Higher frequencies of transitions among point mutations

Vogel, Friedrich; Kopun, Marijana

doi:10.1007/bf01732746

Cited by 82 publications

(42 citation statements)

References 20 publications

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“…The number of transition SNPs was higher than transversions as expected because it is well known that random mutations lead to higher transition rates during evolution (Vogel and Kopun 1977). This higher transition rate was also observed in oil palm.…”

Section: Gbs and Snp Identificationsupporting

confidence: 73%

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Çelik

Bodur²,

Frary

et al. 2016

Mol Breeding

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Recently developed plant genomics approaches (LD mapping and genome-wide selection) require many molecular markers distributed throughout the plant genome. As a result, the availability of an increasing number of markers is essential for maintaining highly efficient and accurate plant breeding programs. In this study, we identified SNP loci in sunflower using a genotyping by sequencing (GBS) approach in an intraspecific F 2 mapping population. A total of 271,445,770 reads were generated by the Genome Analyzer II next-generation sequencing platform and 29.2 % of the reads were aligned to unique locations in the genome. A total of 46,278 SNP loci were identified and 7646 SNP loci were validated in an F 2 population. In addition, a SNP-based linkage map was constructed. This is the first report of SNP discovery in sunflower by GBS. The SNP markers and SNP-based linkage map will be valuable molecular genetics tools for sunflower breeding.

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Section: Gbs and Snp Identificationsupporting

confidence: 73%

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Çelik

Bodur²,

Frary

et al. 2016

Mol Breeding

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“…Understanding the patterns and determinants of sequence variation that predispose to inherited disease has been an important goal of medical genetics for many years (Vogel 1972;Vogel and Kopun 1977). Recent technological progress and the availability of a human genome reference sequence have facilitated studies to systematically discover and analyze the genetic variation present in human populations.…”

mentioning

confidence: 99%

Single Nucleotide Variation Analysis in 65 Candidate Genes for CNS Disorders in a Representative Sample of the European Population

Freudenberg-Hua¹,

Freudenberg²,

Kluck³

et al. 2003

Genome Res.

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The detailed investigation of variation in functionally important regions of the human genome is expected to promote understanding of genetically complex diseases. We resequenced 65 candidate genes for CNS disorders in an average of 85 European individuals. The minor allele frequency (MAF), an indicator of weak purifying selection, was lowest in radical amino acid alterations, whereas similar MAF was observed for synonymous variants and conservative amino acid alterations. In noncoding sequences, variants located in CpG islands tended to have a lower MAF than those outside CpG islands. The transition/transversion ratio was increased among both synonymous and conservative variants compared with noncoding variants. Conversely, the transition/transversion ratio was lowest among radical amino acid alterations. Furthermore, among nonsynonymous variants, transversions displayed lower MAF than did transitions. This suggests that transversions are associated with functionally important amino acid alterations. By comparing our data with public SNP databases, we found that variants with lower allele frequency are underrepresented in these databases. Therefore, radical variants obtain distinctively lower database coverage. However, those variants appear to be under weak purifying selection and thus could play a role in the etiology of genetically complex diseases.

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“…According to the report of Barker et al (1984), FRLPs are detected at a higher frequency in restriction enzyme recognition sites that contain the CpG dimer. In the human genome, most of these dinucleotides are methylated ( Van der Ploeg and Flavell, 1980;Cooper, 1983) and 5-methyl-cytosine is frequently replaced by thymidine due to the deamination of the methylated base (Vogel, 1972;Vogel and Kopun, 1977). That is, both MspI(CCGG) and TaqI (TCGA) would be expected to detect polymorphisms with a higher efficiency than those that do not contain CpG in their recognition sequences.…”

Section: Discussionmentioning

confidence: 99%

Isolation of DNA clones revealing restriction fragment length polymorphisms in the human genome

et al. 1986

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SummaryA recombinant human DNA library was constructed using pUC 18 as the cloning vector. Plasmid DNA isolated from a small scale culture was used as the hybridization probe; many recombinant clones could be easily tested for their ability to detect restriction fragment length polymorphisms (RFLPs). Forty-five arbitrary single copy DNA fragments were isolated from this library and five clones revealed RFLPs. Probe OS-5 had three alleles and probe OS-7, which detected insertion/deletion polymorphisms, had several alleles.Apart from these clones, two polymorphic DNA fragments were isolated from the pBR322 plasmid library and another two from the Charon 4A phage library. Although only four restriction enzymes were employed to detect polymorphisms, the efficiency of detecting polymorphisms was reasonable.These nine clones will serve as useful markers for linkage studies.

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Higher frequencies of transitions among point mutations

Cited by 82 publications

References 20 publications

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

Single Nucleotide Variation Analysis in 65 Candidate Genes for CNS Disorders in a Representative Sample of the European Population

Isolation of DNA clones revealing restriction fragment length polymorphisms in the human genome

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