Development of DNA markers associated with some traits using association mapping in olive (Olea europaea)

In olive breeding, the phenotypic traits associated with the fruit, endocarp and oil are the key factors that determine productivity among the main breeding selection criteria. Association mapping is an efficient method for dissecting the associations between phenotypic variation and gene polymorphisms in existing germplasms, without the development of mapping populations. In the current study, a total of 96 olive genotypes, including both oil and table olive genotypes from Turkish Olive GenBank Resources, were used to examine marker-trait associations. Nine yield-related traits of these olive genotypes were recorded during the years of 2011-2012 and 2013-2014. For olive genotyping, AFLP, SSR and SNP markers data of 96 olive genotypes and GBS marker data of 94 olive genotypes were used to perform association mapping for yield-related traits. The linkage disequilibrium of pair-wise loci was analyzed, followed by association analysis between AFLP, SSR, SNP markers and nine yield related traits and also between GBS markers and 14 yield-related traits. Different approaches were used to control for false-positive results in association tests and compared for their capacity to fit the data. Using AFLP, SSR and SNP markers, eleven significant associations were obtained for fruit weight, fruit shape, stone weight and stone shape when the MLM (Q+K) model was used. Using the GBS markers, seven significant associations were obtained for presence of lenticels while twenty significant associations were obtained for fruit nipple when the GLM (PCs) model was used. Our results suggested that association mapping can be an effective approach for identifying marker-trait associations in olive genotypes, without the development of mapping populations.