Mapping of rabbit chromosome 1 markers generated from a microsatellite‐enriched chromosome‐specific library

Korstanje, Ron; Gillissen, Gert; Bieman, M.G. den; Versteeg, Serge A.; Oost, BA van; Fox, R. R.; Lith, H.A. van; Zutphen, L.F.M. van

doi:10.1046/j.1365-2052.2001.00783.x

Cited by 17 publications

(21 citation statements)

References 11 publications

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“…In order to assess the coverage of individual chromosomes by linkage groups, and to orient linkage groups along chromosomes, it is necessary to map genetic markers belonging to specific linkage groups on metaphase chromosomes. In the present study we describe the chromosomal localization of microsatellite markers that have recently been used for linkage studies (Korstanje et al, 2001a(Korstanje et al, , 2001b, thus providing links between the genetic and the physical maps of the rabbit genome. For the localization of these markers we used the DNA of clones from a rabbit Bacterial Artificial Chromosome (BAC) library as probe for FISH.…”

confidence: 99%

“…Positive clones were cultured and DNA was isolated according to standard procedures. In order to verify the presence of the microsatellite sequences of interest in the selected clones, PCR was performed on the isolated BAC DNA as previously described (Korstanje et al, 2001a(Korstanje et al, , 2001b, and the amplification products were separated on a 3 % MS-8 pronarose (Sphearo Q) gel. Table 2 lists the names of the genes containing the respective microsatellites, the sequences of the primers used, the mean size of the amplification products, the primer references and the EMBL accession numbers for the complete sequences.…”

Section: Fish Probesmentioning

confidence: 99%

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Fourteen chromosomal localizations and an update of the cytogenetic map of the rabbit

Zijlstra¹,

Haan²,

Korstanje

et al. 2002

Cytogenet Genome Res

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In order to improve the informativeness of the cytogenetic map of the rabbit genome, fourteen markers were regionally mapped to individual chromosomes. The localizations comprise eleven gene loci (PRLR, GHR, HK1, ACE, TF, 18S+28S rDNA, CYP2C4, PMP2, TCRB, ALOX15 and MT1) and three microsatellite loci (Sat13, Sol33 and D1Utr6). Five of the genes contain known microsatellite sequences. To achieve these localizations, homologous and heterologous small insert clones, and clones from a rabbit Bacterial Artificial Chromosome (BAC) library were used as probes for fluorescence in situ hybridization experiments. Results indicate that especially BAC clones are a valuable tool for cytogenetic mapping. Some of the genes were selected for mapping on the basis of human- rabbit comparative painting data, to achieve localizations on gene-poor rabbit chromosomes. Our data are, in general, in agreement with the human-rabbit comparative painting data. By mapping microsatellite sequences that have also been used in linkage studies, links are provided between the genetic and physical maps of the rabbit genome. Linkage groups I, VI and XI could be assigned to chromosomes 1, 5 and 3 respectively. Moreover, in this paper we give an overview of the current status of the rabbit cytogenetic map. This map now comprises 62 physically mapped genes, which are scattered over all autosomes, except chromosome 2, and the X chromosome.

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confidence: 99%

Section: Fish Probesmentioning

confidence: 99%

Fourteen chromosomal localizations and an update of the cytogenetic map of the rabbit

Zijlstra¹,

Haan²,

Korstanje

et al. 2002

Cytogenet Genome Res

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“…Linkage mapping was not feasible, because the 2 strains were outbred, and only few genetic markers have been mapped in the rabbit. 7 Another approach to study genetic variation between the 2 strains is expression analysis. In contrast to various other species, expression arrays are not available for rabbits.…”

Section: See Page 237mentioning

confidence: 99%

Identification of Macrophage Arginase I as a New Candidate Gene of Atherosclerosis Resistance

Teupser

Burkhardt

Wilfert

et al. 2006

ATVB

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Objective-Our laboratory has previously created 2 strains of rabbits with genetically determined high-atherosclerotic response (HAR) and low-atherosclerotic response (LAR). The aim of the present study was to identify new genes of atherosclerosis susceptibility in macrophages from the 2 strains. Methods and Results-Suppression subtractive hybridization was used to screen for genes with higher expression in macrophages from LAR rabbits. We identified a cDNA fragment with high homology to human arginase I (AI; 91%) and subsequently cloned the full-length cDNA of the rabbit homologue. Quantitative RT-PCR revealed a significantly higher macrophage AI mRNA expression in LAR rabbits than in HAR rabbits (77428Ϯ10941 versus 34344Ϯ4538; Pϭ0.002; copies/10 6 copies ␤-actin), which also correlated with a significantly higher arginase enzyme activity. Northern blot analysis led to the identification of a size polymorphism of AI mRNA. This was because of a 413 bp C-repeat insertion in the 3Ј untranslated region. The shorter transcript variant was predominantly expressed in LAR rabbits and associated with significantly higher AI mRNA expression levels. Transfection experiments indicated decreased mRNA stability of the long AI variant. Conclusions-High

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“…Construction of short-insert libraries became easier after the introduction of methods for representative amplification of chromosomal DNA as only a few hundred or thousand sorted chromosomes (Miller et al 1992; Vooijs et al 1993; Macas et al 1996) or even a single chromosome (Van Devanter et al 1994) was sufficient as starting material. Chromosome specifics of the libraries facilitated gene mapping and targeted the development of DNA markers in human, animals, and plants (Arumuganathan et al 1994; Grady et al 1996; Lan et al 1999; Korstanje et al 2001; Požárková et al 2002). …”

Section: The Many Important Uses Of Flow-sorted Chromosomesmentioning

confidence: 99%

“…If, however, there is a need to develop markers from a particular genome region, this strategy is highly inefficient. A targeted alternative has been the development of markers from short-insert chromosome-specific DNA libraries (Arumuganathan et al 1994; Grady et al 1996; Lan et al 1999), in some cases enriched for DNA motives of interest (Korstanje et al 2001; Požárková et al 2002; Kofler et al 2008). DNA markers were also developed from clones from chromosome-specific DNA libraries with large inserts after sequencing their ends (Paux et al 2006; Bartoš et al 2008).…”

Section: The Many Important Uses Of Flow-sorted Chromosomesmentioning

confidence: 99%

Chromosomes in the flow to simplify genome analysis

Doležel

Vrána

Šafář

et al. 2012

Funct Integr Genomics

103

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Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 102–104 chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.

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Mapping of rabbit chromosome 1 markers generated from a microsatellite‐enriched chromosome‐specific library

Cited by 17 publications

References 11 publications

Fourteen chromosomal localizations and an update of the cytogenetic map of the rabbit

Fourteen chromosomal localizations and an update of the cytogenetic map of the rabbit

Identification of Macrophage Arginase I as a New Candidate Gene of Atherosclerosis Resistance

Chromosomes in the flow to simplify genome analysis

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