Testing Different Approaches to Construct an Olive (Olea Europaea L.) Core Subset Suitable for Association Genetic Studies

Abstract

Evaluation of genetic diversity is of great interest for the management of germplasm collections and breeding programs. Management can be efficient when the evaluation is focused on a subset of accessions that represents the variability observed in the whole germplasm collection. Most core sets have been developed for seed crops using different approaches and sampling size to select entries on the basis of genetic and/or phenotypic data, while few studies on perennial crops have been published.Here, we proposed a core collection for cultivated olive (Olea europaea L.) using both Simple Sequence Repeat (SSR) markers and phenotypic traits by testing different sampling approaches including stratified and non-stratified methods. Twelve SSR markers were used to construct a core subset from an initial collection of 505 single genotypes sourced from 14 Mediterranean countries. Among all the sampling methods, we showed that a sample size of 12.5% was most suitable in capturing all the observed alleles using the M-method approach. Based on both SSR and phenotypic data, we established an initial core set, including the main Mediterranean varieties, which displayed the highest genetic and phenotypic variability. No obvious genetic structure was indicated when the core subset was analyzed with Principal Coordinate analysis (PCoA). Our results gave an efficient basis as a first step for olive association mapping. The constructed core subset could be further evaluated for traits of agronomic interest, leading to association between the allelic variation and the phenotypic variability.