What proportion of declared QTL in plants are false?

The false discovery rate (FDR) is the probability that a quantitative trait locus (QTL) is false, given that a QTL has been declared. A misconception in QTL mapping is that the FDR is equal to the comparison-wise significance level, α_C. The objective of this simulation study was to determine the FDR in an F₂ mapping population, given different numbers of QTL, population sizes, and trait heritabilities. Markers linked to QTL were detected by multiple regression of phenotype on marker genotype. Phenotypic selection and marker-based recurrent selection were compared. The FDR increased as α_C increased. Notably, the FDR was often 10-30 times higher than the α_C level used. Regardless of the number of QTL, heritability, or size of the genome, the FDR was ≤0.01 when α_C was 0.0001. The FDR increased to 0.82 when α_C was 0.05, heritability was low, and only one QTL controlled the trait. An α_C of 0.05 led to a low FDR when many QTL (30 or 100) controlled the trait, but this lower FDR was accompanied by a diminished power to detect QTL. Larger mapping populations led to both lower a FDR and increased power. Relaxed significance levels of α_C=0.1 or 0.2 led to the largest responses to marker-based recurrent selection, despite the high FDR. To prevent false QTL from confusing the literature and databases, a detected QTL should, in general, be reported as a QTL only if it was identified at a stringent significance level, e.g., α_C≅0.0001.