P4048 Comparison of three methods to discover copy number variants in Nellore and Angus cattle. (1st September 2016)

• Record Type: Journal Article
• Authors: Xing, Y.; Gill, C. A.
• Is Part Of: Journal of animal science. Volume 94(2016)Supplement 4
• Page Start: 102
• Page End: 102
• Publication Date: 2016-09-01
• Subjects: Copy number variants -- CNV-seq -- gene ontology enrichment; Livestock -- Periodicals; Livestock; Electronic journals; Periodicals; 636.005
• DOI: 10.2527/jas2016.94supplement4102x
• Languages: English
• ISSNs: 0021-8812

Abstract

Abstract: Copy Number Variants (CNV) are insertions and deletions of 1 kb or larger in a genome that are present in a variable number of copies compared with a reference genome. Differential expression of genes, in part due to gene dosage effects, can affect phenotypic variation. Our objective was to discover CNV using whole genome sequences of the Nellore and Angus founders of our mapping population. Illumina paired-end 100 bp reads of seven Nellore ( Bos taurus indicus ) bulls and six Angus ( Bos taurus taurus ) cows (33–88x coverage) were aligned with BWA and GATK 3.2 to the UMD3.1 bovine assembly of a Hereford ( Bos taurus taurus ) cow. We compared CNV-seq, RAPTR-SV and BreakDancer for CNV discovery. CNV-seq identifies CNV based on differences in read depth after normalization for depth of coverage across the genome; one Angus cow was the reference individual for all pairwise comparisons. BreakDancer identifies CNV based on read pair information, and RAPTR-SV combines read pair and split read approaches for CNV discovery. CNV-seq and RAPTR-SV both detected insertions and deletions, whereas BreakDancer only detected deletions. Putative CNV regions (CNVR) were detected on all 29 autosomes and the X chromosome. CNV-seq was the most conservative detection method, and CNV counts per animal ranged from 141 to 1914. There were 492 CNVR found by all three applications. We used DAVID for CNVR gene ontology (GO) enrichment analysis and applied a within-category Benjamini-Hochberg correction to control the false discovery rate. Of the enriched GO terms in Nellore animals, 75% were enriched in Angus animals too. Enriched GO terms were olfactory transduction, phosphate metabolic process, MHC protein complex and nucleotide binding.