COMBINING DIFFERENT LINE CROSSES FOR MAPPING QUANTITATIVE TRAIT LOCI USING THE IDENTICAL BY DESCENT-BASED VARIANCE COMPONENT METHOD

Mapping quantitative trait loci (QTLs) is usually conducted with a sin gle line cross. The power of such QTL mapping depends highly on the tw o parental lines. If the two lines are fixed for the same allele at a putative QTL, the QTL is undetectable. On the other hand, if a QTL is segregating in the line cross and is detected, the estimated variance of the QTL cannot be extrapolated beyond the statistical inference spa ce of the two parental lines. To reduce the likelihood of missing a QT L and to increase the statistical inference space of the estimated QTL variance, we present a consensus QTL mapping strategy. We adopt the i dentical by descent (IBD)-based variance component method originally a pplied to human linkage analysis by combining multiple line crosses as independent families. Mle explore the properties of consensus QTL map ping and demonstrate the method with F-2, backcross (BC), and full-sib (FS) families. In addition, we examine the effects of the QTL heritab ility, marker informativeness, QTL position, the number of families, a nd family size. We show that F-2 families notably outperform BC and FS families in detecting a QTL. There is a substantial reduction in the standard deviation of the estimated QTL position and the separation of the QTL and polygenic variance. Finally, we show that the power to de tect a QTL is greater when using a small number of large families than a large number of small families.