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Discovery, validation and characterization of 1039 cattle single nucleotide polymorphisms
R Donthu1, D M Larkin, M P Heaton
1Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Animal Genetics
|December 5, 2009
Summary
Researchers identified 1039 validated single nucleotide polymorphisms (SNPs) in cattle, creating a valuable resource for genome-wide association studies and improving animal breeding through genetic analysis.
Area of Science:
- Genomics
- Animal Genetics
Background:
- Bovine genome assembly Btau 1.0 and BAC-end sequences were used to identify potential single nucleotide polymorphisms (SNPs).
- A comprehensive panel of 186 cattle DNA samples from 18 breeds was utilized for genotyping.
Purpose of the Study:
- To identify and validate a significant number of polymorphic single nucleotide polymorphisms (SNPs) in cattle.
- To create a valuable genetic resource for genome-wide association studies (GWAS) and animal breeding applications.
Main Methods:
- Comparison of repeat-masked BAC-end sequences with whole-genome shotgun contigs.
- Genotyping of identified SNPs on a diverse cattle breed panel.
- In silico mapping of validated SNPs to cattle chromosomes using Btau 4.0 assembly.
Main Results:
- Approximately 13,000 putative SNPs were initially identified.
- 1039 SNPs were validated as polymorphic, with 998 having a minor allele frequency > or =0.25.
- 974 validated SNPs were mapped to cattle chromosomes in Btau 4.0, averaging one SNP per 3 Mbp.
Conclusions:
- The 1039 validated SNPs represent a robust resource for cattle genomics.
- These SNPs will facilitate genome-wide association studies and enhance marker-assisted selection in animal breeding programs.
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