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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.
PLoS One. 2013; 8(9):e73674.Plos

Abstract

BACKGROUND

The 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 FINDINGS

Next-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/SIGNIFICANCE

This 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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Authors+Show Affiliations

Kaya HB
Department of Bioengineering, Ege University, Izmir, Turkey.
Cetin O
No affiliation info available
Kaya H
No affiliation info available
Sahin M
No affiliation info available
Sefer F
No affiliation info available
Kahraman A
No affiliation info available
Tanyolac B
No affiliation info available

MeSH

Amplified Fragment Length Polymorphism AnalysisExpressed Sequence TagsGenetic MarkersGenome, PlantGenotypeHigh-Throughput Nucleotide SequencingMicrosatellite RepeatsOleaPhylogenyPhylogeographyPolymorphism, Single NucleotideQuantitative Trait LociTranscriptomeTurkey

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24058483

Citation

Kaya, Hilal Betul, et al. "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." PloS One, vol. 8, no. 9, 2013, pp. e73674.
Kaya HB, Cetin O, Kaya H, et al. 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. PLoS One. 2013;8(9):e73674.
Kaya, H. B., Cetin, O., Kaya, H., Sahin, M., Sefer, F., Kahraman, A., & Tanyolac, B. (2013). 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. PloS One, 8(9), e73674. https://doi.org/10.1371/journal.pone.0073674
Kaya HB, et al. 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. PLoS One. 2013;8(9):e73674. PubMed PMID: 24058483.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Kaya,Hilal Betul, AU - Cetin,Oznur, AU - Kaya,Hulya, AU - Sahin,Mustafa, AU - Sefer,Filiz, AU - Kahraman,Abdullah, AU - Tanyolac,Bahattin, Y1 - 2013/09/13/ PY - 2013/05/23/received PY - 2013/07/19/accepted PY - 2013/9/24/entrez PY - 2013/9/24/pubmed PY - 2014/6/4/medline SP - e73674 EP - e73674 JF - PloS one JO - PLoS One VL - 8 IS - 9 N2 - BACKGROUND: The 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 FINDINGS: Next-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/SIGNIFICANCE: This 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. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/24058483/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_ L2 - https://dx.plos.org/10.1371/journal.pone.0073674 DB - PRIME DP - Unbound Medicine ER -