SSR Marker-Based DNA Fingerprinting and Cultivar Identification of Olives (Olea europaea)

Erċışlı, Sezai; İpek, Ahmet; Barut, Erdoğan

doi:10.1007/s10528-011-9430-z

Cited by 70 publications

(50 citation statements)

References 18 publications

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“…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%

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: 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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“…Olive is also the second most important oil fruit crop cultivated worldwide after oil palm (Baldoni and Belaj 2009). Olea species were evaluated by using various genetic markers such as SSRs genotyping (Taamalli et al 2008;Ercisli et al 2011, Gomes et al 2009, Carriero et al 2002; RAPDs genotyping (Bogani et al 1994;Belaj et al 2004); AFLPs genotyping (Owen et al 2005;Baldoni et al 2006), SNPs (Reale et al 2006), Ribosomal DNA polymorphisms (Hess et al 2000, Besnard et al 2007, and organelle DNA polymorphisms (Besnard et al 2002;Intrieri et al 2007).…”

Section: Introductionmentioning

confidence: 99%

In Silico chloroplast SSRs mining of Olea species

Filiz

Koç

2012

Biodiversitas

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Filiz E, Koc E. 2012. In Silico chloroplast SSRs mining of Olea species. Biodiversitas 13: 114-117. Simple sequence repeat (SSR) markers are highly informative and have been widely applied as molecular markers in genetic studies. The purpose of present study is to analyze the occurrence and distribution of chloroplast SSRs in genic and intergenic regions from Olea species viz., Olea europaea, Olea europaea subsp. cuspidate, Olea europaea subsp. europaea, Olea europaea subsp. maroccana, Olea woodiana subsp. woodiana by using bioinformatics tools. We identified 1149 chloroplast SSRs (cpSSRs) in all genome and a total of 340 (29.6%) was located in genic regions. It was observed that the most abundant repeat types were found mononucleotide SSR (66.7 %) followed by trinucleotide SSR (28.3 %), dinucleotide (2.7%), tetranucleotide (1.5%) and pentanucleotide (0.8%). cpSSRs located in genic regions were identified only mono-and trinucleotide motifs, the most abundant of which was trinucleotide (16.2%) followed by mononucleotide (14.3%). All types of repeat motif (mono-, di-, tri-, tetra-and pentanucleotide) were detected except hexanucleotide motifs. According to SSRs analysis, the most abundant observed motifs were identified for mono-, di-, tri-, tetra-and pentanucleotide cpSSRs A/T, AT/TA, AAG/CTT, AAAG/AGTTT, and AATCC/ATTGG respectively. This study results provided scientific base for phylogenetics, evolutionary genetics and diversity studies on different Olea species in future.

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“…Moreover, SSR markers were averagely selected from above 6 clustering DEG groups to avoid biases and specificity in selecting SSR marker. Additionally, microsatellites are one of the most powerful genetic markers in biology, and they provide a number of advantages that increase the suitability of microsatellites for genetic diversity analyses39, marker-assisted selection40, cultivar identification41, high-density linkage maps42, and QTL mapping38. Two single-copy nuclear genes containing microsatellite loci of the (TC) n motif of intron 7 of AG1 and the (GGC) n motif of exon 1 of PHYB have been successfully used for palm phylogenetics43.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana)

Zhao

Sun

et al. 2017

Sci Rep

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Rattan is an important group of regenerating non-wood climbing palm in tropical forests. The cirrus is an essential climbing organ and provides morphological evidence for evolutionary and taxonomic studies. However, limited data are available on the molecular mechanisms underlying the development of the cirrus. Thus, we performed in-depth transcriptomic sequencing analyses to characterize the cirrus development at different developmental stages of Daemonorops jenkinsiana. The result showed 404,875 transcripts were assembled, including 61,569 high-quality unigenes were identified, of which approximately 76.16% were annotated and classified by seven authorized databases. Moreover, a comprehensive analysis of the gene expression profiles identified differentially expressed genes (DEGs) concentrated in developmental pathways, cell wall metabolism, and hook formation between the different stages of the cirri. Among them, 37 DEGs were validated by qRT-PCR. Furthermore, 14,693 transcriptome-based microsatellites were identified. Of the 168 designed SSR primer pairs, 153 were validated and 16 pairs were utilized for the polymorphic analysis of 25 rattan accessions. These findings can be used to interpret the molecular mechanisms of cirrus development, and the developed microsatellites markers provide valuable data for assisting rattan taxonomy and expanding the understanding of genomic study in rattan.

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SSR Marker-Based DNA Fingerprinting and Cultivar Identification of Olives (Olea europaea)

Cited by 70 publications

References 18 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

In Silico chloroplast SSRs mining of Olea species

Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana)

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