Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery

Stothard, Paul, Choi, Jung-Woo, Basu, Urmila, Sumner-Thomsen, Jennifer M., Meng, Yan, Liao, Xiaoping and Moore, Stephen S. (2011) Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics, 12 559: 1-14.


Author Stothard, Paul
Choi, Jung-Woo
Basu, Urmila
Sumner-Thomsen, Jennifer M.
Meng, Yan
Liao, Xiaoping
Moore, Stephen S.
Title Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2011-11
Sub-type Article (original research)
DOI 10.1186/1471-2164-12-559
Volume 12
Issue 559
Start page 1
End page 14
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2012
Language eng
Formatted 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 andHolstein 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.  
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Queensland Alliance for Agriculture and Food Innovation
 
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Created: Thu, 09 Feb 2012, 15:07:17 EST by Stephen Moore on behalf of Qld Alliance for Agriculture and Food Innovation