To clean or not to clean phenotypic datasets for outlier plants in genetic analyses?

ALVAREZ PRADO, SANTIAGO; SANCHEZ, ISABELLE; CABRERA-BOSQUET, LLORENÇ; GRAU, ANTONIN; WELCKER, CLAUDE; TARDIEU, FRANÇOIS; HILGERT, NADINE

JOURNAL OF EXPERIMENTAL BOTANY

OXFORD UNIV PRESS

Lugar: Oxford; Año: 2019

0022-0957

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.