach that used identified QTL on other chromosomes as cofactors toincrease mapping power. In the multiple-QTL analysis, two genome-widesignificant QTL (BTA17 and X/Y(ps)) and four genome-wide suggestive QTL (BTA1,6, 13, and 19) were revealed. The QTL identified here using linkage analysis donot overlap with regions previously identified using TDT analysis. One factorthat may explain the disparity between the results is that a more extensive dataset was used in the present study. Furthermore, methodological differencesbetween TDT and linkage analyses may affect the power of these approaches.Copyright 2004 Genetics Society of America