Nov 16, 2011

Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

BMC Genomics
Bujie ZhanChristian Bendixen

Abstract

Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes. We report the integration of the whole genome sequence of a single Holstein Friesian bull with data from single nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) array technologies to determine a comprehensive spectrum of genomic variation. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent (IBD) or in copy number variation (CNV) with results from SNP array genotyping. Coding insertions and deletions (indels) were found to be enriched for size in multiples of 3 and were located near the N- and C-termini of proteins. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural varia...Continue Reading

  • References91
  • Citations38

Citations

Mentioned in this Paper

Metabolic Process, Cellular
Real-Time Polymerase Chain Reaction
Genome-Wide Association Study
Short Interspersed Nucleotide Elements
Biochemical Pathway
DNA Copy Number Changes
Genome
Dopa-Responsive Dystonia
Firecrest
Murine

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