The DcMaster Transposon Display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome

Grzebelus, Dariusz; Jagosz, Barbara; Simon, Philipp W.

doi:10.1016/j.gene.2006.07.041

Cited by 31 publications

(27 citation statements)

References 21 publications

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“…DNA restriction with MseI, ligation of adaptors, as well as preselective and selective PCR amplification were performed as described previously (Grzebelus et al 2007). Six different combinations of 3 selective nucleotides at the 3' end of the adaptor-specific primers (Table 2) were used for the final round of amplification.…”

Section: Identification Of Dcmtd Markersmentioning

confidence: 99%

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

Macko

Grzebelus

2008

J Appl Genet

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In recent years, transposon insertion polymorphisms have been utilized as molecular markers, and a range of techniques tailored towards identification of insertion sites of various transposable elements have been developed. In the present paper we describe the application of a recently developed DcMaster transposon display system to analyse the genetic diversity of Polish breeding materials of carrot (Daucus carota) and to identify polymorphisms useful for hybrid seed purity testing. Using 3 sets of breeding materials (each consisting of the cytoplasmic male sterility stock, the maintainer, the pollinator, and the corresponding F1 hybrid), we identified 56 DcMTD markers. DcMaster insertion sites proved to be highly polymorphic in cultivated carrot, as 79% of all insertion sites differentiated between individual plants. Fourteen stock-specific DcMTD markers were further selected as potentially useful for hybrid seed purity testing.

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Section: Identification Of Dcmtd Markersmentioning

confidence: 99%

“…Grzebelus et al (2007) reported that around 70% of DcMTD amplification products were polymorphic between the cultivated carrot line B493 and the wild carrot QAL. In the present study we obtained a similar, or even slightly higher level of polymorphism, reaching 79%.…”

Section: Dcmtd Markers As a Tool For Evaluation Of Genetic Diversitymentioning

confidence: 99%

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

Macko

Grzebelus

2008

J Appl Genet

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“…Moreover, they can serve as useful tools for the functional genomics of model and crop plant species. While the application of transposable elements generally uses well characterised elements, such as Ac/Ds from maize, for mutagenesis in heterologous systems, endogenous elements can also be used as "tags" to clone genes or as markers for evaluating linkage analyses in progeny of genetic crosses (Ramachandran and Sundaresan 2001;Queen et al 2004;Grzebelus et al 2007). Therefore, while of interest in their own right, members of these classes of transposable elements in cassava may have the potential to assist with the genetic characterisation or improvement of this important crop.…”

Section: Discussionmentioning

confidence: 99%

Diversity of LTR-retrotransposons and Enhancer/Suppressor Mutator-like transposons in cassava (Manihot esculenta Crantz)

2008

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Cassava (Manihot esculenta Crantz), though a major world crop with enormous potential, is very under studied. Little is known about its genome structure and organisation. Transposable elements have a key role in the evolution of genome structure, and can be used as important tools in applied genetics. This paper sets out to survey the diversity of members of three major classes of transposable element within the cassava genome and in relation to similar elements in other plants. Members of two classes of LTR-retrotransposons, Ty1/copia-like and Ty3/gypsy-like, and of Enhancer/Suppressor Mutator (En/Spm)-like transposons were isolated and characterised. Analyses revealed 59 families of Ty1/copia, 26 families of Ty3/gypsy retrotransposons, and 40 families of En/Spm in the cassava genome. In the comparative analyses, the predicted amino acid sequences for these transposon classes were compared with those of related elements from other plant species. These revealed that there were multiple lineages of Ty1/copia-like retrotransposons in the genome of cassava and suggested that vertical and horizontal transmission as the source of cassava Mecops may not be mutually exclusive. For the Ty3/gypsy elements network, two groups of cassava Megyps were evident including the Arabidopsis Athila lineage. However, cassava En/Spm-like elements (Meens) constituted a single group within a network of plant En/Spm-like elements. Hybridisation analysis supported the presence of transposons in the genome of cassava in medium (Ty3/gypsy and En/Spm) to high (Ty1/copia) copy numbers. Thus the cassava genome was shown to contain diverse members of three major classes of transposable element; however, the different classes exhibited contrasting evolutionary histories.

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“…Of these, 15 markers were included in the carrot reference linkage map, constructed previously using an F 2 population derived from a cross between the dark orange inbred B493 and a wild white-rooted carrot Queen Anne's Lace (QAL) Simon 2002, 2004;Grzebelus et al 2007;Just et al 2007;Cavagnaro et al 2009Cavagnaro et al , 2010. These markers were distributed across all nine linkage groups (Grzebelus et al 2007;Just et al 2007;Cavagnaro et al 2009Cavagnaro et al , 2010 and included eight STS markers (based on putative carotenoid biosynthetic gene sequences), four simple sequence repeats (SSRs), one sequencecharacterized amplified region (SCAR), and two PCR markers (for Rs and DCOR sequences; Table 1). In addition, two other markers from different carrot linkage maps were used to screen the BAC library and develop potential FISH probes.…”

Section: Methodsmentioning

confidence: 99%

“…The developed chromosome-specific carrot BACs provided us a tool to localize additional DNA sequences that were either not mapped or mapped in genetic backgrounds unrelated to the B493×QAL population used to construct the reference linkage map Simon 2002, 2004;Grzebelus et al 2007;Just et al 2007;Cavagnaro et al 2010). Thus, we were able to assign chromosomal positions to the rDNA gene clusters, and to six BAC probes (four unanchored and Table 1.…”

Section: Fish Mapping Of Additional Dna Sequencesmentioning

confidence: 99%

Comparative FISH mapping of Daucus species (Apiaceae family)

et al. 2011

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The cytogenetic characterization of the carrot genome (Daucus carota L., 2n = 18) has been limited so far, partly because of its somatic chromosome morphology and scant of chromosome markers. Here, we integrate the carrot linkage groups with pachytene chromosomes by fluorescent in situ hybridization (FISH) mapping genetically anchored bacterial artificial chromosomes (BACs). We isolated a satellite repeat from the centromeric regions of the carrot chromosomes, which facilitated the study of the pachytene-based karyotype and demonstrated that heterochromatic domains were mainly confined to the pericentromeric regions of each chromosome. Chromosome-specific BACs were used to: (1) physically locate genetically unanchored DNA sequences, (2) reveal relationships between genetic and physical distances, and (3) address chromosome evolution in Daucus. Most carrot BACs generated distinct FISH signals in 22-chromosome Daucus species, providing evidence for syntenic chromosome segments and rearrangements among them. These results provide a foundation for further cytogenetic characterization and chromosome evolution studies in Daucus.

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The DcMaster Transposon Display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome

Cited by 31 publications

References 21 publications

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

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

Diversity of LTR-retrotransposons and Enhancer/Suppressor Mutator-like transposons in cassava (Manihot esculenta Crantz)

Comparative FISH mapping of Daucus species (Apiaceae family)

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