Analysis of plant diversity with retrotransposon-based molecular markers

Kalendar, Ruslan; Flavell, Andrew J.; Ellis, Noel; Sjakste, Tatjana; Moisy, Cédric; Schulman, Alan H.

doi:10.1038/hdy.2010.93

Cited by 230 publications

(155 citation statements)

References 109 publications

(135 reference statements)

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“…The simplicity and unequivocal scoring of RBIP markers were previously demonstrated, while multiallelic SSR markers might be less accurate (Cieslarová et al 2011a, b). We applied both markers derived from repetitive sequences and routinely used them in germplasm description (Kalendar et al 2011, Smýkal et al 2011. SSR markers showed a higher polymorphism per locus (average PIC= 0.60, Table 1), since their polymorphism is based on various lengths (alleles) of the amplified fragment from the given locus, while for retrotransposon insertion markers the information is of only one of three possible types (average PIC= 0.32, Table 5).…”

Section: Molecular Data Analysismentioning

confidence: 99%

Molecular analysis of temporal genetic structuring in pea (Pisum sativum L.) cultivars bred in the Czech Republic and in former Czechoslovakia since the mid-20th century

Cieslarová¹,

Hýbl²,

Griga³

et al. 2012

Czech J. Genet. Plant Breed.

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Changes in genetic diversity of peas bred in the Czech Republic and in former Czechoslovakia since the mid-20 th century were analysed using 38 molecular marker loci, including retrotransposons and microsatellites, differentiating a total of 84 alleles. Both marker types were comparably effective in revealing the genetic diversity, with a high correlation (r = 0.81), although the pairwise genetic distances of each marker type differed. In total, 175 accessions, selected from the Czech pea gene bank collection and representing the pea cultivars collected or bred in the country, were divided into three groups according to their date of sampling or variety registration. The first group contained 70 old cultivars and landraces collected prior to 1961. The second group contained 46 cultivars released from 1961 to 1980. The third group contained 59 cultivars released between 1981 and 2004. In spite of the decline in several diversity measures, differences in allele frequencies and even allele loss in three microsatellite loci were recorded over the 70-year period, while these differences between the groups were not statistically significant. In addition, genetic heterogeneity was detected in 29 accessions (15%). This indicates that although no genetic erosion could be observed since then, it is important to monitor the genetic diversity, furthermore it highlights the vital role of germplasm collections for the crop diversity conservation.

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Section: Molecular Data Analysismentioning

confidence: 99%

Molecular analysis of temporal genetic structuring in pea (Pisum sativum L.) cultivars bred in the Czech Republic and in former Czechoslovakia since the mid-20th century

Cieslarová¹,

Hýbl²,

Griga³

et al. 2012

Czech J. Genet. Plant Breed.

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“…Amplifications were performed according to Kalendar et al (2011) in a 25 µl reaction volume, containing PCR Buffer (1x final concentration, invitrogen), 2,5 mM MgCl2, 0,4 mM of each dNTP, 0,4 mM IRAP primer, 50 ng genomic DNA, and 2 unit Taq DNA polymerase. Amplification conditions (thermocycler Model-9700, PerkinElmer, Boston, MA, USA) were as follows: initial denaturation at 95 °C for 3 min, 35 cycles at 95 °C for 15 sec, 55 °C for 30 sec, a ramp to 72 °C reaching in 3 min, followed by a 10 min lag at this temperature, and an indefinite holding at 4 °C, respectively.…”

Section: Irap (Inter-retroelement Amplified Polymorphisms) Pcrmentioning

confidence: 99%

Using Two Retrotransposon Based Marker Systems (IRAP and REMAP) for Molecular Characterization of Olive (<i>Olea europaea</i> L.) Cultivars

Kaya

YILMAZ-GOKDOGAN

2016

Not Bot Horti Agrobo

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Olive (Olea europaea L.) is one of the most characteristic agricultural trees of the Mediterranean region and has a large number of cultivar diversity. Olive cultivar characterization is very important especially for the fruit productivity and olive oil quality. In the present study, 46 clones belonging to Turkey (eight cultivars, each having five clones) and Italy (two cultivars, each having three clones) were assessed for cultivar characterization via inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) marker systems using 10 LTR and 10 ISSR primers. In total, 368 band profiles were obtained, 358 of which are polymorphic (97.28% polymorphism). The cultivars were segregated into three main groups, each group having several branches, where all the clones of each cultivar were belonging to the same main group. The only exception to that was the distribution of the clones of cultivar Yaglik, 'Yaglik 4' and 'Yaglik 5', into different main groups. IRAP and REMAP analysis showed a high level of genetic variability among the olive cultivars in this study and this marker systems would be useful tool for clonal selection programs.

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“…DNA markers have been developed using various methods like random amplified polymorphic DNA, restriction fragment length polymorphism, simple sequence repeats, amplified fragment length polymorphism (AFLP), sequence characterized amplified region, and single nucleotide polymorphism (Agarwal et al 2008;Kalendar et al 2011;Varshney et al 2013). Moreover, development of polymorphic markers between close relatives or same species are laborious and time consuming due to its high homologous nature.…”

Section: Introductionmentioning

confidence: 99%

“…TE-based molecular markers such as inter-retrotransposon amplified polymorphism, retrotransposon-microsatellite amplified polymorphism, sequence-specific amplification polymorphism, insertion polymorphism based on retrotransposon and DNA transposon, inter-MITE polymorphism and transposon display (TD) (Agarwal et al 2008;Kalendar et al 2011;Shirasawa et al 2012) have been successfully applied for the various genomics purposes such as genetic diversity, inspection of clonal variation, identifying unambiguous gene flow between closely related species and breeding (Deragon and Zhang 2006;Bire and Rouleux-Bonnin 2012;Carrier et al 2012). DNA polymorphisms are used to identify molecular markers for important agronomic traits controlled by single gene or quantitative trait loci (Monden et al 2009;Kalendar et al 2011;Fattash et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

Perumal¹,

Waminal²,

Lee³

et al. 2016

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea ABSTRACT Miniature transposable elements (mTEs) such as miniature inverted-repeat transposable element (MITE), terminal repeat retrotransposon in miniature, and short interspersed element are exquisite sources for marker development. mTEs are short, non-autonomous and stably inherited. The high-copy members are widely distributed into the gene rich euchromatic regions. Here, we conducted a modified transposon display (TD) for a high-copy MITE family, BraSto-2 (Bs2). The Bs2-specific primers derived from conserved sequences of Bs2 members as well as MseI adapter primers were used for polymerase chain reaction (PCR) in two Brassica rapa accessions, 'Chiifu' and 'Kenshin'. The pooled PCR products were sequenced by Illumina sequencing platform instead of high-resolution gel electrophoresis. Subsequent in silico-based insertion polymorphism (IP) analysis (next-generation sequencing [NGS]-based Bs2 transposon display) was conducted, which generated more than 99 putative polymorphic insertion sites between 'Chiifu' and 'Kenshin'. Among 90 successful PCR amplification, 34 showed Bs2 IP (IP-Bs2) between 'Chiifu' and 'Kenshin' accessions, 27 and seven 'Chiifu'-and 'Kenshin'-unique insertions, respectively. When the 90 IP-Bs2 primer sets were applied to 10 Brassica accessions, including four additional B. rapa and B. oleracea accessions, 69 (76%) showed insertion olymorphism among accessions. The IP-Bs2 were evenly distributed through all the chromosomes and provide rich polymorphism among various B. rapa and B. oleracea accessions demonstrating the usefulness of these markers for various genetic diversity and molecular breeding studies in Brassica. In addition, NGS-based TD will be applicable to various high copy transposable elements family for high throughput and rapid polymorphic marker development which will be helpful for efficient plant genomics and breeding purposes.

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Analysis of plant diversity with retrotransposon-based molecular markers

Cited by 230 publications

References 109 publications

Molecular analysis of temporal genetic structuring in pea (Pisum sativum L.) cultivars bred in the Czech Republic and in former Czechoslovakia since the mid-20th century

Molecular analysis of temporal genetic structuring in pea (Pisum sativum L.) cultivars bred in the Czech Republic and in former Czechoslovakia since the mid-20th century

Using Two Retrotransposon Based Marker Systems (IRAP and REMAP) for Molecular Characterization of Olive (<i>Olea europaea</i> L.) Cultivars

Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

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