Next generation sequencing of African and Indicine cattle to identify single nucleotide polymorphisms
W. Barris A , B. E. Harrison A , S. McWilliam A , R. J. Bunch A , M. E. Goddard B and W. Barendse A C
+ Author Affiliations
- Author Affiliations
C. R. C. for Beef Genetic Technologies
A CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia.
B Department of Primary Industries Victoria, 1 Park Drive, Bundoora, Vic. 3083, Australia.
C Corresponding author. Email: bill.barendse@csiro.au
Animal Production Science 52(3) 133-142 https://doi.org/10.1071/AN11095
Submitted: 1 June 2011 Accepted: 27 November 2011 Published: 19 January 2012
Journal Compilation © CSIRO Publishing 2012 Open Access CC BY-NC-ND
Abstract
We sequenced the genomes of a Brahman, an Africander and a Tuli bull because tropically adapted breeds of cattle have so far not been well characterised at the level of DNA variation. In excess of 16 Gb of Illumina GA-II sequence was obtained for each animal in the form of 75-bp paired-end reads, generating more than 6× coverage of each genome, and between 86.7 and 88.8% of the bases of each genome sequence was covered by one or more sequence reads. A total of 6.35 million single nucleotide polymorphisms (SNP) were discovered in the three animals, adding 3.56 million new SNP to dbSNP. The Brahman animal had nearly twice as many SNP as either the Tuli or the Africander. Comparing genome sequence to genotypic array data, genotype accuracy from sequencing was more than 98% for homozygotes that had at least six high quality sequence reads and for heterozygotes that had at least two high quality reads containing the alternative allele. Intergenic and intronic SNP were found at higher densities closer to coding sequences, and there was a reduction in numbers of SNP within 5 bp of a splice site, features consistent with genetic selection. On average, slightly more SNP per Mb, and slightly higher average reads per SNP per Mb, were found towards the ends of chromosomes, especially towards the telomeric end of the chromosome. At least one autosome in each animal showed a large stretch of homozygosity, the largest was 58 Mb long in the Tuli, although the animals are not known to have recent inbreeding.
Additional keywords: Africander, Brahman, cattle, genome, selection, sequence, Tuli.
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