Selective genotyping for QTL detection using sib pair analysis in outbred populations with hierarchical structures

A simulation study illustrates the effects of the inclusion of half-sib pai rs as well as the effects of selective genotyping on the power of detection and the parameter estimates in a sib pair analysis of data from an outbred population. The power of QTL detection obtained from samples of sib pairs selected according to their within family variance or according to the mean within family variance within half sib family was compared and contrasted with the power obtained when only full sib pair analysis was used. There wa s an increase in power (4-16%) and decrease in the bias of parameter estima tes with the use of half-sib information. These improvements in power and p arameter estimates depended on the number of the half sib pairs (half sib f amily size). Almost the same power as that obtained using all the available sib pairs could be achieved by selecting only 50-60% the animals. The most effective method was a select both full and half sib pairs on the basis of high within full sib family variance for the trait in question. The QTL po sition estimates were in general slightly biased towards the center of the chromosome and the QTL variance estimates were biased upwards, there being quite large differences in bias depending on the selection method.