Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovická

Baránek, Miroslav; Mészáros, Martin; Sochorová, Jana; Čechová, Jana; Raddová, Jana

doi:10.1016/j.scienta.2012.05.022

Cited by 47 publications

(50 citation statements)

References 15 publications

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“…Recently, the iPBS method has been considered a good molecular marker system since it requires no previous knowledge of the genome and only minimal amount of DNA [34]. Despite these advantages, only few plants have been investigated in terms of their genetic diversity using this [15], Guo et al [17]. And Duan et al [35].…”

Section: Discussionmentioning

confidence: 99%

Determination of the Population Structure of Fig Genotypes from Algeria and Turkey Using Inter Primer Binding Site-Retrotransposon and Simple Sequence Repeat Markers

Belttar¹,

Yahia²,

Nemli³

et al. 2017

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In order to identify the variation and estimate the genetic diversity among the fig (Ficus carica L.) genotypes collected from Algeria and Turkey, the genetic relationships between 86 genotypes were investigated using 23 inter primer binding sites (iPBS)-retrotransposon and 16 simple sequence repeat (SSR) primers. A total of 63 polymorphic bands for the iPBS-retrotransposon markers and 25 alleles for the SSR markers were identified with an average of 2.7 and 1.6 per primer, respectively. The average value of polymorphism information content (PIC) for the iPBS markers (0.73) was higher than that for the SSR markers (0.69). Applying the neighbor-joining method to the combined iPBS-retrotransposon and SSR data, the fig genotypes were clustered into two groups. The STRUCTURE software was used to determine the population structure. Among the genotypes studied, two populations (K = 2) were identified indicating a low diversity between the Algerian and Turkish varieties. Both types of markers were able to differentiate all the fig genotypes and were efficient in discriminating the closely related genotypes. Our data also showed that as a universal marker, iPBS-retrotransposon is a useful tool for the molecular characterization of fig genotypes.How to cite this paper: Belttar, H., Yahia,

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Section: Discussionmentioning

confidence: 99%

Determination of the Population Structure of Fig Genotypes from Algeria and Turkey Using Inter Primer Binding Site-Retrotransposon and Simple Sequence Repeat Markers

Belttar¹,

Yahia²,

Nemli³

et al. 2017

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“…Furthermore, it was observed that a rapid mutational process in plants caused by TE during environmental stress, could be adventitious for the particular group of organisms, by rapidly increasing genotypic variability, which may be associated with adaptation for abiotic stress (Wessler 1996;Kalendar et al 2000;Finatto et al 2015). The development of iPBS technique allowed for tracking genomic changes induced by TE in species for which genomic information is limited: Prunus arme− niaca (Baránek et al 2012), Malus x domestica (Kuras et al 2013), Cicer species (Andeden et al 2013), Psidium guajava (Mehmood et al 2013), Myrica rubra (Chen and Liu 2014). However, so far, iPBS genotyping has not been applied to the analysis of genetic variability shaped in environmental stress gradient.…”

Section: Discussionmentioning

confidence: 99%

“…Only Baránek et al (2012) reported lower level of polymorphism for iPBS markers (4.88%), but their analyses aimed at genetic identification of clones of the apricot cultivar.…”

Section: Discussionmentioning

confidence: 99%

Genetic variability of Colobanthus quitensis from King George Island (Antarctica)

Androsiuk¹,

Chwedorzewska²,

Szandar³

et al. 2015

Polish Polar Research

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Antarctic pearlwort (Colobanthus quitensis) is one of the flowering plant species considered native to maritime Antarctica. Although the species was intensively analyzed towards its morphological, anatomical and physiological adaptation to local environment, its genetic variability is still poorly studied. In the presented study, a recently developed retrotransposon−based DNA marker system (inter Primer Binding Site -iPBS) was applied to assess the genetic diversity and differentiation of C. quitensis populations from King George Island (South Shetland Islands, West Antarctic). A total of 143 scoreable bands were detected using 7 iPBS primers among 122 plant specimens representing 8 populations. 55 (38.5%) bands were found polymorphic, with an average of 14.3% polymorphic frag− ments per primer. Nine of all observed fragments were represented as a private bands de− ployed unevenly among populations. Low genetic diversity (on average H e = 0.040 and I = 0.061) and moderate population differentiation (F ST = 0.164) characterize the analyzed material. Clustering based on PCoA revealed, that the populations located on the edges of the study area diverge from the central populations. The pattern of population differentia− tion corresponds well with their geographic location and the characteristics of the sampling sites. Due to the character of iPBS markers, the observed genetic variability of populations may be explained by the genome rearrangements caused by mobilization of mobile genetic elements in the response to various stress factors. Additionally, this study demonstrates the usefulness of iPBS markers for genetic diversity studies in wild species.

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“…The inter-primer binding site (iPBS) method has proven to be a powerful DNA fingerprinting technique without the need for previous knowledge of a sequence, and is referred to as a universal marker system because iPBS-retrotransposons comprise the only retrotransposon-based marker system that has allowed polymorphism visualization throughout the plant kingdom. iPBSretrotransposon DNA markers have been successfully employed in evaluating the genetic diversity of Saussurea esthonica, apricot, grapevine, Cicer species, guava, Chinese bayberry (Myrica rubra), and cultivated and wild Lens species (Gailite et al, 2011;Baránek et al, 2012;Guo et al, 2012;Andeden et al, 2013;Mehmood et al, 2013;Fang-Yong and Ji-Hong, 2014;Baloch et al, 2015). However, iPBS-retrotransposon markers have not yet been used in genetic diversity studies of rice.…”

Section: Introductionmentioning

confidence: 99%

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data

Cömertpay¹,

Baloch²,

Derya³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine interprimer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon-and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBSretrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.

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Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovická

Cited by 47 publications

References 15 publications

Determination of the Population Structure of Fig Genotypes from Algeria and Turkey Using Inter Primer Binding Site-Retrotransposon and Simple Sequence Repeat Markers

Determination of the Population Structure of Fig Genotypes from Algeria and Turkey Using Inter Primer Binding Site-Retrotransposon and Simple Sequence Repeat Markers

Genetic variability of Colobanthus quitensis from King George Island (Antarctica)

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data

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