WP4 - Novel approaches to reveal disease resistance (INRAE)
The overall objectives of WP4 is to establish new ways to interrogate the genomic and phenotypic basis for disease resistance in fishes, including by developing methods to enhance our understanding of and ability to measure immune cellular phenotypes and tools to functionally validate genomic regulatory elements responsible for host-defense responses. The work proposed exploits both in vivo and in vitro salmonid model systems and functional genomic investigations carried out at the tissue and cellular levels, and will provide many new methods for understanding immune mechanisms and cellular phenotypes underpinning susceptibility to bacterial and viral infection in fish.
Achieve a detailed functional annotation analysis of clonal rainbow trout lines with contrasted susceptibility to bacterial and viral infection.
Describe fish immune cell subsets for the first time using scRNA-Seq.
Validate genomic regions underlying immune responses via gene editing.
Links with other WPs
WP4 is complementary to WP3, as the data will provide insights into particular immune cell subtypes that may be responsible for functional-genomic responses recorded in the ImmunoMaps. Hence, there will be an extensive crosschecking of datasets between WP3 and WP4. WP4 interacts with other WPs where immune-relevant functional annotation is performed (WP3, WP5; which provide candidate genomic regions for functional validation, subgoal 4.3). WP4 interacts with WP6, as the functional annotation data will be run through comparative analysis pipelines.
WP1 - Functional annotation assays
WP2- Bioinformatics and data analysis
WP3 - Genomic basis of immune phenotypes
WP4 - Novel approaches to reveal disease resistance
WP5 - Exploiting genome functional annotation to enhance fish breeding
WP6 - Comparative analyses
WP7 - Dissemination, exploitation and communication
WP8 - Management and coordination
WP9 - Ethics Requirements