h-TBP: an approach based on intron-length polymorphism for the rapid isolation and characterization of the multiple members of the β-tubulin gene family in Camelina sativa (L.) Crantz

Galasso, Incoronata; Manca, Antonella; Braglia, Luca; Martinelli, Tommaso; Morello, Laura; Breviario, Diego

doi:10.1007/s11032-010-9515-0

Cited by 27 publications

(22 citation statements)

References 23 publications

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“…Anticipated results of TBP fingerprinting are shown in Additional file 1. Galasso et al [61] introduced new primers for amplification of the entire β -tubulin region, containing the partial exons 1 and 3 and the full sequences of introns I and II, as well as exon 2. They named this variant h-TBP (horse-TBP).…”

Section: Gene-targeted and Functional Markers (Gtms And Fms)mentioning

confidence: 99%

“…However, novel primer design may become problematic if genomic annotations of conserved sequences are missing. It has also been shown that conserved DNA based markers are able to discriminate between different species, that the number of amplified bands correlates well with ploidy levels [61], and that banding patterns can reflect rearrangements of polyploid genomes. Such experiments have also been performed using AAD markers, with various results [113,114].…”

Section: Utility and Limitations Of Conserved Dna Based Markersmentioning

confidence: 99%

“…The extent of this problem seems to vary between different techniques. Galasso et al [61] cloned a number of TBP fragments and found no amplicons from analogous sites. Cernák et al [103] proved the amplification of targeted introns from the corresponding gene using simple restriction digestion.…”

Section: Utility and Limitations Of Conserved Dna Based Markersmentioning

confidence: 99%

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Advances in plant gene-targeted and functional markers: a review

et al. 2013

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Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.

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Section: Gene-targeted and Functional Markers (Gtms And Fms)mentioning

confidence: 99%

Section: Utility and Limitations Of Conserved Dna Based Markersmentioning

confidence: 99%

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Advances in plant gene-targeted and functional markers: a review

et al. 2013

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“…Conserved DNA regions sharing the same priming site may be distributed across the genomes of different genotypes in different patterns; therefore polymorphisms can be detected within species . The priming site is also a subject of study in the characterization of conserved regions …”

Section: Introductionmentioning

confidence: 99%

Genetic assessment of common bean (Phaseolus vulgaris L.) accessions by peroxidase gene‐based markers

2013

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“…Among the two types of polymorphisms, intron length polymorphism (ILP) is easily detected by a PCR-based approach, namely, exon-primed intron-crossing PCR (EPIC-PCR) (Palumbi 1995 ), where primers are designed in exonic regions fl anking the target introns. Very few reports are available on the development of such markers (Wei et al 2005 ;Feltus et al 2006 ;Chen et al 2011 ;Braglia et al 2010 ;Galasso et al 2010 ;Poczai et al 2010 ;Shang et al 2010 ;Tamura et al 2012 ;Liu et al 2011 ;Gupta et al 2011Gupta et al , 2012Xia et al 2012 ) in various crop species. Availability of whole-genome (Wang et al 2005 ) and soybean (Shu et al 2010 ).…”

Section: Development Of Intron Polymorphism Markersmentioning

confidence: 99%

Molecular Marker Development Using Bioinformatic Tools

Rajendrakumar

2015

Sorghum Molecular Breeding

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h-TBP: an approach based on intron-length polymorphism for the rapid isolation and characterization of the multiple members of the β-tubulin gene family in Camelina sativa (L.) Crantz

Cited by 27 publications

References 23 publications

Advances in plant gene-targeted and functional markers: a review

Advances in plant gene-targeted and functional markers: a review

Genetic assessment of common bean (Phaseolus vulgaris L.) accessions by peroxidase gene‐based markers

Molecular Marker Development Using Bioinformatic Tools

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