title: Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery.
abstract: BACKGROUND
  One of the goals of livestock genomics research is to identify the genetic differences responsible for variation in phenotypic traits, particularly those of economic importance. Characterizing the genetic variation in livestock species is an important step towards linking genes or genomic regions with phenotypes. The completion of the bovine genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of the genetic variations present in cattle. Here we describe the whole-genome resequencing of two Bos taurus bulls from distinct breeds for the purpose of identifying and annotating novel forms of genetic variation in cattle.
  
  
  RESULTS
  The genomes of a Black Angus bull and a Holstein bull were sequenced to 22-fold and 19-fold coverage, respectively, using the ABI SOLiD system. Comparisons of the sequences with the Btau4.0 reference assembly yielded 7 million single nucleotide polymorphisms (SNPs), 24% of which were identified in both animals. Of the total SNPs found in Holstein, Black Angus, and in both animals, 81%, 81%, and 75% respectively are novel. In-depth annotations of the data identified more than 16 thousand distinct non-synonymous SNPs (85% novel) between the two datasets. Alignments between the SNP-altered proteins and orthologues from numerous species indicate that many of the SNPs alter well-conserved amino acids. Several SNPs predicted to create or remove stop codons were also found. A comparison between the sequencing SNPs and genotyping results from the BovineHD high-density genotyping chip indicates a detection rate of 91% for homozygous SNPs and 81% for heterozygous SNPs. The false positive rate is estimated to be about 2% for both the Black Angus and Holstein SNP sets, based on follow-up genotyping of 422 and 427 SNPs, respectively. Comparisons of read depth between the two bulls along the reference assembly identified 790 putative copy-number variations (CNVs). Ten randomly selected CNVs, five genic and five non-genic, were successfully validated using quantitative real-time PCR. The CNVs are enriched for immune system genes and include genes that may contribute to lactation capacity. The majority of the CNVs (69%) were detected as regions with higher abundance in the Holstein bull.
  
  
  CONCLUSIONS
  Substantial genetic differences exist between the Black Angus and Holstein animals sequenced in this work and the Hereford reference sequence, and some of this variation is predicted to affect evolutionarily conserved amino acids or gene copy number. The deeply annotated SNPs and CNVs identified in this resequencing study can serve as useful genetic tools, and as candidates in searches for phenotype-altering DNA differences.
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
authors.forename: Jung-Woo
authors.initials: JW
authors.lastname: Choi
authors.forename: Urmila
authors.initials: U
authors.lastname: Basu
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Sumner-Thomson
authors.forename: Yan
authors.initials: Y
authors.lastname: Meng
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Liao
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Moore
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D056915:DNA Copy Number Variations; D016678:Genome; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques; D008297:Male; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
references.citation: Genome Res. 2009 Sep;19(9):1527-41
references.pmid: 19546169
references.citation: Genomics. 2006 Apr;87(4):527-33
references.pmid: 16469480
references.citation: BMC Genomics. 2009 Apr 24;10:180
references.pmid: 19393050
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Genome. 2010 Nov;53(11):876-83
references.pmid: 21076503
references.citation: Science. 2009 Apr 24;324(5926):522-8
references.pmid: 19390049
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6
references.pmid: 21045057
references.citation: Nat Rev Genet. 2009 Jun;10(6):381-91
references.pmid: 19448663
references.citation: Genome Res. 2008 Nov;18(11):1711-23
references.pmid: 18687881
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9
references.pmid: 21051339
references.citation: Bioinformatics. 2011 Aug 15;27(16):2300-1
references.pmid: 21697123
references.citation: Genome Res. 2010 May;20(5):693-703
references.pmid: 20212021
references.citation: BMC Genomics. 2010 Apr 09;11:232
references.pmid: 20377913
references.citation: PLoS Comput Biol. 2010 Sep 16;6(9):
references.pmid: 20862353
references.citation: Science. 2009 Apr 24;324(5926):528-32
references.pmid: 19390050
references.citation: J Anim Sci. 2009 Apr;87(14 Suppl):E3-10
references.pmid: 19028854
references.citation: BMC Bioinformatics. 2009 Mar 06;10:80
references.pmid: 19267900
references.citation: BMC Genomics. 2010 May 06;11:284
references.pmid: 20459598
references.citation: Genome Biol. 2009;10(4):R42
references.pmid: 19393038
references.citation: Nat Methods. 2010 May;7(5):365-71
references.pmid: 20440878
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W635-41
references.pmid: 16845089
references.citation: Mamm Genome. 2007 Jan;18(1):1-4
references.pmid: 17245610
references.citation: Genome Biol. 2009;10(8):R82
references.pmid: 19660108
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51
references.pmid: 21097890
references.citation: J Comput Biol. 2000 Feb-Apr;7(1-2):203-14
references.pmid: 10890397
references.citation: Hum Mutat. 2003 Jun;21(6):577-81
references.pmid: 12754702
references.citation: Nat Rev Genet. 2011 May;12(5):363-76
references.pmid: 21358748
references.citation: Nat Genet. 2009 Oct;41(10):1061-7
references.pmid: 19718026
references.citation: BMC Bioinformatics. 2009 Dec 15;10:421
references.pmid: 20003500
references.citation: PLoS Genet. 2006 Feb;2(2):e20
references.pmid: 16482228
references.citation: Nat Methods. 2008 Mar;5(3):247-52
references.pmid: 18297082
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W64-70
references.pmid: 20435677
references.citation: J Dairy Sci. 2006 Apr;89(4):1349-61
references.pmid: 16537966