QTL ANALYSIS - UNRELIABILITY AND BIAS IN ESTIMATION PROCEDURES

Several statistical methods which employ multiple marker data are curr ently available for the analysis of quantitative trait loci (QTL) in e xperimental populations. Although comparable estimates of QTL location and effects have been obtained by these methods, using simulated and real data sets, their accuracy and reliability have not been extensive ly investigated. The present study specifically examines the merit of using F-2 and doubled haploid populations for locating QTL and estimat ing their effects. Factors which may affect accuracy and reliability o f QTL mapping, such as the number and position of the markers availabl e, the accuracy of the marker locations and the size of the experiment al population used, are considered. These aspects are evaluated for QT L of differing heritabilities and locations along the chromosome. A po pulation of 300 F-2 individuals and 150 doubled haploid lines gave est imates of QTL position and effect which were comparable, albeit extrem ely unreliable. Even for a QTL of high heritability (10%), the confide nce interval was 35 cM. There was little increase in reliability to be obtained from using 300, rather than 200, F-2 individuals and 100 dou bled haploid lines gave similar results to 150. QTL estimates were not significantly improved either by using the expected, rather than the observed, marker positions or by using a dense map of markers rather t han a sparse map. A QTL which was asymmetrically Located in the linkag e group resulted in inaccurate estimates of QTL position which were se riously biassed at low heritability of the QTL. In a population of 300 F-2 individuals the bias increased from 4 cM to 20 cM, for a QTL with 10% and 2% heritability respectively.