Maximization of minority classes in core collections designed for association studies

Abstract

Core collections are nowadays widely employed in diverse studies on plant genetics. The more extensively used method to build core collections (maximization strategy) is based on the selection, from a global collection, of those accessions which maximize the number of different alleles and phenotypic classes (classes’ richness). However, different core collections should be created for different types of studies, and though several years ago most of core collections were developed to make the characterization and use of germplasm collections easier with a smaller sample size, for either conservation or breeding purposes, today, they are widely employed for association studies that are broadly applied in plant genetic improvement. Following the M strategy, some alleles or phenotypic classes often appear in a very low frequency, which may reduce the power of the analysis, avoiding the detection of real associations (false negatives). In this work, we propose and evaluate a new way to build core collections using the maximization strategy in several sequential steps, to maximize the frequency of minority classes, thus increasing the statistical power of the association study.