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Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery

Sebastian H Eck1, Anna Benet-Pagès1, Krzysztof Flisikowski2, Thomas Meitinger13, Ruedi Fries2 and Tim M Strom13*

Author Affiliations

1 Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr., 85764 Neuherberg, Germany

2 Lehrstuhl für Tierzucht, Technische Universität München, Hochfeldweg, 85354 Freising-Weihenstephan, Germany

3 Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Trogerstr., 81675 München, Germany

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Genome Biology 2009, 10:R82  doi:10.1186/gb-2009-10-8-r82

Published: 6 August 2009

Abstract

Background

The majority of the 2 million bovine single nucleotide polymorphisms (SNPs) currently available in dbSNP have been identified in a single breed, Hereford cattle, during the bovine genome project. In an attempt to evaluate the variance of a second breed, we have produced a whole genome sequence at low coverage of a single Fleckvieh bull.

Results

We generated 24 gigabases of sequence, mainly using 36-bp paired-end reads, resulting in an average 7.4-fold sequence depth. This coverage was sufficient to identify 2.44 million SNPs, 82% of which were previously unknown, and 115,000 small indels. A comparison with the genotypes of the same animal, generated on a 50 k oligonucleotide chip, revealed a detection rate of 74% and 30% for homozygous and heterozygous SNPs, respectively. The false positive rate, as determined by comparison with genotypes determined for 196 randomly selected SNPs, was approximately 1.1%. We further determined the allele frequencies of the 196 SNPs in 48 Fleckvieh and 48 Braunvieh bulls. 95% of the SNPs were polymorphic with an average minor allele frequency of 24.5% and with 83% of the SNPs having a minor allele frequency larger than 5%.

Conclusions

This work provides the first single cattle genome by next-generation sequencing. The chosen approach - low to medium coverage re-sequencing - added more than 2 million novel SNPs to the currently publicly available SNP resource, providing a valuable resource for the construction of high density oligonucleotide arrays in the context of genome-wide association studies.