BackgroundThe olive tree (Olea europaea L.) is a diploid (2n = 2x = 46) outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP) discovery in olive. The objectives of this study were (1) to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2) to characterize 96 olive genotypes originating from different regions of Turkey.Methodology/Principal FindingsNext-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers.Conclusions/SignificanceThis study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL) analysis, association mapping and map-based gene cloning in the olive. High levels of genetic variation among Turkish olive genotypes revealed by SNPs, AFLPs and SSRs allowed us to characterize the Turkish olive genotype.

Olive (Olea europaea L.) is one of the most important fruit trees especially in the Mediterranean countries due to high consumption of table olive and olive oil. In olive breeding, the phenotypic traits associated to fruit are the key factors that determine productivity. Association mapping has been used in some tree species and a lot of crop plant species, and here, we perform an initial effort to detect marker-trait associations in olive tree. 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. For olive genotyping, SNP, AFLP, and SSR marker data were selected from previously published study and association analysis was performed between these markers and 5 yield-related traits. Three different approaches were used to check for false-positive results in association tests, and association results obtained from these models were compared. Using the model utilizing both population structure and relative kinship, eleven associations were significant with FDR ≤ 0.05. The largest number of significant associations was detected for fruit weight and stone weight. Our results suggested that association mapping could be an effective approach for identifying marker-trait associations in olive genotypes, without the development of mapping populations. This study shows for the first time the use of association mapping for identifying molecular markers linked to important traits in olive tree.

Bu çalışma ile Türkiye zeytin ağaç varlığında önemli bir yer tutan Saurani, Nizip yağlık ve Uslu çeşitlerinin döllenme biyolojileri araştırılmıştır. Bu amaçla 3 yıl süre ile serbest tozlanma, karşılıklı tozlama ve kendileme uygulamaları yapılarak çeşitlerin kendine verimlilik durumu ve uygun tozlayıcıları incelenmiştir. Çalışma neticesinde çeşitlerin kendine verimliliği ve tozlayıcıların etkinlik derecelerinin yıllar arasında değişebileceği görülmüştür. Bununla birlikte, yabancı tozlanmanın kendileme uygulamasına göre birçok durumda meyve tutumunu arttırdığı saptanmıştır. Bu nedenle kendine verimli olduğu düşünülen çeşitlerde dahi yabancı tozlanmanın gerekliliği ortaya konmuştur. Çalışmada, Nizip yağlık çeşidi kısmen kendine verimli olarak değerlendirilmiştir. Memecik ve Kilis yağlık çeşitlerinin Nizip yağlık çeşidi için uygun tozlayıcılar olabileceği düşünülmektedir. Saurani zeytin çeşidi verimlilik indeks değerlerine göre kendine verimli olarak bulunmuştur. Ancak meyve tutumunu arttırmak için Halhalı çelebi, Gemlik, Memecik ve Nizip yağlık çeşitlerinin uygun tozlayıcılar olarak kullanılabileceği düşünülmektedir. Uslu çeşidi de verimlilik indeks değerlerine göre kendine verimli olarak saptanmıştır. Bununla birlikte Gemlik, Memecik ve Erkence çeşitlerinin meyve tutumunu arttırmada etkili olduğu görülmüştür.

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Olive breeding is an important method for improving of olive oil quality. In the early 1990’s, a controlled cross breeding project was started on Turkish domestic olive cultivars by Bornova Olive Research Institute, Izmir. This study was carried out with a total of 11 hybrids and 2 parents and these oil samples were obtained from “Memecik” [5 samples (MG) + 1 parent (MEM)] and “Gemlik” [6 samples (GM) + 1 parent (GEM)] domestic olive cultivars grown under the same agronomic and pedoclimatic conditions. In this study, agronomic criteria (ripening index), some nutritional values (total phenolic contents, major fatty acids [palmitic, oleic, linoleic acid, linolenic acid] and their parameters (linoleic/linolenic ratio, quality index), and sensory properties (panel test) of olive (Memecik and Gemlik) hybrid oils were analyzed during 2005–2008 four harvest years. All results showed that 11 advanced domestic olive hybrids had different oil characteristics relative to the parents of hybrids based on nutritional and sensory profiles. The Pearson correlation coefficients and principal components factor loadings observed among chemical/sensory characteristics and fatty acid profile (GM 19, GM 39, MG 11, MG 5 and MG 123 promising hybrids) could be of interest in future olive breeding programs. Considering the main objectives of olive breeding project, the hybrids of GM 19 and MG 5 exhibited superior agronomic (maturation–regular yield), technological–nutritional (high total polyphenol content, balanced omega3/omega6 ratio), and sensorial (high pungent and bitter qualifications) features. The official registrations of these hybrids were carried out by Ministry of Agriculture and Forestry of Turkey.