Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds

PloS One
Mekki BoussahaDominique Rocha

Abstract

High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant reg...Continue Reading

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Mar 26, 2016·Frontiers in Genetics·Mikolaj M RaszekGraham S Plastow
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Methods Mentioned

BETA
electrophoresis
PCR
genotyping
chip
PCA

Software Mentioned

Genome Analysis Tool Kit
UnifiedGenotyer
Ensembl Biomart
- UnifiedGenotyper
pca
R package ade4
Biomart
BWA
dudi
Picard

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