Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines

Li, J; Klindworth, Daryl L.; Shireen, Fareeha; Cai, Xiwen; Hu, Jinguo; Xu, Steven S.

doi:10.1139/g06-114

Cited by 20 publications

(21 citation statements)

References 24 publications

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“…An additional study used this technique for developing chromosome-specific TRAP markers in wheat. The combination of ten fixed primers and two arbitrary primers generated 307 markers, and the authors considered that the chromosome-specific markers developed provided an identity for each chromosome, facilitating the molecular and genetic characterisation of the individual chromosome, including genetic mapping and gene identification (Li et al, 2007). Miklas et al (2006) used the TRAP technique for mapping and tagging disease resistance traits in common bean.…”

Section: Resultsmentioning

confidence: 99%

Identification and Validation of Est-Derived Molecular Markers, Trap and Vntrs, for Banana Research

Garcia¹,

Talebi²,

Ferreira³

et al. 2011

Acta Hortic.

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The advent of high-throughput sequencing technology has generated abundant information on DNA sequences for the genomes of many plant species. Expressed Sequence Tags (ESTs), which are unique DNA sequences derived from a cDNA library and therefore representing genes transcribed in specific tissues or at some stage of development, are one type of DNA sequences highly available today for many important crop species. Molecular markers are used for bridging DNA sequence information with particular phenotypes and are useful tools for genotyping germplasm collections and also for tagging genes involved in desirable agronomic traits. In this sense, there is always a strong demand for suitable marker techniques to better utilise existing sequence information. A transcriptome database from banana (Musa spp.), DATAMusa, containing 42,724 ESTs from 11 different cDNA libraries and encompassing approximately 24 Mb of DNA sequence, was used in this study for the design of primers to PCR-amplify two types of EST-derived molecular markers, Variable Nucleotide Tandem Repeat (VNTR) and Target Region Amplification Polymorphism (TRAP). These primers were then validated against a panel of 14 diploid Musa genotypes and produced 32 (VNTR) and 119 (TRAP) alleles. Used separately or together, both types of markers were able to discriminate Musa genotypes from different genome background (A or B genomes). The TRAP alleles identified were derived from only one EST, while the VNTR alleles were derived from 12 unigenes. Based on the results of this study, EST-derived markers can be an important source of polymorphism to be used in genetic diversity and gene discovery studies in banana.

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Section: Resultsmentioning

confidence: 99%

Identification and Validation of Est-Derived Molecular Markers, Trap and Vntrs, for Banana Research

Garcia¹,

Talebi²,

Ferreira³

et al. 2011

Acta Hortic.

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“…The NBS-LRR sites have been implicated in disease resistance in many crop plants (Meyers et al, 2003;Maleki et al, 2003;Belkhadir et al, 2004). Documentation exists that TRAP markers indeed target genie regions (Alwala et al, 2006;J. Li et al, 2006) and the possibility of arbitrary primer potentially amplifying random portions of the genome is minimal due to increased T^ temperature in the PCR.…”

Section: Discussionmentioning

confidence: 99%

Molecular Markers Associated with Resistance toAspergillus flavusin Maize Grain: QTL and Discriminant Analyses

Alwala

Kimbeng

Williams

et al. 2008

Journal of New Seeds

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Aflatoxin contamination of maize {Zea mays L.) grain caused by Aspergillus flavus is a serious health hazard to animals and humans. Resistance to infection by A. flavus is poorly understood. The objectives of this investigation were to identify potential candidate markers associated with resistance in maize kernels and pollen grains to A. flavus using a mapping population derived from a cross between Mp313E (resistant) and SC212m (susceptible) inbred lines. The parents, F,, and F2 plants, were planted in the field in 2005. Each Fj plant was self-pollinated to produce F2.3 seed. Fresh pollen collected from parental lines, F,, and each Fj plant was germinated on a growth medium in the presence of A. flavus conidia. Selfed seeds from parents, F,, and Fj plants, were challenged with A. flavus conidial suspension and incubated using a medium-free method. Percent kernels uninfected (PKU) and number of pollen grains germinated (NPG) were recorded. A linkage map was constructed with JoinMap 3.0 using DNA profiles of all F2 individuals produced from amplified fragment length polymorphism (AFLP) and target region amplification polymorphism (TRAP) markers. Interval mapping and multiple-QTL model (MQM) mapping analyses were performed using MapQTL 4.0 software. Three marker-QTL associations were observed for log-transformed PKU. Potential markers associated with this trait were also identified via discriminant analysis (DA). The markers identified via DA pointed to the same genomic regions as identified via the QTL-mapping strategy. For log-transformed NPG, five marker-QTL associations were detected. One QTL was associated with a TRAP marker. The DA confirmed the existence of three QTL. The QTL detected for NPG were different from the QTL detected for PKU. Thus, resistances of pollen and kernels to A. flavus appeared to be controlled by different genetic systems/mechanisms. Correlation between pollen germination and percent kernel infection was negligible (r -0.067), suggesting that the two traits can be improved independently. KEYWORDS.Amplified fragment length polymorphism (AFLP), Aspergillus flavus, discriminant analysis (DA), maize (Zea mays L.), quantitative trait loci (QTL), target region amplification polymorphism (TRAP)

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“…For genetic diversity assessment of germplasm collections, SRAP markers are also considered to be superior to AADs as they seem to be more congruent with morphological variation and evolutionary history [220]. TRAP markers show similar features to SRAPs, but in polyploid genomes TRAPs are unequally distributed among some homologous groups [221]. Moreover, in sunflower, Hu [222] was able to define linkage groups in telomeric regions.…”

Section: Characteristics Of Tfm Markersmentioning

confidence: 99%

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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Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines

Cited by 20 publications

References 24 publications

Identification and Validation of Est-Derived Molecular Markers, Trap and Vntrs, for Banana Research

Identification and Validation of Est-Derived Molecular Markers, Trap and Vntrs, for Banana Research

Molecular Markers Associated with Resistance toAspergillus flavusin Maize Grain: QTL and Discriminant Analyses

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

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