COMPARISON OF THREE QTL DETECTION METHODS WHEN TWO QTL ARE LINKED ON THE SAME CHROMOSOME WITH DIFFERENT EFFECTS AND MARKER SPACINGS

¹ ForBio Research Pty Ltd, 50 Meiers Road, Indooroopilly QLD 4068, Australia

² Genetic Solutions, PO Box 6082, Fairfield Gardens QLD 4103, Australia

A computer simulation study was performed to determine if QTL can be detected by a range of analytical techniques under a defined set of parameters and varying marker spacing. Marker spacing is important because it determines the number of primers and markers that need to be genotyped on the full family for QTL detection analyses. The three analytical approaches examined were Interval Mapping (IM), Composite Interval Mapping (CIM) and Multiple Interval Mapping (MIM). Two linked QTL of different size were simulated in phase (same direction of effects) and out of phase (opposite direction of effects). Only data for a single linkage group were simulated, with QTL separated by 29 cM in the centre of the linkage group. The marker spacings were 6 cM, 15 cM, 25 cM and 30 cM. IM was shown to have significant power in detecting a region where one or more QTL are segregating. CIM has less power, but can resolve linked QTL and is easy to implement. MIM has similar power to CIM, except in the case of linked QTL that are out of phase, where it has higher power than both CIM and IM. Both CIM and MIM provide more accurate estimates of QTL parameters than IM.