Significance Thresholds in Genome Scans – Which Threshold to Use to Maximise the Accuracy of Subsequent Marker Assisted Selection

Our aim was to investigate the effect of the level of stringency of quantitative trait loci (QTL) detection in a genome scan on the accuracy of subsequent maker assisted selection (MAS). A genome scan and subsequent MAS were performed in a population of simulated pigs. The accuracy of MAS was greatest when QTL with P < 0.10 (on an individual gene basis) in the genome scan were used in MAS. More stringent thresholds reduced the proportion of genetic variance accounted for by detected QTL. Lowering the significance threshold from P<0.10 to P<0.25 resulted in a large number of false positive results, with the consequence that the variance accounted for by marked QTL was overestimated. and accuracy of MAS reduced. While criteria P<0.10 maximised the accuracy of MAS, it may not be the most profitable threshold. Using more stringent thresholds greatly reduced the number of markers to be typed without greatly reducing accuracy of MAS.