ARS | Publication request: Mapping cattle copy number variation by population-scale genome sequencing

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: May 1, 2012
Publication Date: July 15, 2012
Citation: Liu, G. 2012. Mapping cattle copy number variation by population-scale genome sequencing. Meeting Abstract. p. 146.

Technical Abstract: Copy number variation (CNV) is abundant in livestock, differing from SNPs in extent, origin and functional impact. Despite progress in CNV discovery, the nucleotide resolution architecture of most CNVs remains elusive. As a pilot population study of cattle CNV, we sequenced 100 representative cattle at 4 to 10-fold coverage. This panel comprises both dairy and beef breeds such as Holstein, Jersey, Angus, Brahman, Limosin, Nelore, Gir and others. We evaluated a dozen of screen methods developed by the 1000 Human Genomes Project. These approaches included read pair (RP) mapping, read depth (RD) analysis, split read (SR) alignment, assembly of sequence reads (AS) and hybrid approaches integrating RP and RD features (PD). After customized and optimized for cattle, our best-performing RD (mrsFAST+WSSD) and PD (Genome STRiP) pipelines generate thousands of deletions and other CNVs, including insertions and tandem duplications. We further confirmed selected events with complementary CNV discovery approaches (high density CGH and SNP arrays) and experimental validations (PCR and FISH). With the price of next generation sequencing dropping, the genomes of influential livestock around the world will be generated. Our analytical framework and high resolution CNV map will serve as a resource for these sequencing-based comparative genomic studies. Combining with SNPs, CNVs in their haplotype contexts will support genome-assisted animal selection studies.