DcMaster transposon display markers as a tool for diversity evaluation of carrot breeding materials and for hybrid seed purity testing

Macko, A.; Grzebelus, Dariusz

doi:10.1007/bf03195246

Cited by 15 publications

(9 citation statements)

References 24 publications

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“…It combines and adapts established methods of Transposon Display [19,20,38], high-throughput sequencing [39], and sample indexing [26-35]. Genomic DNA (Figure 1A) is sheared by sonication.…”

Section: Resultsmentioning

confidence: 99%

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

et al. 2010

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BackgroundMobile elements (MEs) are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and substrates for further genomic rearrangements. Research on the impacts, population dynamics, and evolution of MEs is constrained by the difficulty of ascertaining rare polymorphic ME insertions that occur against a large background of pre-existing fixed elements and then genotyping them in many individuals.ResultsHere we present a novel method for identifying nearly all insertions of a ME subfamily in the whole genomes of multiple individuals and simultaneously genotyping (for presence or absence) those insertions that are variable in the population. We use ME-specific primers to construct DNA libraries that contain the junctions of all ME insertions of the subfamily, with their flanking genomic sequences, from many individuals. Individual-specific "index" sequences are designed into the oligonucleotide adapters used to construct the individual libraries. These libraries are then pooled and sequenced using a ME-specific sequencing primer. Mobile element insertion loci of the target subfamily are uniquely identified by their junction sequence, and all insertion junctions are linked to their individual libraries by the corresponding index sequence. To test this method's feasibility, we apply it to the human AluYb8 and AluYb9 subfamilies. In four individuals, we identified a total of 2,758 AluYb8 and AluYb9 insertions, including nearly all those that are present in the reference genome, as well as 487 that are not. Index counts show the sequenced products from each sample reflect the intended proportions to within 1%. At a sequencing depth of 355,000 paired reads per sample, the sensitivity and specificity of ME-Scan are both approximately 95%.ConclusionsMobile Element Scanning (ME-Scan) is an efficient method for quickly genotyping mobile element insertions with very high sensitivity and specificity. In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species.

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Section: Resultsmentioning

confidence: 99%

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

et al. 2010

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“…Transposon insertion polymorphisms are widely used as molecular markers and a range of techniques exploring that type of variability has been developed (Grzebelus 2006). Examples of the use of MITE insertion polymorphisms using a highly efficient Transposon Display (TD) system include population diversity studies and genetic mapping in maize (Casa et al 2000(Casa et al , 2002 and carrot (Macko andGrzebelus 2008, Grzebelus andSimon 2009). If sequences flanking the transposon are known, a codominant site-specific assay can be developed.…”

Section: Introductionmentioning

confidence: 99%

Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula

Grzebelus

Gładysz

Macko-Podgórni

et al. 2009

Gene

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“…DcMaster Transposon Display (DcMTD), a system for the identification of DcMaster insertion polymorphisms was developed. It was used to investigate genomic localisation of insertions (Grzebelus et al 2007a) and to examine genetic diversity in carrot breeding materials (Macko and Grzebelus 2008). Here, we present the experimental evidence for the presence of other groups of DcMaster-like elements in the carrot genome, characterize their structure and possible evolutionary relationships.…”

Section: Introductionmentioning

confidence: 99%

Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome

Grzebelus

Simon

2008

Genetica

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Transposable elements constitute a significant fraction of plant genomes. Both autonomous and non-autonomous elements of the DcMaster family, residing in the carrot genome, were described previously. DcMaster elements were classified as members of the PIF/Harbinger superfamily. In the present paper we report on the identification of other groups of DcMaster-like elements. Beside the previously described, relatively highly abundant miniature inverted repeat element (MITE) family Krak (ca. 3,600 copies, ca. 80% intra-family similarity), three other families, i.e. 1.1 kb long KrakL1 (ca. 3,000 copies, ca. 98% intra-family similarity), 1.2 kb long KrakL2 (a single identified element, 71.1% similar to KrakL1 consensus), and 2.2 kb long Midi (few elements, 99% intra-family similarity), were revealed. The fact that all members within each of the newly found families were almost identical in their sequence suggests their very recent activity. The families differed in terms of their similarity to the canonical DcMaster element. They also differed in copy number, from just a few copies of Midi to few thousand copies of Krak. A modification of the DcMaster Transposon Display (DcMTD) marker system, targeted specifically towards Krak elements, was used to investigate their insertion polymorphism. It was shown that Krak insertion sites, similarly to those of the DcMaster elements, were highly polymorphic between the wild and the cultivated Daucus carota.

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DcMaster transposon display markers as a tool for diversity evaluation of carrot breeding materials and for hybrid seed purity testing

Cited by 15 publications

References 24 publications

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula

Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome

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