Discovery and Potential of SNP Markers in Characterization of Tunisian Olive Germplasm

Hakim, Imen Rekik; Kammoun, Naziha Grati; Makhloufi, Emna; Rebaï, Ahmed

doi:10.3390/d2010017

Cited by 35 publications

(23 citation statements)

References 23 publications

(22 reference statements)

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“…Until a recently published study (Kaya et al 2013), only a small number of SNP loci had been identified in olives (Hakim et al 2010;Macedo et al 2009;Muleo et al 2009;Reale et al 2006). Kaya's study used deep sequencing for the identification of 2987 SNPs in olives (Kaya et al 2013 Fig.…”

Section: Snps Identification Strategymentioning

confidence: 98%

“…Various DNA markers have been used in these studies including restriction fragment length polymorphism (RFLP) (Bazakos et al 2012;Besnard and Berville 2002), amplified fragment length polymorphism (AFLP) (Albertini et al 2011;Angiolillo et al 1999;Baldoni et al 2006), random amplified polymorphic DNA (RAPD) (Awan et al 2011;Leva and Petruccelli 2012;Parra-Lobato et al 2012), sequence-characterized amplified regions (SCAR) (Marieschi et al 2011), DaRT (Domínguez-García et al 2012, SSR (Beghe et al 2011;Biton et al 2012;Corrado et al 2011;Delgado-Martinez et al 2012;Ercisli et al 2011;Rehman et al 2012;Rotondi et al 2011) and single nucleotide polymorphism (SNP) Hakim et al 2010;Macedo et al 2009;Muleo et al 2009;Reale et al 2006).…”

Section: Introductionmentioning

confidence: 99%

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Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

et al. 2015

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The olive (Olea europaea L.) was domesticated in the Mediterranean area over 6000 years ago and is currently one of the area's most important oleaginous crops. Due to its economic, cultural and ecological importance, breeding programs aimed at obtaining new olive cultivars have been developed in most olive-producing countries. An efficient breeding program requires a large and genetically variable germplasm collection. In this study, we used nextgeneration sequencing technology for the identification of 145,974 single nucleotide polymorphism (SNPs) loci. A subset of 138 SNPs was then used to analyze the genetic relationships between 119 cultivars making up most of the Israeli germplasm collection. The various cultivars did not cluster according to their geographic origin but rather showed a high correlation with their function (oil, table or dual purpose). Comparison of genetic diversity between 15 cultivars using SSRs and SNPs revealed that for the purposes of analyzing genetic variation between olive cultivars, the SSR marker seems more suitable. However, based on the analysis of several trees of the same cultivar sampled from different nurseries, the SNP marker proved to be a more reliable criterion for cultivar identification. This study presents the most comprehensive SNP analysis of olive phylogeny to date. Based on the rapid development of SNP genotyping methods over the last few years, we believe that in the near future, we will be able to genotype many sample genomes using the appropriate SNPs at a reasonably low cost. Therefore, we can expect that in the future, SNPs will definitely be the marker of choice for biodiversity analysis as well as for gene cloning and QTL identification in olives.

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Section: Snps Identification Strategymentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

et al. 2015

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“…But, they have also similar olive oil compositions. Rekik Hakim, Grati-Kamoun, Makhloufi, and Rebai (2010) found a similarity of 92% using the Simple Sequences Repeats (SSR) on the leaves. Ben-Ayed, GratiKamoun, Sans-Grout, Moreau, and Rebai (2012) using SSR on DNA extracted oils, found less similarity between these two varieties.…”

Section: Fatty Acid ''Morphotypes''mentioning

confidence: 99%

Authentication of Tunisian virgin olive oils by chemometric analysis of fatty acid compositions and NIR spectra. Comparison with Maghrebian and French virgin olive oils

et al. 2015

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Six Tunisian virgin olive oil (VOO) varieties, Chemlali Sfax, Chetoui, Chemchali, Oueslati, Zarrazi and Zalmati, were characterised by two analytical methods. The gas chromatography allowed the determination of 14 fatty acids and squalene amounts. With fatty acids of each variety, a characteristic "morphotypes" for each oil variety was established. Chemlali Sfax and Zalmati showed strong similarities. Gas chromatography of fatty acid methyl esters (FAME) and near infrared (NIR) spectra of oils, associated to chemometric treatment, allowed the study of the inter-varietal variability and the verification of the variety origins of some Tunisian commercial VOOs. The specificity of Tunisian VOOs was evaluated by comparing the samples to Algerian, Moroccan and French Protected Designation of Origin VOOs. Classification in varietal origins by SIMCA used the FAME compositions and NIR spectra of the most represented varieties (Chemlali Sfax, Chetoui and Oueslati) showed a high potential to authenticate the varietal origin of Tunisian VOOs.

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“…In order to exploit genetic diversity for targeted olive cultivar improvements, several Tunisian research teams have used PCR-based markers for basic and applied research to assess the genetic diversity of Tunisian olive cultivars. These markers types include RAPD (Zitoun et al, 2008), AFLP (Grati-Kamoun et al, 2006;Taamalli et al, 2006), SSR (Taamalli et al, 2007;Hannachi et al, 2008;Rekik et al, 2008) and SNP (Rekik et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Genetic similarity among Tunisian cultivated olive estimated through SSR markers

Abdelhamid

Grati-Kamoun

Marra

et al. 2013

Sci. agric. (Piracicaba, Braz.)

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Olive (Olea europaea L. subsp. europaea var. europaea) is one of the oldest fruit tree in the Mediterranean basin, and is cultivated for oil and canned fruit. Part of this interest is driven by the economic importance of olive oil which is increasing throughout the world due to its beneficial effect to human health. In Tunisia, olive has great socio-economic importance, with more than 60 millions olive trees cultivated for olive oil production including a wide range of cultivars which are widely extended from the north to the south regions of the country for its high economic value. Here, we applied microsatellites (SSRs) molecular markers to assess the genetic variability of the most important Tunisian olive cultivars. In total, the 10 simple sequence repeats (SSR) loci revealed 73 alleles with a mean number of 07 alleles per locus were detected.The polymorphism index content (PIC) values were high (0.72) ranging from 0.86 at GAPU 103 to 0.56 at EMO 90. The analysis of the dendrogram showed six main separate groups.

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Discovery and Potential of SNP Markers in Characterization of Tunisian Olive Germplasm

Cited by 35 publications

References 23 publications

Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection

Authentication of Tunisian virgin olive oils by chemometric analysis of fatty acid compositions and NIR spectra. Comparison with Maghrebian and French virgin olive oils

Genetic similarity among Tunisian cultivated olive estimated through SSR markers

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