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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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Published on: June 21, 2018

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.

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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.