Towards the development of genomic tools to optimise selection in the rainbow trout

INRA scientists have shown that it is possible to exploit existing genomic resources in the rainbow trout in order to identify SNP genetic markers, which are of considerable value to analysing different traits.  These markers will enable the development of essential selection tools for the trout-rearing industry so that it can achieve gains in competitiveness and sustainability.

Rainbow trout. © INRA, MARIE Didier

The usefulness of genomic selection

Technological advances in the field of high-throughput genomics have enabled sequencing of the full genome of several livestock species (cattle, pigs, horses and chickens).  These sequencing projects have also led to the development of several hundreds of thousands of SNPs (Single Nucleotide Polymorphisms, or point mutations)..  With the advent of new genomic tools such as DNA arrays, there is now a tendency to select breeding animals that display valuable zootechnical performance based only on the sequence polymorphism of their DNA rather than on the performance of their progeny (see the article entitled "A new DNA chip to enable less costly genomic selection in dairy cattle").  These genomic data enable significant savings in time, are cost effective and facilitate the selection of traits that are difficult to observe or measure (for example, disease resistance).

The rainbow trout: from mRNA to SNP markers

As the most common farmed fish species, rainbow trout is of economic importance in both France and Europe. In addition to its commercial interest, rainbow trout is also a model species for a wide range of genome-related research activities.  It occupies a unique taxonomic position among fish, belonging to a family that is specific for having undergone recent whole genome duplication (WGD)..  This evolutionary history offers an opportunity, at different stages of divergence, to study the modes of evolution and rediploidisation in a recently duplicated genome, but partial duplication of the remaining genome seriously complicates standard molecular genetic approaches.  In particular, it may lead to confusion regarding variations between duplicated genomic regions (false SNPs) and variations within a given region (true SNPs).
Major efforts have enabled the development of genomic resources for this species, and sequencing of the complete genome is currently under way.  However,  sequencing of the rainbow trout genome has been performed using a doubled haploid homozygous DNA sample which hinders the identification of new SNPs. Therefore, the identification of SNP markers requires a specific approach.  The INRA scientists thus explored mutations detected during the sequencing of trout mRNA (genomic regions coding genes) using EST (Expressed Sequence Tag) databanks that had already been constituted and were available at a low cost.

A first step towards genomic tools in the trout

In the context of a research project funded by INRA, the scientists tried to identify and then validate SNPs from trout EST sequences available at the INRA bioinformatics platform, SIGENAE (see box).  A preliminary bioinformatics study performed by SIGENAE enabled the identification of approximately 40,000 putative SNPs, but it was anticipated that a proportion of these SNPs might be linked to artefacts, particularly because of the complex structure of the trout genome.  

To estimate the proportion of markers that could actually be exploited, it was essential to test the SNPs on a certain number of individuals.  After applying a succession of qualitative filters to enable pre-selection of the most probable SNPs, the scientists chose a "test" sample of 1152 SNPs.  They then verified the presence of these SNPs in the trout genome.  To achieve this, each of these SNPs was determined by genotyping a population of 480 trout from different genetic origins at the INRA genomics GET PlaGe core facility  using Illumina GoldenGate  Assay ®,.  A fraction of these SNPs could not be amplified (poor quality of the DNA fragments generated).  Approximately 608 genomic sites out of the remaining 958 proved to be non-informative, either because they were not polymorphic (identical sequence in all individuals) or because they corresponded to sequences arising from duplicated regions in the genome.  The remaining 350 genomic sites were confirmed as containing a validated SNP.

Contact(s)
Scientific contact(s):

Associated Division(s):
Attribute Type Value
node_id string 101415
parent_node_id string 232
main_node_id string 101415
contentobject_id string 94875
contentobject_version string 46
contentobject_is_published string 1
depth string 3
sort_field string 1
sort_order string 1
priority string 1
modified_subnode string 1499259538
path_string string '/1/2/232/101415/'
path_identification_string string 'sitedept/deptunite26'
remote_id string '6f946cb09ca61fe9d58b30886969541d'
is_hidden string 0
is_invisible string 0
name string 'Animal Genetics '
data_map array Array(33)
>seo object[eZContentObjectAttribute] Object
>title object[eZContentObjectAttribute] Object
>bloc_xml_introduction object[eZContentObjectAttribute] Object
>bloc_xml_presentation object[eZContentObjectAttribute] Object
>shortchapo object[eZContentObjectAttribute] Object
>zoom_news object[eZContentObjectAttribute] Object
>url object[eZContentObjectAttribute] Object
>mail_contact object[eZContentObjectAttribute] Object
>contact object[eZContentObjectAttribute] Object
>address object[eZContentObjectAttribute] Object
>robots object[eZContentObjectAttribute] Object
>metadescription object[eZContentObjectAttribute] Object
>centercode object[eZContentObjectAttribute] Object
>pathprefix object[eZContentObjectAttribute] Object
>display_twitterbar object[eZContentObjectAttribute] Object
>url_communitylink1 object[eZContentObjectAttribute] Object
>logo_communitylink1 object[eZContentObjectAttribute] Object
>url_communitylink2 object[eZContentObjectAttribute] Object
>logo_communitylink2 object[eZContentObjectAttribute] Object
>url_communitylink3 object[eZContentObjectAttribute] Object
>logo_communitylink3 object[eZContentObjectAttribute] Object
>url_communitylink4 object[eZContentObjectAttribute] Object
>logo_communitylink4 object[eZContentObjectAttribute] Object
>bloc_edito_intro object[eZContentObjectAttribute] Object
>bloc_edito_presentation object[eZContentObjectAttribute] Object
>jobdisplay object[eZContentObjectAttribute] Object
>visual object[eZContentObjectAttribute] Object
>credits object[eZContentObjectAttribute] Object
>mentions object[eZContentObjectAttribute] Object
>arborh object[eZContentObjectAttribute] Object
>extranet_link object[eZContentObjectAttribute] Object
>jobteaser object[eZContentObjectAttribute] Object
>urlteaser object[eZContentObjectAttribute] Object
object object[eZContentObject] Object
>id string 94875
>section_id string 1
>owner_id string 14
>contentclass_id string 50
>name string 'Animal Genetics '
>published string 1358170625
>modified string 1452781289
>current_version string 46
>status string 1
>remote_id string '9f05d84502c04d6f694847fe28baa97c'
>language_mask string 6
>initial_language_id string 2
>current object[eZContentObjectVersion] Object
>versions array Array(9)
>author_array array Array(3)
>class_name string 'Département : Site'
>content_class object[eZContentClass] Object
>contentobject_attributes array Array(33)
>owner object[eZContentObject] Object
>related_contentobject_array array Array(1)
>related_contentobject_count string 4
>reverse_related_contentobject_array array Array(0)
>reverse_related_contentobject_count string 2
>linked_contentobject_array array Array(0)
>linked_contentobject_count string 0
>reverse_linked_contentobject_array array Array(0)
>reverse_linked_contentobject_count string 2
>embedded_contentobject_array array Array(0)
>embedded_contentobject_count string 0
>reverse_embedded_contentobject_array array Array(0)
>reverse_embedded_contentobject_count string 0
>can_read boolean true
>can_pdf boolean true
>can_diff boolean false
>can_create boolean false
>can_create_class_list array Array(0)
>can_edit boolean false
>can_translate boolean false
>can_remove boolean false
>can_move boolean false
>can_move_from boolean false
>can_view_embed boolean false
>data_map array Array(33)
>grouped_data_map array Array(1)
>main_parent_node_id string 232
>assigned_nodes array Array(1)
>parent_nodes array Array(1)
>main_node_id string 101415
>main_node object[eZContentObjectTreeNode] Object
>default_language string 'eng-GB'
>content_action_list boolean false
>class_identifier string 'inra_departement'
>class_group_id_list array Array(1)
>match_ingroup_id_list boolean false
>current_language string 'eng-GB'
>current_language_object object[eZContentLanguage] Object
>initial_language object[eZContentLanguage] Object
>initial_language_code string 'fre-FR'
>available_languages array Array(1)
>language_codes array Array(1)
>language_js_array string '[{"locale":"eng-GB","name":"English (United Kingdom)"}]'
>languages array Array(1)
>all_languages array Array(2)
>can_edit_languages array Array(0)
>can_create_languages array Array(0)
>always_available integer 0
>allowed_assign_section_list array Array(1)
>allowed_assign_state_id_list array Array(1)
>allowed_assign_state_list array Array(0)
>state_id_array array Array(1)
>state_identifier_array array Array(1)
subtree array Array(28)
>0 object[eZContentObjectTreeNode] Object
>1 object[eZContentObjectTreeNode] Object
>2 object[eZContentObjectTreeNode] Object
>3 object[eZContentObjectTreeNode] Object
>4 object[eZContentObjectTreeNode] Object
>5 object[eZContentObjectTreeNode] Object
>6 object[eZContentObjectTreeNode] Object
>7 object[eZContentObjectTreeNode] Object
>8 object[eZContentObjectTreeNode] Object
>9 object[eZContentObjectTreeNode] Object
>10 object[eZContentObjectTreeNode] Object
>11 object[eZContentObjectTreeNode] Object
>12 object[eZContentObjectTreeNode] Object
>13 object[eZContentObjectTreeNode] Object
>14 object[eZContentObjectTreeNode] Object
>15 object[eZContentObjectTreeNode] Object
>16 object[eZContentObjectTreeNode] Object
>17 object[eZContentObjectTreeNode] Object
>18 object[eZContentObjectTreeNode] Object
>19 object[eZContentObjectTreeNode] Object
>20 object[eZContentObjectTreeNode] Object
>21 object[eZContentObjectTreeNode] Object
>22 object[eZContentObjectTreeNode] Object
>23 object[eZContentObjectTreeNode] Object
>24 object[eZContentObjectTreeNode] Object
>25 object[eZContentObjectTreeNode] Object
>26 object[eZContentObjectTreeNode] Object
>27 object[eZContentObjectTreeNode] Object
children array Array(8)
>0 object[eZContentObjectTreeNode] Object
>1 object[eZContentObjectTreeNode] Object
>2 object[eZContentObjectTreeNode] Object
>3 object[eZContentObjectTreeNode] Object
>4 object[eZContentObjectTreeNode] Object
>5 object[eZContentObjectTreeNode] Object
>6 object[eZContentObjectTreeNode] Object
>7 object[eZContentObjectTreeNode] Object
children_count string 8
view_count integer 0
contentobject_version_object object[eZContentObjectVersion] Object
>id string 342527
>contentobject_id string 94875
>creator_id string 95415
>version string 46
>status string 1
>created string 1452781190
>modified string 1452781287
>workflow_event_pos string 0
>user_id string 0
>language_mask string 7
>initial_language_id string 2
>creator object[eZContentObject] Object
>name string 'Génétique animale'
>version_name string 'Génétique animale'
>main_parent_node_id string 232
>contentobject_attributes array Array(33)
>related_contentobject_array array Array(1)
>reverse_related_object_list array Array(0)
>parent_nodes array Array(1)
>can_read boolean false
>can_remove boolean false
>data_map array Array(33)
>node_assignments array Array(1)
>contentobject object[eZContentObject] Object
>initial_language object[eZContentLanguage] Object
>language_list array Array(2)
>translation boolean false
>translation_list array Array(2)
>complete_translation_list array Array(2)
>temp_main_node object[eZContentObjectTreeNode] Object
sort_array array Array(1)
>0 array Array(2)
can_read boolean true
can_pdf boolean true
can_create boolean false
can_edit boolean false
can_hide boolean false
can_remove boolean false
can_move boolean false
can_move_from boolean false
can_add_location boolean false
can_remove_location boolean false
can_view_embed boolean false
is_main boolean true
creator object[eZContentObject] Object
>id string 95415
>section_id string 2
>owner_id string 14
>contentclass_id string 4
>name string 'Deretz Severine'
>published string 1358178906
>modified string 1477910105
>current_version string 2
>status string 1
>remote_id string '09060e970ff3c83c049b2ab588287fbb'
>language_mask string 3
>initial_language_id string 2
>current object[eZContentObjectVersion] Object
>versions array Array(2)
>author_array array Array(2)
>class_name string 'User'
>content_class object[eZContentClass] Object
>contentobject_attributes array Array(5)
>owner object[eZContentObject] Object
>related_contentobject_array array Array(0)
>related_contentobject_count string 0
>reverse_related_contentobject_array array Array(0)
>reverse_related_contentobject_count string 0
>linked_contentobject_array array Array(0)
>linked_contentobject_count string 0
>reverse_linked_contentobject_array array Array(0)
>reverse_linked_contentobject_count string 0
>embedded_contentobject_array array Array(0)
>embedded_contentobject_count string 0
>reverse_embedded_contentobject_array array Array(0)
>reverse_embedded_contentobject_count string 0
>can_read boolean false
>can_pdf boolean false
>can_diff boolean false
>can_create boolean false
>can_create_class_list array Array(0)
>can_edit boolean false
>can_translate boolean false
>can_remove boolean false
>can_move boolean false
>can_move_from boolean false
>can_view_embed boolean false
>data_map array Array(5)
>grouped_data_map array Array(1)
>main_parent_node_id string 312
>assigned_nodes array Array(3)
>parent_nodes array Array(3)
>main_node_id string 101973
>main_node object[eZContentObjectTreeNode] Object
>default_language string 'eng-GB'
>content_action_list boolean false
>class_identifier string 'user'
>class_group_id_list array Array(1)
>match_ingroup_id_list boolean false
>current_language string 'fre-FR'
>current_language_object object[eZContentLanguage] Object
>initial_language object[eZContentLanguage] Object
>initial_language_code string 'fre-FR'
>available_languages array Array(0)
>language_codes array Array(0)
>language_js_array boolean false
>languages array Array(0)
>all_languages array Array(1)
>can_edit_languages array Array(0)
>can_create_languages array Array(0)
>always_available integer 1
>allowed_assign_section_list array Array(1)
>allowed_assign_state_id_list array Array(1)
>allowed_assign_state_list array Array(0)
>state_id_array array Array(1)
>state_identifier_array array Array(1)
path_with_names string 'sitedept/deptunite26'
path array Array(2)
>0 object[eZContentObjectTreeNode] Object
>1 object[eZContentObjectTreeNode] Object
path_array array Array(4)
>0 integer 1
>1 integer 2
>2 integer 232
>3 integer 101415
parent object[eZContentObjectTreeNode] Object
>node_id string 232
>parent_node_id string 2
>main_node_id string 232
>contentobject_id string 219
>contentobject_version string 64
>contentobject_is_published string 1
>depth string 2
>sort_field string 9
>sort_order string 1
>priority string 2
>modified_subnode string 1513094126
>path_string string '/1/2/232/'
>path_identification_string string 'sitedept'
>remote_id string '702cee6c5bb3a0f2459eb4705cbf71aa'
>is_hidden string 0
>is_invisible string 0
>name string 'INRA Divisions'
>data_map array Array(23)
>object object[eZContentObject] Object
>subtree array Array(835)
>children array Array(17)
>children_count string 17
>view_count integer 0
>contentobject_version_object object[eZContentObjectVersion] Object
>sort_array array Array(1)
>can_read boolean true
>can_pdf boolean true
>can_create boolean false
>can_edit boolean false
>can_hide boolean false
>can_remove boolean false
>can_move boolean false
>can_move_from boolean false
>can_add_location boolean false
>can_remove_location boolean false
>can_view_embed boolean false
>is_main boolean true
>creator object[eZContentObject] Object
>path_with_names string 'sitedept'
>path array Array(1)
>path_array array Array(3)
>parent object[eZContentObjectTreeNode] Object
>url string 'sitedept'
>url_alias string 'sitedept'
>class_identifier string 'inra_site_departements'
>class_name string 'Départements : Dispatch'
>hidden_invisible_string string '-/-'
>hidden_status_string string 'Visible'
>classes_js_array string '[{"classID":57,"name":"Actualit\u00e9"},{"classID":131,"name":"Annuaire : Rubrique"},{"classID":16,"name":"Article"},{"classID":17,"name":"Article (main-page)"},{"classID":18,"name":"Article (sub-page)"},{"classID":42,"name":"Banner"},{"classID":19,"name":"Blog"},{"classID":81,"name":"Blog : Billet"},{"classID":101,"name":"Blog : Billet marque blanche"},{"classID":62,"name":"Blog : Blog"},{"classID":99,"name":"Blog : Blog marque blanche"},{"classID":82,"name":"Blog : Rubrique additionnelle"},{"classID":20,"name":"Blog post"},{"classID":127,"name":"Br\u00e8ve"},{"classID":60,"name":"Carrousel : Actu de carrousel"},{"classID":143,"name":"Carrousel : Diapositive autonome"},{"classID":168,"name":"Carrousels"},{"classID":56,"name":"Centre : Site"},{"classID":94,"name":"Centres : Dispatch"},{"classID":13,"name":"Comment"},{"classID":50,"name":"D\u00e9partement : Site"},{"classID":95,"name":"D\u00e9partements : Dispatch"},{"classID":71,"name":"Digital Asset (Media)"},{"classID":24,"name":"Documentation page"},{"classID":154,"name":"Dossier"},{"classID":116,"name":"Dossier 'Parutions'"},{"classID":76,"name":"Dossier 'Quizs'"},{"classID":169,"name":"Dossier actu secondaire"},{"classID":89,"name":"Ev\u00e9nement"},{"classID":88,"name":"Ev\u00e9nements : Racine"},{"classID":40,"name":"Event"},{"classID":41,"name":"Event calendar"},{"classID":22,"name":"Feedback form"},{"classID":28,"name":"File"},{"classID":29,"name":"Flash"},{"classID":1,"name":"Folder"},{"classID":37,"name":"Forum"},{"classID":39,"name":"Forum reply"},{"classID":38,"name":"Forum topic"},{"classID":43,"name":"Forums"},{"classID":23,"name":"Frontpage"},{"classID":35,"name":"Gallery"},{"classID":36,"name":"Geo Article"},{"classID":145,"name":"Glossaire : Mot"},{"classID":30,"name":"Image"},{"classID":25,"name":"Infobox"},{"classID":130,"name":"Instit : Fiche Annuaire"},{"classID":140,"name":"Instit : Nous trouver"},{"classID":48,"name":"Instit : Racine"},{"classID":133,"name":"Instit : Rubrique 'Actu'"},{"classID":139,"name":"Instit : Th\u00e8me 'Annuaire'"},{"classID":134,"name":"Instit : Th\u00e8me 'Missions'"},{"classID":137,"name":"Instit : Th\u00e8me 'Organisation'"},{"classID":135,"name":"Instit : Th\u00e8me 'Rep\u00e8res'"},{"classID":136,"name":"Instit : Th\u00e8me 'Strat\u00e9gie'"},{"classID":46,"name":"Kiosque : Racine"},{"classID":31,"name":"Link"},{"classID":201,"name":"Logo"},{"classID":72,"name":"Magazine"},{"classID":142,"name":"Mediath\u00e8que : Mot cl\u00e9"},{"classID":149,"name":"Mediath\u00e8que : Playlist"},{"classID":52,"name":"Mediath\u00e8que : Racine"},{"classID":150,"name":"Mediath\u00e8que : Rubrique 'Mots cl\u00e9s'"},{"classID":148,"name":"Mediath\u00e8que : Rubrique 'Playlist'"},{"classID":141,"name":"Mediath\u00e8que : Rubrique 'Zoom'"},{"classID":199,"name":"Mediath\u00e8que : Rubrique simple"},{"classID":121,"name":"M\u00e9taprogramme : Site"},{"classID":96,"name":"M\u00e9taprogrammes : Dispatch"},{"classID":161,"name":"Mon Compte"},{"classID":124,"name":"Mon Compte : Utilisateur Front"},{"classID":26,"name":"Multicalendar"},{"classID":119,"name":"Newsletter : Abonn\u00e9"},{"classID":104,"name":"Newsletter : Bloc s\u00e9l\u00e9ction"},{"classID":105,"name":"Newsletter : Bloc texte"},{"classID":103,"name":"Newsletter : Campagne simple"},{"classID":102,"name":"Newsletter : Campagne sp\u00e9ciale"},{"classID":120,"name":"Newsletter : Dossier 'Abonn\u00e9s'"},{"classID":122,"name":"Newsletter : Dossier 'D\u00e9sinscrits'"},{"classID":125,"name":"Newsletter : Dossier 'Entreprises'"},{"classID":126,"name":"Newsletter : Entreprise"},{"classID":100,"name":"Newsletter : Newsletter"},{"classID":92,"name":"Parution"},{"classID":27,"name":"Poll"},{"classID":47,"name":"Portail : Canal"},{"classID":45,"name":"Portail : Racine"},{"classID":53,"name":"Portail : Th\u00e8me"},{"classID":185,"name":"Portrait"},{"classID":163,"name":"Portrait Old"},{"classID":87,"name":"Presse : Accueil public"},{"classID":108,"name":"Presse : Biographie"},{"classID":91,"name":"Presse : Communiqu\u00e9"},{"classID":118,"name":"Presse : Dossier 'Biographies'"},{"classID":112,"name":"Presse : Dossier 'Communiqu\u00e9s'"},{"classID":115,"name":"Presse : Dossier 'Dossiers de presse'"},{"classID":203,"name":"Presse : Dossier 'Kits de presse'"},{"classID":107,"name":"Presse : Dossier de presse"},{"classID":63,"name":"Presse : Inscription"},{"classID":205,"name":"Presse : Kit de presse"},{"classID":51,"name":"Presse : Racine"},{"classID":21,"name":"Product"},{"classID":32,"name":"Quicktime"},{"classID":73,"name":"Quiz : Accueil"},{"classID":74,"name":"Quiz : Question"},{"classID":195,"name":"Quiz : question - r\u00e9ponse"},{"classID":75,"name":"Quiz : R\u00e9ponse"},{"classID":69,"name":"Racine"},{"classID":34,"name":"Real video"},{"classID":179,"name":"RH : Annonce permanente"},{"classID":176,"name":"RH : Annonce temporaire"},{"classID":181,"name":"RH : Article simple"},{"classID":172,"name":"RH : Campagne permanente"},{"classID":180,"name":"RH : Campagne temporaire"},{"classID":207,"name":"RH : Connexion Espagnole"},{"classID":187,"name":"RH : Discipline scientifique"},{"classID":193,"name":"RH : Domaine professionnel"},{"classID":165,"name":"RH : dossier 'Portraits'"},{"classID":177,"name":"RH : Dossier Reportages"},{"classID":183,"name":"RH : Fichier description"},{"classID":184,"name":"RH : Fichier inscription"},{"classID":178,"name":"RH : Folder annonces"},{"classID":197,"name":"RH : mobilit\u00e9 internationale"},{"classID":171,"name":"RH : Proc\u00e9dure"},{"classID":49,"name":"RH : Racine"},{"classID":175,"name":"RH : R\u00e9gion"},{"classID":167,"name":"RH : Rubrique"},{"classID":164,"name":"RH : Rubrique 'Actu'"},{"classID":170,"name":"RH : Rubrique emploi"},{"classID":174,"name":"RH : textes candidatures"},{"classID":189,"name":"RH : Type d'annonce"},{"classID":191,"name":"RH : Type nature de contrat"},{"classID":106,"name":"RSS : Flux"},{"classID":129,"name":"Rubrique texte simple"},{"classID":146,"name":"SEO : Robots txt"},{"classID":147,"name":"SEO : Sitemap xml"},{"classID":151,"name":"SEO : Valeurs par d\u00e9faut"},{"classID":44,"name":"Silverlight"},{"classID":166,"name":"Sites : Rubrique"},{"classID":33,"name":"Windows media"},{"classID":182,"name":"Xiti : Identifiants Home"}]'
>is_container string 1
url string 'sitedept/deptunite26'
url_alias string 'sitedept/deptunite26'
class_identifier string 'inra_departement'
class_name string 'Département : Site'
hidden_invisible_string string '-/-'
hidden_status_string string 'Visible'
classes_js_array string '[{"classID":57,"name":"Actualit\u00e9"},{"classID":131,"name":"Annuaire : Rubrique"},{"classID":16,"name":"Article"},{"classID":17,"name":"Article (main-page)"},{"classID":18,"name":"Article (sub-page)"},{"classID":42,"name":"Banner"},{"classID":19,"name":"Blog"},{"classID":81,"name":"Blog : Billet"},{"classID":101,"name":"Blog : Billet marque blanche"},{"classID":62,"name":"Blog : Blog"},{"classID":99,"name":"Blog : Blog marque blanche"},{"classID":82,"name":"Blog : Rubrique additionnelle"},{"classID":20,"name":"Blog post"},{"classID":127,"name":"Br\u00e8ve"},{"classID":60,"name":"Carrousel : Actu de carrousel"},{"classID":143,"name":"Carrousel : Diapositive autonome"},{"classID":168,"name":"Carrousels"},{"classID":56,"name":"Centre : Site"},{"classID":94,"name":"Centres : Dispatch"},{"classID":13,"name":"Comment"},{"classID":50,"name":"D\u00e9partement : Site"},{"classID":95,"name":"D\u00e9partements : Dispatch"},{"classID":71,"name":"Digital Asset (Media)"},{"classID":24,"name":"Documentation page"},{"classID":154,"name":"Dossier"},{"classID":116,"name":"Dossier 'Parutions'"},{"classID":76,"name":"Dossier 'Quizs'"},{"classID":169,"name":"Dossier actu secondaire"},{"classID":89,"name":"Ev\u00e9nement"},{"classID":88,"name":"Ev\u00e9nements : Racine"},{"classID":40,"name":"Event"},{"classID":41,"name":"Event calendar"},{"classID":22,"name":"Feedback form"},{"classID":28,"name":"File"},{"classID":29,"name":"Flash"},{"classID":1,"name":"Folder"},{"classID":37,"name":"Forum"},{"classID":39,"name":"Forum reply"},{"classID":38,"name":"Forum topic"},{"classID":43,"name":"Forums"},{"classID":23,"name":"Frontpage"},{"classID":35,"name":"Gallery"},{"classID":36,"name":"Geo Article"},{"classID":145,"name":"Glossaire : Mot"},{"classID":30,"name":"Image"},{"classID":25,"name":"Infobox"},{"classID":130,"name":"Instit : Fiche Annuaire"},{"classID":140,"name":"Instit : Nous trouver"},{"classID":48,"name":"Instit : Racine"},{"classID":133,"name":"Instit : Rubrique 'Actu'"},{"classID":139,"name":"Instit : Th\u00e8me 'Annuaire'"},{"classID":134,"name":"Instit : Th\u00e8me 'Missions'"},{"classID":137,"name":"Instit : Th\u00e8me 'Organisation'"},{"classID":135,"name":"Instit : Th\u00e8me 'Rep\u00e8res'"},{"classID":136,"name":"Instit : Th\u00e8me 'Strat\u00e9gie'"},{"classID":46,"name":"Kiosque : Racine"},{"classID":31,"name":"Link"},{"classID":201,"name":"Logo"},{"classID":72,"name":"Magazine"},{"classID":142,"name":"Mediath\u00e8que : Mot cl\u00e9"},{"classID":149,"name":"Mediath\u00e8que : Playlist"},{"classID":52,"name":"Mediath\u00e8que : Racine"},{"classID":150,"name":"Mediath\u00e8que : Rubrique 'Mots cl\u00e9s'"},{"classID":148,"name":"Mediath\u00e8que : Rubrique 'Playlist'"},{"classID":141,"name":"Mediath\u00e8que : Rubrique 'Zoom'"},{"classID":199,"name":"Mediath\u00e8que : Rubrique simple"},{"classID":121,"name":"M\u00e9taprogramme : Site"},{"classID":96,"name":"M\u00e9taprogrammes : Dispatch"},{"classID":161,"name":"Mon Compte"},{"classID":124,"name":"Mon Compte : Utilisateur Front"},{"classID":26,"name":"Multicalendar"},{"classID":119,"name":"Newsletter : Abonn\u00e9"},{"classID":104,"name":"Newsletter : Bloc s\u00e9l\u00e9ction"},{"classID":105,"name":"Newsletter : Bloc texte"},{"classID":103,"name":"Newsletter : Campagne simple"},{"classID":102,"name":"Newsletter : Campagne sp\u00e9ciale"},{"classID":120,"name":"Newsletter : Dossier 'Abonn\u00e9s'"},{"classID":122,"name":"Newsletter : Dossier 'D\u00e9sinscrits'"},{"classID":125,"name":"Newsletter : Dossier 'Entreprises'"},{"classID":126,"name":"Newsletter : Entreprise"},{"classID":100,"name":"Newsletter : Newsletter"},{"classID":92,"name":"Parution"},{"classID":27,"name":"Poll"},{"classID":47,"name":"Portail : Canal"},{"classID":45,"name":"Portail : Racine"},{"classID":53,"name":"Portail : Th\u00e8me"},{"classID":185,"name":"Portrait"},{"classID":163,"name":"Portrait Old"},{"classID":87,"name":"Presse : Accueil public"},{"classID":108,"name":"Presse : Biographie"},{"classID":91,"name":"Presse : Communiqu\u00e9"},{"classID":118,"name":"Presse : Dossier 'Biographies'"},{"classID":112,"name":"Presse : Dossier 'Communiqu\u00e9s'"},{"classID":115,"name":"Presse : Dossier 'Dossiers de presse'"},{"classID":203,"name":"Presse : Dossier 'Kits de presse'"},{"classID":107,"name":"Presse : Dossier de presse"},{"classID":63,"name":"Presse : Inscription"},{"classID":205,"name":"Presse : Kit de presse"},{"classID":51,"name":"Presse : Racine"},{"classID":21,"name":"Product"},{"classID":32,"name":"Quicktime"},{"classID":73,"name":"Quiz : Accueil"},{"classID":74,"name":"Quiz : Question"},{"classID":195,"name":"Quiz : question - r\u00e9ponse"},{"classID":75,"name":"Quiz : R\u00e9ponse"},{"classID":69,"name":"Racine"},{"classID":34,"name":"Real video"},{"classID":179,"name":"RH : Annonce permanente"},{"classID":176,"name":"RH : Annonce temporaire"},{"classID":181,"name":"RH : Article simple"},{"classID":172,"name":"RH : Campagne permanente"},{"classID":180,"name":"RH : Campagne temporaire"},{"classID":207,"name":"RH : Connexion Espagnole"},{"classID":187,"name":"RH : Discipline scientifique"},{"classID":193,"name":"RH : Domaine professionnel"},{"classID":165,"name":"RH : dossier 'Portraits'"},{"classID":177,"name":"RH : Dossier Reportages"},{"classID":183,"name":"RH : Fichier description"},{"classID":184,"name":"RH : Fichier inscription"},{"classID":178,"name":"RH : Folder annonces"},{"classID":197,"name":"RH : mobilit\u00e9 internationale"},{"classID":171,"name":"RH : Proc\u00e9dure"},{"classID":49,"name":"RH : Racine"},{"classID":175,"name":"RH : R\u00e9gion"},{"classID":167,"name":"RH : Rubrique"},{"classID":164,"name":"RH : Rubrique 'Actu'"},{"classID":170,"name":"RH : Rubrique emploi"},{"classID":174,"name":"RH : textes candidatures"},{"classID":189,"name":"RH : Type d'annonce"},{"classID":191,"name":"RH : Type nature de contrat"},{"classID":106,"name":"RSS : Flux"},{"classID":129,"name":"Rubrique texte simple"},{"classID":146,"name":"SEO : Robots txt"},{"classID":147,"name":"SEO : Sitemap xml"},{"classID":151,"name":"SEO : Valeurs par d\u00e9faut"},{"classID":44,"name":"Silverlight"},{"classID":166,"name":"Sites : Rubrique"},{"classID":33,"name":"Windows media"},{"classID":182,"name":"Xiti : Identifiants Home"}]'
is_container string 1
Animal Genetics
Associated Centre(s):
Jouy-en-Josas

The SIGENAE Platform

The SIGENAE platform centralizes data harvested during the partial or total sequencing of transcriptomes from six livestock species (cattle, pigs, rabbit, sheep, chicken, trout).  This platform was set up in the context of the AGENAE Scientific Interest Group (Groupement d'Intérêt Scientifique AGENAE - Analyse du GENome des Animaux d'Elevage, or Analysis of the Genome of Farmed Livestock). The GIS AGENAE brings together researchers from CIRAD and INRA as well as representatives from the different sectors concerned.  Created in 2002 for a period of 5 years (and renewed in 2008), this GIS has enabled some major discoveries, notably in genomics, in species of importance to livestock farming in France.
For more information:
http://www.sigenae.org
http://www.agenae.fr/

The Get-PlaGe core facility

Get-PlaGe is a core facility that provides both the private and public scientific community with state-of-the-art technologies and expertise in next generation sequencing, genotyping and transcriptomics. This facility was set up by the INRA Animal Genetics Division and the Toulouse Midi-Pyrénées Genopole (http://www.genotoul.fr/). Get-PlaGe forms part of the national genomic platform infrastructure “France Genomique”, supported by a French “Investissements d’Avenir” (Investments for the Future) grant, created to optimize and strengthen French capacity in the fields of high-throughput genomics and related bioinformatics.
For more information:
http://www.genotoul.fr/

for further information

  • Boussaha Mekki, Guyomard René, Cabau Cédric, Esquerré Diane, Quillet Edwige. Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout". 2012  BMC Genomics. 13, 238