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Updated: Jul 17, 2026
05:53
Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
BcSNPdb: bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci.
Sunjin Moon1, Hyoung Doo Shin, Hyun Sub Cheong
1Laboratory of Bioinformatics and Population Genetics, School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea.
Journal of Biochemistry and Molecular Biology
|January 25, 2007
Summary
Researchers identified thousands of bovine single nucleotide polymorphisms (SNPs) to aid in mapping quantitative trait loci (QTL). These SNPs are valuable resources for understanding genetic variations influencing economically important traits in cattle.
Area of Science:
- Genomics
- Animal Genetics
- Bioinformatics
Background:
- Fine mapping of bovine quantitative trait loci (QTL) is crucial for understanding economically important traits.
- Identifying single nucleotide polymorphisms (SNPs) within coding regions is essential for precise genetic analysis.
Purpose of the Study:
- To identify and characterize bovine SNPs in coding regions for QTL fine mapping.
- To develop a comprehensive database of bovine SNPs linked to QTL information.
Main Methods:
- In silico analysis of 692,763 bovine SNPs from UniGene clusters.
- Experimental validation of candidate SNPs through genotyping in 186 animals across 14 breeds.
- Development of a program for identifying non-synonymous SNPs (nsSNPs) and correcting frameshift errors.
Main Results:
- Identified 53,446 candidate SNPs with a depth >3.
- Validated 43% of randomly selected candidate SNPs with frequencies ranging from 0.009 to 0.498.
- Discovered 17,735 nsSNPs using a novel coding region identification program.
- Integrated SNP and QTL data into the bovine SNP database, BcSNPdb, featuring 43 quantitative traits.
Conclusions:
- The identified SNPs provide valuable resources for genomic variation studies in cattle.
- These SNPs facilitate the exploitation of genetic variations influencing economically and agriculturally important traits in cows.
- BcSNPdb serves as a centralized resource for bovine genetic research and breeding applications.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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