Plant DNA fingerprinting with radioactive and digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences

Weising, Kurt; Beyermann, Birgit; Ramser, Juliane; Kahl, Günter

doi:10.1002/elps.1150120211

Cited by 113 publications

(40 citation statements)

References 57 publications

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“…Lyophilized material was ground using a mill (Retsch MM200). Genomic DNA was prepared from lyophilized material using a modified CTAB protocol (Weising et al, 1991).…”

Section: Molecular Marker Analysismentioning

confidence: 99%

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Muylle¹,

Baert²,

Bockstaele

et al. 2005

Heredity

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Crown rust resistance is an important selection criterion in ryegrass breeding. The disease, caused by the biotrophic fungus Puccinia coronata, causes yield losses and reduced quality. In this study, we used linkage mapping and QTL analysis to unravel the genomic organization of crown rust resistance in a Lolium perenne population. The progeny of a pair cross between a susceptible and a resistant plant were analysed for crown rust resistance. A linkage map, consisting of 227 loci (AFLP, SSR, RFLP and STS) and spanning 744 cM, was generated using the two-way pseudo-testcross approach from 252 individuals. QTL analysis revealed four genomic regions involved in crown rust resistance. Two QTLs were located on LG1 (LpPc4 and LpPc2) and two on LG2 (LpPc3 and LpPc1). They explain 12.5, 24.9, 5.5 and 2.6% of phenotypic variance, respectively. An STS marker, showing homology to R genes, maps in the proximity of LpPc2. Further research is, however, necessary to check the presence of functional R genes in this region. Synteny at the QTL level between homologous groups of chromosomes within the Gramineae was observed.LG1 and LG2 show homology with group A and B chromosomes of oat on which crown rust-resistance genes have been identified, and with the group 1 chromosomes of the Triticeae, on which leaf rustresistance genes have been mapped. These results are of major importance for understanding the molecular background of crown rust resistance in ryegrasses. The identified markers linked to crown rust resistance have the potential for use in marker-assisted breeding. Heredity (2005) 95, 348-357.

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“…Lyophilized material was ground using a mill (Retsch MM200). Genomic DNA was prepared from lyophilized material using a modified CTAB protocol (Weising et al, 1991).…”

Section: Molecular Marker Analysismentioning

confidence: 99%

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Muylle¹,

Baert²,

Bockstaele

et al. 2005

Heredity

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“…Prior to DNA extraction, the tissues were digested with RNase A (200 mg/ml) and proteinase K (1 mg/ml) after the tissues had been homogenized. DNA was then extracted with the QIAGEN Genomic DNA Kit (QIAGEN, Hilden, Germany) (Mischiati et al, 1993;Weising et al, 1991).…”

Section: Specimens and Dna Extractionmentioning

confidence: 99%

High frequency of p16INK4A gene alterations in hepatocellular carcinoma

et al. 1999

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The tumor suppressor gene p16 (CDKN2/MTS-1/ INK4A) is an important component of the cell cycle and inactivation of the gene has been found in a variety of human cancers. In order to investigate the role of p16 gene in the tumorigenesis of hepatocellular carcinoma (HCC), 48 cases of HCC were analysed for p16 alterations by: methylation-speci®c PCR (MSP) to determine the methylation status of the p16 promoter region; comparative multiplex PCR to detect homozygous deletion; PCR ± SSCP and DNA sequencing analysis to identify mutation of the p16 gene. We found high frequency of hypermethylation of the 5' CpG island of the p16 gene in 30 of 48 cases (62.5%) of HCC tumors. Moreover, homozygous deletion at p16 region were present in ®ve of 48 cases (10.4%); and missense mutation were detected in three of 48 cases (6.3%). The overall frequency of p16 alterations, including homozygous deletion, mutation and hypermethylation, in HCC tumors was 70.8% (34 of 48 cases). These ®ndings suggest that: (a) the inactivation of the p16 is a frequent event in HCC; (b) the p16 gene is inactivated by multiple mechanisms including homozygous deletion, promoter hypermethylation and point mutation; (c) the most common somatic alteration of the p16 gene in HCC is de novo hypermethylation of the 5' CpG island; and (d) in contrast to other studies, high frequency of genomic alterations are not uncommon in the 9p21 of the p16 gene. Our results strongly suggest that the p16 gene plays an important role in the pathogenesis of HCC.

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“…Several strategies have been developed to exploit the polymorphic behavior of microsatellites and their flanking sequences for genome analysis. The first strategy employs synthetic oligonucleotide probes complementary to simple tandem repeats as hybridization probes t o restriction enzymedigested, electrophoretically separated DNA [5,6,8]. This so-called oligonucleotide fingerprinting approach often P. C. Sharma er al.…”

Section: Introductionmentioning

confidence: 99%

The potential of microsatellites for hybridization‐ and polymerase chain reaction‐based DNA fingerprinting of chickpea (Cicer arietinum L.) and related species

et al. 1995

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The genetic variability in agronomically important chickpea accessions (Cicer arietinum L.) as detected by single-locus restriction fragment length polymorphism (RFLP) probes, random amplified polymorphic DNA (RAPD) and isoenzyme markers, is rather low. Recently, highly polymorphic microsatellites became the markers of choice for linkage mapping and population studies. We are currently following two main strategies to exploit the variability of microsatellites and adjacent sequences for genetic studies in chickpea. (i) In an approach referred to as oligonucleotide fingerprinting, microsatellite-complementary oligonucleotides were employed as multilocus probes for in-gel hybridization. A total of 38 different probes representing di-, tri- and tetranucleotide repeats were used to analyze variability between and within four accessions of C. arietinum. Hybridization signals were obtained with 35 probes. While the abundance and level of polymorphism of different target sequences varied considerably, distinct, intraspecifically informative banding patterns were obtained with the majority of probes and all restriction enzymes tested. No obvious correlation existed between abundance, fingerprint quality, and sequence characteristics of a particular motif. (ii) In a recently developed strategy called microsatellite primed polymerase chain reaction (MP-PCR), microsatellite-complementary oligonucleotides serve as single PCR primers for genomic DNA templates. We tested the general applicability of MP-PCR by amplifying DNA samples from tomato, chickpea and two related annual Cicer species with a variety of di-, tri- and tetranucleotide repeat primers. Most but not all primers generated distinct fingerprint-like banding patterns after agarose gel electrophoresis and ethidium bromide staining of the amplification products. Since the method proved to be sensitive to reaction conditions in a way similar to RAPD analysis, we increased the PCR specificity by the introduction of a modified "touch-down" protocol. In chickpea, touch-down MP-PCR generated highly reproducible banding patterns which predominantly revealed interspecific polymorphisms. The potential of different microsatellite-based strategies for genome analysis in chickpea is discussed.

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Plant DNA fingerprinting with radioactive and digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences

Cited by 113 publications

References 57 publications

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

High frequency of p16INK4A gene alterations in hepatocellular carcinoma

The potential of microsatellites for hybridization‐ and polymerase chain reaction‐based DNA fingerprinting of chickpea (Cicer arietinum L.) and related species

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