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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Structural and functional impacts of copy number variations on the cattle genome

Authors
item LIU, GE
item BICKHART, DEREK

Submitted to: Lecture
Publication Type: Abstract Only
Publication Acceptance Date: June 18, 2013
Publication Date: October 8, 2013
Citation: Liu, G., Bickhart, D.M. 2013. Structural and functional impacts of copy number variations on the cattle genome (abstract). Lecture. p.3.

Technical Abstract: Although there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs), similar realizations for larger, more complex forms of genetic variation have just emerged. Several recent publications reveal that copy number variations (CNVs) are common and associated with cattle health and breed formation. Array based platforms, such as array comparative genomic hybridization (aCGH) and SNP arrays, indirectly assay CNVs, do not resolve the structure of the events and are limited to assaying sequence represented in the cattle genome reference sequence. Sequence-based resolution of CNV and the development of high throughput genotyping platforms are required to assess their association with economic traits. We have developed a general integrated framework to detect, classify and compare CNVs by jointly using existing NGS, aCGH and SNP genotyping data; we have applied it to cattle datasets and evaluated its performances through computational comparison and experimental validation; we also tested functional impacts of cattle CNVs by associating them with animal production and health traits. This project will also significantly improve annotation of the cattle reference genome by filling in novel sequence information. It will provide the second generation cattle CNV map (many events at base resolution) - a crucial resource for developing CNV genotyping platforms and cattle population sequencing projects.

Last Modified: 9/10/2014
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