Know more

Our use of cookies

Cookies are a set of data stored on a user’s device when the user browses a web site. The data is in a file containing an ID number, the name of the server which deposited it and, in some cases, an expiry date. We use cookies to record information about your visit, language of preference, and other parameters on the site in order to optimise your next visit and make the site even more useful to you.

To improve your experience, we use cookies to store certain browsing information and provide secure navigation, and to collect statistics with a view to improve the site’s features. For a complete list of the cookies we use, download “Ghostery”, a free plug-in for browsers which can detect, and, in some cases, block cookies.

Ghostery is available here for free: https://www.ghostery.com/fr/products/

You can also visit the CNIL web site for instructions on how to configure your browser to manage cookie storage on your device.

In the case of third-party advertising cookies, you can also visit the following site: http://www.youronlinechoices.com/fr/controler-ses-cookies/, offered by digital advertising professionals within the European Digital Advertising Alliance (EDAA). From the site, you can deny or accept the cookies used by advertising professionals who are members.

It is also possible to block certain third-party cookies directly via publishers:

Cookie type

Means of blocking

Analytical and performance cookies

Realytics
Google Analytics
Spoteffects
Optimizely

Targeted advertising cookies

DoubleClick
Mediarithmics

The following types of cookies may be used on our websites:

Mandatory cookies

Functional cookies

Social media and advertising cookies

These cookies are needed to ensure the proper functioning of the site and cannot be disabled. They help ensure a secure connection and the basic availability of our website.

These cookies allow us to analyse site use in order to measure and optimise performance. They allow us to store your sign-in information and display the different components of our website in a more coherent way.

These cookies are used by advertising agencies such as Google and by social media sites such as LinkedIn and Facebook. Among other things, they allow pages to be shared on social media, the posting of comments, and the publication (on our site or elsewhere) of ads that reflect your centres of interest.

Our EZPublish content management system (CMS) uses CAS and PHP session cookies and the New Relic cookie for monitoring purposes (IP, response times).

These cookies are deleted at the end of the browsing session (when you log off or close your browser window)

Our EZPublish content management system (CMS) uses the XiTi cookie to measure traffic. Our service provider is AT Internet. This company stores data (IPs, date and time of access, length of the visit and pages viewed) for six months.

Our EZPublish content management system (CMS) does not use this type of cookie.

For more information about the cookies we use, contact INRA’s Data Protection Officer by email at cil-dpo@inra.fr or by post at:

INRA
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

INRA GABI Unit

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. 

Results

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.

Perspectives

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).

Valorisation

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.