Fleckvieh genome, Vanstein
Whole genome re-sequencing of a single Bos taurus animal for SNP discovery
Background: The approximately 2 million bovine SNPs available in dbSNP have mainly been identified in the Hereford breed by the bovine genome project and by sequencing reduced representation libraries of various breeds. To increase this resource, we used whole-genome re-sequencing of a single Fleckvieh bull.  Results: We generated 24 Gbases 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. 9360 of these SNPs cause non-synonymous substitutions within coding regions. We further identified 115.000 small indels. Comparison with the genotypes of the same animal generated on a 50k 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 oligonucleotide array data and genotypes determined for 196 randomly selected SNPs, was approximately 1%. Accounting for these detection rates, we estimated a nucleotide diversity of approximately 9.4 x 10-4 or 1 SNP per 1093 bp, which is in accordance with previous estimates. 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 minimal allele frequency (MAF) of 24.5%. The distribution of the minor allele frequency of tested SNPs was nearly uniform with 83% of the SNPs having a MAF 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 - identified more than 2 million novel SNPs providing a valuable resource for the construction of high density oligonucleotide arrays in the context of genome-wide association studies.