CONICET | Buscador de Institutos y Recursos Humanos

Based on case studies, we discuss the extent to which genome-wide association studies are affected by outlier plants, i.e. those deviating from multi-criteria plant distribution. The results depended on the cleaning method. No-cleaning resulted in the highest number of dubious QTLs, especially at loci with highly unbalanced allelic frequencies. A trade-off was identified between the risk of false positive (with no-cleaning and/or a low threshold for minor allele frequency) and the risk of missing interesting rare alleles. Cleaning can lower the latter risk by making acceptable a higher threshold.