Dataset Information

Single nucleotide polymorphism discovery and haplotype analysis of Ca2+-dependent K+ channel beta-1 subunit.

ABSTRACT: The large-conductance, Ca-dependent K channel plays a key role in the control of vascular tone. Variation in the gene encoding the beta-1 subunit of the Ca-dependent K channel (KCNMB1) has been reported to be associated with hypertension, however, variants in KCNMB1 have not been systematically characterized to date. In this study, we have performed the most comprehensive evaluation to date of single nucleotide polymorphisms in KCNMB1 using genomic DNA from 60 individuals of European, African and native American ancestry. We identified and characterized single nucleotide polymorphisms in the exons, intron/exon junctions, upstream region and 3' untranslated regions of KCNMB1 using denaturing high-performance liquid chromatography combined with direct DNA sequencing. A total of 25 single nucleotide polymorphisms in KCNMB1 were identified. Seven of the polymorphisms (28%) are novel single nucleotide polymorphisms not reported previously. Allele frequencies range from less than 1.7 to 50% and 19 single nucleotide polymorphisms had a minor allele frequency greater than 5%. A lack of strong linkage disequilibrium among the 25 single nucleotide polymorphisms was observed in all three race/ethnicity groups; therefore the identification of haplotype 'tag' single nucleotide polymorphisms for genetic association studies is not likely to be appropriate for KCNMB1. Multiple species comparative analysis and in-silico functional analysis were performed to identify potential functionally important single nucleotide polymorphisms within the gene. These data highlight that a tag single nucleotide polymorphism approach will not be appropriate for the study of genes such as KCNMB1, although potentially important functionally significant single nucleotide polymorphisms are suggested for future studies investigating the influence of this gene's variability on disease and drug response.

SUBMITTER: Gong Y

PROVIDER: S-EPMC2713575 | biostudies-literature | 2007 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Single nucleotide polymorphism discovery and haplotype analysis of Ca2+-dependent K+ channel beta-1 subunit.

Gong Yan Y Beitelshees Amber L AL Wessel Jennifer J Langaee Taimour Y TY Schork Nicholas J NJ Johnson Julie A JA

Pharmacogenetics and genomics 20070401 4

The large-conductance, Ca-dependent K channel plays a key role in the control of vascular tone. Variation in the gene encoding the beta-1 subunit of the Ca-dependent K channel (KCNMB1) has been reported to be associated with hypertension, however, variants in KCNMB1 have not been systematically characterized to date. In this study, we have performed the most comprehensive evaluation to date of single nucleotide polymorphisms in KCNMB1 using genomic DNA from 60 individuals of European, African an ...[more]

PMID: 17496725

Similar Datasets

Project description:BackgroundCurrent breeding approaches in potato rely almost entirely on phenotypic evaluations; molecular markers, with the exception of a few linked to disease resistance traits, are not widely used. Large-scale sequence datasets generated primarily through Sanger Expressed Sequence Tag projects are available from a limited number of potato cultivars and access to next generation sequencing technologies permits rapid generation of sequence data for additional cultivars. When coupled with the advent of high throughput genotyping methods, an opportunity now exists for potato breeders to incorporate considerably more genotypic data into their decision-making.ResultsTo identify a large number of Single Nucleotide Polymorphisms (SNPs) in elite potato germplasm, we sequenced normalized cDNA prepared from three commercial potato cultivars: 'Atlantic', 'Premier Russet' and 'Snowden'. For each cultivar, we generated 2 Gb of sequence which was assembled into a representative transcriptome of ~28-29 Mb for each cultivar. Using the Maq SNP filter that filters read depth, density, and quality, 575,340 SNPs were identified within these three cultivars. In parallel, 2,358 SNPs were identified within existing Sanger sequences for three additional cultivars, 'Bintje', 'Kennebec', and 'Shepody'. Using a stringent set of filters in conjunction with the potato reference genome, we identified 69,011 high confidence SNPs from these six cultivars for use in genotyping with the Infinium platform. Ninety-six of these SNPs were used with a BeadXpress assay to assess allelic diversity in a germplasm panel of 248 lines; 82 of the SNPs proved sufficiently informative for subsequent analyses. Within diverse North American germplasm, the chip processing market class was most distinct, clearly separated from all other market classes. The round white and russet market classes both include fresh market and processing cultivars. Nevertheless, the russet and round white market classes are more distant from each other than processing are from fresh market types within these two groups.ConclusionsThe genotype data generated in this study, albeit limited in number, has revealed distinct relationships among the market classes of potato. The SNPs identified in this study will enable high-throughput genotyping of germplasm and populations, which in turn will enable more efficient marker-assisted breeding efforts in potato.

Dataset Information

Single nucleotide polymorphism discovery and haplotype analysis of Ca2+-dependent K+ channel beta-1 subunit.

Publications

Single nucleotide polymorphism discovery and haplotype analysis of Ca2+-dependent K+ channel beta-1 subunit.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets