Molecular characterization of olive cultivars using amplified fragment length polymorphism markers

Erċışlı, Sezai; Barut, Erdoğan; İpek, Ahmet

doi:10.4238/vol8-2gmr576

Cited by 22 publications

(21 citation statements)

References 13 publications

(14 reference statements)

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“…The results indicated that the 96 olive genotypes possessed a high-level of genetic variation. The genetic similarity values found in our study are comparable to the values previously found in other studies for the identification of Turkish olive genotypes using the AFLP [101], SSR [36], [44], and SRAP [36] markers. Isık et al [36] investigated the genetic diversity in 66 Turkish olive varieties using SSR markers.…”

Section: Discussionsupporting

confidence: 90%

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

Kaya

Çetin²,

Kaya³

et al. 2013

PLoS ONE

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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.

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Section: Discussionsupporting

confidence: 90%

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

Kaya

Çetin²,

Kaya³

et al. 2013

PLoS ONE

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“…Randomly amplified polymorphic DNA (RAPD) markers were the first molecular markers used to identify olive cultivars (Bogani et al, 1994). Later, amplified fragment length polymorphism (AFLP) markers were found to be useful for the assessment of genetic diversity between olive cultivars, wild genotypes, and Olea species (Angiolillo et al, 1999;Owen et al, 2005;Ercisli et al, 2009). Simple sequence repeat (SSR) markers are another choice of marker technology for the characterization of olive genotypes and a considerable number of SSR markers have been developed for the olive genome in recent years (e.g., Rallo et al, 2000;Sefc et al, 2000;Ipek et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits

et al. 2015

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ABSTRACT. The purpose of this study was to characterize olive core collection with amplified fragment length polymorphism (AFLP) markers and fruit traits and to determine AFLP markers significantly associated with these fruit characters in olive. A total of 168 polymorphic AFLP markers generated by five primer combinations and nine fruit traits were used to characterize relationships between 18 olive cultivars. Although all olive cultivars were discriminated from each other by either AFLP markers (<0.75 similarity level) or fruit traits, clustering based on the AFLP markers and fruit traits was not significantly correlated (r = 0.13). Partial clustering of olive cultivars by AFLP markers according to their geographical origin was observed. Associations of AFLP markers with fruits were determined using a multiple-regression analysis with stepwise addition of AFLP markers. Significant associations between eight AFLP markers and fruit traits were identified. While five AFLP markers demonstrated significant negative correlation with fruit and stone weight, width and length and total polyphenols (P < 0.05), three AFLP markers displayed significant positive correlation with α-tocopherol and γ-tocopherol (P < 0.01). This is the first report on the association of molecular markers with fruit traits in olive. Molecular markers associated with morphological and agronomic traits could be utilized for the breeding of olive cultivars. However, the association power of these markers needs to be confirmed in larger populations, and highly correlated markers should then be converted to PCR-based DNA markers such as sequence-characterized amplified region markers for better utilization.

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“…Morphological and pomological characteristics of common Turkish olive cultivars were previously determined by Canozer (1991). Genetic variation among some Turkish olive cultivars was analyzed using DNA based molecular markers (Owen et al, 2005;Ozkaya et al, 2006;Ercisli et al, 2009;Ipek et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Assessment of inter- and intra-cultivar variations in olive using SSR markers

İpek

Barut

Gülen

et al. 2012

Sci. agric. (Piracicaba, Braz.)

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Olive (Olea europaea L.) production in the world has been made by using many cultivars, and the genetic uniformity of commercial cultivars is important for standard olive oil and table olive production. The genetic variation among and within commonly cultivated olive cultivars in Turkey was analyzed using SSR markers. A total of 135 leaf samples were collected from 11 commonly cultivated olive cultivars from 11 provinces in four geographical regions of Turkey. Seven SSR primer pairs generated 46 SSR markers, and the number of SSR markers per primer pair ranged from 4 (UDO-14) to 9 (GAPU-89) with an average of 6.57. This high level of SSR polymorphism suggests that olive production in Turkey has been made using genetically diverse olive cultivars and this high level of genetic variation is probably due to the location of However, there was some confusion about the identification of cultivars with similar phenotypic traits. To prevent misidentification of olive cultivars and to minimize intra-cultivar variation, certified propagation materials which were characterized using DNA based molecular markers should be used during the establishment of new olive orchards.

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Molecular characterization of olive cultivars using amplified fragment length polymorphism markers

Cited by 22 publications

References 13 publications

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits

Assessment of inter- and intra-cultivar variations in olive using SSR markers

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