Mapping of multiple quantitative trait loci by simple regression in half-sib designs

Detection of QTL in outbred half-sib family structures has mainly been base d on interval mapping of single QTL on individual chromosomes. Methods to a ccount for linked and unlinked QTL have been developed, but most of them ar e only applicable in designs with inbred species or pose great demands on c omputing facilities. This study describes a strategy that allows for rapid analysis, involving multiple QTL, of complete genomes. The methods combine information from individual analyses after which trait scores for a specifi c linkage group are adjusted for identified QTL at other linkage groups. Re gression methods are used to estimate QTL positions and effects; permutatio n tests are used to obtain empirical threshold values. The description of t he methods is complemented by an example of the combined analysis of 28 bov ine chromosomes and their associations with milk yield in Finnish Ayrshire cattle. In this example, the individual analysis revealed five suggestive Q TL affecting milk yield. Following the strategy presented in this paper, th e final combined analysis showed eight significant QTL affecting milk yield . This clearly demonstrates the potential gain of using the combined analys is. The use of regression methods, with low demands on computing resources, makes this approach very practical for total genome scans.