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Confirming single nucleotide polymorphisms from expressed sequence tag datasets derived from three cattle cDNA
Seung-Hwan Lee1, Eung-Woo Park, Yong-Min Cho
1Animal Genomics & Bioinformatics Division, National Livestock Research Institute, RDA, Suwon 441-350, Korea.
Journal of Biochemistry and Molecular Biology
|April 6, 2006
Summary
Researchers identified 201 candidate coding single nucleotide polymorphisms (cSNPs) in Hanwoo cattle using expressed sequence tags (ESTs). A high prediction rate (71%) suggests ESTs are valuable for rapid genetic marker discovery in cattle.
Area of Science:
- Genomics
- Animal Genetics
Background:
- The Hanwoo breed (Korean native cattle) is economically important.
- Genetic markers are crucial for improving livestock traits through marker-assisted selection.
Purpose of the Study:
- To identify candidate coding single nucleotide polymorphisms (cSNPs) in Hanwoo cattle using expressed sequence tags (ESTs).
- To assess the efficiency of SNP prediction from EST data for genetic marker development.
Main Methods:
- Assembling 7,600 ESTs from liver, M. longissimus dorsi, and intermuscular fat cDNA libraries using the Phrap assembler.
- Identifying candidate cSNPs using the Phred/Phrap/Polyphred/Consed pipeline.
- Verifying predicted cSNPs through BLASTX analysis and examining their location (coding regions, 3'-UTRs).
Main Results:
- Assembled 829 contigs from 7,600 ESTs.
- Identified 201 candidate cSNPs in 129 contigs, with transitions (69%) being more frequent than transversions (31%).
- Verified 12 out of 17 selected SNPs, with 5 identified as nonsynonymous, 5 as synonymous, and 2 in 3'-UTRs.
Conclusions:
- A high SNP prediction rate (71%) from a large EST database is achievable.
- EST data provides a rapid and efficient method for generating abundant cSNPs.
- Identified cSNPs can serve as valuable genetic markers for Hanwoo cattle improvement.