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24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay


GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

Bovine genome structure variations

Bovine genome structure variations
The variations between different genomes of the same species include anything from simple nucleotide polymorphisms (SNP and Indels) to larger structure variants (SV). This study is one of the first to identify the SV of the bovine genome from high-throughput sequencing data and then to identify their phenotypic effects.

Context and stakes

Structure variants (SV) are defined as genomic alterations (insertions, deletions, duplications, inversions and translocations) that affect the DNA segments in over 50 nucleotides. At the genome scale the SV are less frequent than small variants (SNP and indels) but concern an important part of the genome and have a greater impact on function and evolution. At the functionnal level, the SV impact every region and may therefore have an effect on the expression of certain genes and as a consequence on the corresponding phenotypes. The SV have been greatly studied in some species. In man for example, approximately 50% of solid tumors and 85% of the hematopoietic neoplasia are the direct consequences of SV. In fact, chimeric genes caused by SV are very frequent in some types of cancer. In cattle, however, SV have been very little studied. Most studies have used fluorescence analysis of SNP microarrays which does not allow mapping and provides only a rough characterization. More recent results obtained through whole genome sequencing (WGS) have begun to appear, but they remain limited by the number of individuals characterized with this tool. This study is the first performed in French breeds. 


This study allowed identifying 6426 putative SV from WGS for 62 bulls representing the three main French dairy breeds. These genomic variations affect DNA segments of more than 50 pairs of bases and correspond to 3138 deletions, 2227 insertions and 1061 tandem duplications.

The functional annotation of the regions containing these SV has allowed identifying 2415 variations affecting either whole genes or coding and/or regulating regions of genes. They therefore have a greater probability of affect gene expression and as a consequence having an effect on some important phenotypes.

An experimental validation was performed on 331 SV using a new high-throughput genotyping approach with a custom LD chip developed by our team. We were able to abtain good quality genotypes for 255 SV and amongst these 191 (75%) have been validated.

This study is a pangenomic analysis of SV in cattle and provides a new glance at the architecture of the bovine genome.


The analysis is currently being applicated to all the whole genome sequence data available for several hundred bulls representing a large number of dairy and beef cattle breeds in order to identify and characterize the SV, validate a large number of different experimental approaches and to study their effects on a large number of agronomically important traits through association analysis.

We have also expanded this work to other farm species for the study of SV in chicken as part of the Domestichick project coordinated by Michèle TIXIER-BOICHARD (UMR1313 – GABI).


Boussaha M, Esquerré D, Barbieri J, Djari A, Pinton A, Letaief R, Salin G, Escudié F, Roulet A, Fritz S, Samson F, Grohs C, Bernard M, Klopp C, Boichard D, Rocha D. Genome-wide study of structural variants in bovine Holstein, Montbéliarde and Normande dairy breeds. PLoS One. 2015, 10: e0135931. doi: 10.1371/journal.pone.0135931. PubMed PMID: 26317361.