Deep whole genome sequencing of 62 bulls representing the three major dairy breeds in France was performed in order to investigate chromosomal alterations between individual samples across the genome.. GENOME-WIDE STUDY OF STRUCTURAL VARIANTS IN BOVINE HOLSTEIN, MONTBELIARDE AND NORMANDE DAIRY BREEDS

In this work, we performed a large scale study to investigate both small Indels ( 50 bp) in cattle by sequencing the whole-genome of 62 bulls from the three major dairy breeds in France (Holstein, Montbéliarde and Normande breeds). Genomic DNAs were extracted from peripheral venous blood or from semen, using the Wizard Genomic DNA Purification Kit (Promega, Charbonnières-les-Bains, France) or using a standard phenol-chloroform method, respectively. A quality control inspection of the purified DNA sample was performed by agarose gel electrophoresis. DNA concentration was then measured with a Nanodrop ND-100 instrument (Thermo Scientific, Ilkirch, France). Genomic libraries were subsequently prepared using the TruSeq DNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions. Libraries were then checked on an Agilent Technologies 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit and quantified by quantitative PCR with the QPCR NGS Library Quantification kit (Agilent Technologies, Massy, France). Libraries were finally used for 2×100 bp paired-end sequencing on an Illumina HiSeq2000 with a TruSeq SBS v3-HS Kit (Illumina).