iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species

Andeden, Enver Ersoy; Baloch, Faheem Shehzad; Derya, Muazzez; Kilian, Benjamin; Özkan, Hakan

doi:10.1007/s13562-012-0175-5

Cited by 71 publications

(63 citation statements)

References 47 publications

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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%

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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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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“…PCR amplifications were performed in an Eppendorf DNA Thermal Master Gradient Cycler (Eppendorf Netheler Hinz, Hamburg, Germany), and were conducted in a 25-µL reaction mixture containing 25 ng template DNA, 1X Dream Taq Green Buffer (Fermentas), 0.2 mM dNTP (Fermentas), 1 µM primer for 12-to 13-nt primers or 0.6 µM for 18-nt primers, 1.5 U Dream Taq DNA polymerase (Fermentas), and 0.04 U PFU DNA polymerase (Fermentas) (Baloch et al, 2015). The PCR thermal cycling profile was as follows: initial denaturation at 95°C for 3 min, 30 cycles at 95°C for 15 s, 50-65°C annealing temperature (depending upon the primer) for 1 min, 68°C for 1 min, and a final extension at 72°C for 5 min (Andeden et al, 2013). All of the PCR products were separated by 1.7% (w/v) agarose gel electrophoresis with 0.5X TBE buffer for 2 h, stained with ethidium bromide, and visualized using an ultraviolet transilluminator (Infinity ST5, Vilber Lourmat, France).…”

Section: Ipbs-retrotransposon Analysismentioning

confidence: 99%

“…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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“…LTR retrotransposons predominate in plant genomes and can be used as molecular markers due to their ubiquitous distribution, abundant copy number, high heterogeneity, and random nature of insertional polymorphisms resulting from different retrotransposon insertion mechanisms (Shen et al, 2011;Guo et al, 2014c). In addition, LTR retrotransposons contain highly conserved regions for primer design in the development of retrotransposon-based markers (Andeden et al, 2013). Another important feature of LTR retrotransposons is their stability over millions of years due to the nature of their insertion (Sanz et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…The iPBS marker method has several advantages compared with other retrotransposon markers: iPBSs can discriminate among genotypes without prior sequence knowledge and are highly reproducible due to their primer length and the high stringency achieved by the annealing temperature (Guo et al, 2014b). Indeed, this marker system has been used successfully for several genetic diversity studies in plants, such as apricot (Baranek et al, 2012), Cicer species (Andeden et al, 2013), and Vitis vinifera (Guo et al, 2014a(Guo et al, , 2014b. Chen and Liu (2014) also reported that iPBS and start codon-targeted polymorphism markers are effective marker systems for discriminating genotypes in Myrica rubra.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers

Nemli¹,

Kianoosh²,

Tanyolaç³

2015

Turk J Agric For

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IntroductionThe common bean (Phaseolus vulgaris L.) is one of the most ancient legumes and one of the five cultivated species of the genus Phaseolus (Broughton et al., 2003). The common bean originated in Latin America and has become a major food for human consumption (Broughton et al., 2003), providing vital nutrients such as proteins, vitamins, and minerals in diets in many developing countries, especially in Africa (Broughton et al., 2003). Globally, the annual production of green and dry beans is 17 million tons (FAO, 2010) and is almost twice that of the second most important legume, chickpea (Cicer arietinum L.) (Gepts et al., 2008). The common bean, a self-pollinated crop, is a true diploid (n = 11) with a small genome of 588 megabase pairs (Arumuganthan and Earle, 1991).Transposable elements (TEs) are discrete regions of DNA that can move within genomes (Baranek et al., 2012). TEs are important for phylogenetic analysis because they can change their genomic location, creating genomic diversity (Baranek et al., 2012). Recent studies have shown that, depending on its function, a TE in a gene may be conserved in different plant species, subspecies, and cultivars (Xu and Ramakrishna, 2008). TEs can be classified into two major groups according to their mode of transposition: DNA transposons (group I), which replicate directly via a DNA intermediate, and retrotransposons (group II), which replicate through an RNA intermediary (Casacuberta and Santiago, 2003). Retrotransposons play important roles in plant genomes according to genome size (increasing genome size), structure, evolution, variable copy number, and random distribution (Kumar and Bennetzen, 1999). Furthermore, retrotransposons are the most abundant and widely distributed mobile genetic element in eukaryotic genomes and show polymorphism within and between species (Kumar and Bennetzen, 1999). Retrotransposons comprise 35% of the common bean genome (Schmutz et al., 2014). Retrotransposons can be divided into two primary groups according to the presence or absence of a long terminal repeat (LTR): LTR and non-LTR retrotransposons. LTR retrotransposons predominate in plant genomes and can be used as molecular markers due to their ubiquitous distribution, abundant copy number, high heterogeneity, and random nature of insertional polymorphisms resulting from different retrotransposon

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iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species

Cited by 71 publications

References 47 publications

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

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

Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers

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