DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey

Baloch, Faheem Shehzad; Alsaleh, Ahmad; Miera, Luis E. Sáenz de; Hatipoğlu, Rüştü; Çi̇ftçi̇, Vahdettin; Karaköy, Tolga; Yıldız, Mehtap; Özkan, Hakan

doi:10.1016/j.bse.2015.06.017

Cited by 64 publications

(64 citation statements)

References 24 publications

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“…The high iPBS marker polymorphism detected in lentil agrees with previous results in pea [23]. Upon comparing the number of polymorphic iPBS loci (presence vs. absence of an amplified fragment) among the cultivated lentil and its wild ancestor, cultivar Lupa generated a slightly higher (106) number than that retrieved in the wild L .…”

Section: Discussionsupporting

confidence: 87%

Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.)

et al. 2017

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Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type) none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry out further genetic analyses.

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Section: Discussionsupporting

confidence: 87%

Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.)

et al. 2017

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“…1.32. For calculation of the PIC values, the criterion ofBaloch et al (2015a) was followed. Pairwise genetic similarity (GS) values among the accessions were calculated using Jaccard's similarity coefficient(Jaccard, 1908), with the statistical software XLSTAT v.19.7.49007.…”

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confidence: 99%

Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposon- based markers

Yıldız¹,

Koçak²,

Nadeem³

et al. 2020

Turk J Agric For

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Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, including Turkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversity and population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers. A total of 20 iPBS primers were used that generated 172 bands (mean = 8.6 bands/primer), of which ~92% were polymorphic in the entire germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content of the markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPGMA, STRUCTURE, and principal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a few subclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level, the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between the iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing the genetic diversity and population structure in the Turkish pepper germplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties.

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“…Previously, this system has successfully been employed in evaluating the genetic diversity in grapes (Guo et al, 2014), apricot (Baránek et al, 2012), Cicer (Andeden et al, 2013), cultivated and wild Lens species (Baloch et al, 2015a), and field pea (Baloch et al, 2015b). iPBS-retrotransposon markers have not yet been used for genetic diversity studies in okra.…”

Section: Introductionmentioning

confidence: 99%

Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment

2015

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ABSTRACT. Lack of requisite genetic variation in Turkish okra has necessitated the use of different types of markers for estimating the genetic diversity and identifying the source of variation. Transposable elements, present abundantly in plant genomes, generate genomic diversity through their replication and are thus an excellent source of molecular markers. We hypothesized that inter-primer binding site (iPBS)-retrotransposons could be the source of variation because of their genome plasticity nature. In the present study, genetic diversity of 66 okra landraces was analyzed using iPBS-retrotransposon markers. iPBS-retrotransposons detected 88 bands with 40.2% polymorphism and an average of 6.8 bands per primer. Gene diversity and Shannon's information index ranged from 0.01 to 0.13 and 0.02 to 0.21 for iPBS-retrotransposons and from 0.06 to 0.46 and 0.14 to 0.65 for simple sequence repeat (SSR) markers, respectively. Polymorphism information content value for retrotransposons varied between 0.12 and 0.99, while that for SSR was from 0.52 to 0.81. Neighbor joining analysis based on retrotransposons and SSRs divided all the accessions into 10589 Utility of iPBS retrotransposons in okra ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (3): 10588-10602 (2015) four clusters; however, SSR markers were more efficient in clustering the landraces based on their origin. Using the STRUCTURE software for determining population structure, and two populations (at the number of hypothetical subpopulations, K = 2) were identified among the landraces. Low genetic diversity in Turkish okra highlights the need for the introduction of plants from countries with greater genetic diversity for these crops. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in okra.

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DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey

Cited by 64 publications

References 24 publications

Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.)

Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.)

Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposon- based markers

Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment

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