Acronym NA
Category
Aquaculture
Title Breeding for disease resistance in Atlantic salmon in the genome era: novel application of genomic tools and high resolution phenotypes Programme National Programme
Instrument (FP6)
Contact Type (FP7)
Strand (Interreg)
NA
Theme (FP7)
Activity Area (FP6)
Regional Area (Interreg)
Action (COST)
NA
Specific Programme (FP7)
NA
Funding source National Coordinator Hooman Moghadam Coordinator email NA
Coordinator institution
NOFIMA - Norwegian Institute of Food, Fisheries and Aquaculture Research (Norway)
Institutions involved
NA
Start year 2016 End year 2020 Funding (€) € 870,500 Website https://prosjektbanken.forskningsradet.no/project/FORISS/254880?Kilde=FORISS&distribution=Ar&chart=bar&calcType=funding&Sprak=no&sortBy=date&sortOrder=desc&resultCount=30&offset=0&Prosjektleder=Nicholas+Robinson Summary Disease resistance in aquaculture is in many cases a highly complex trait, with resistance and tolerance sometimes poorly defined. In this study, we plan to use high resolution qPCR based gene expression tests of host immune response genes as high resolution phenotypes in a controlled challenge tests for salmonid alphavirus, a pathogen causing pancreas disease (PD) that causes major losses to the industry from both mortality and secondary effects. Using families from a commercial breeding program, we will investigate the genetic correlation between a simple binary dead/alive phenotype and immune response parameters measured by qPCR in a mixed intraperitoneal and cohabitant challenge scenario. We will use RNA-seq to analyse whole transcriptome responses of fish from families that have known high and low breeding values for PD resistance, and we will perform an integrated analysis of methylome and transcriptome to even more deeply investigate the architecture of PD resistance. Opportunistic sampling of field outbreaks of PD, CMS and HSMI from industry partners will be carried out in parallel, and a large set of samples genotyped using a 57K SNP array to estimate heritability and perform GWAS for resistance, comparing results to the controlled challenge tests. Finally, we will take the findings from multiple GWAS analyses together with the transcriptomic and metholome data to select a set of SNPs for PD resistance that have been enriched with functional variants and potential causative mutations. These SNPs will be genotyped using a novel genotyping-by-sequencing approach using amplicon based sequencing, and genomic breeding value accuracies validated using challenge test data and compared benchmark high-density SNP arrays. Together, this study will shed new light on the genetic basis of disease resistance in Atlantic salmon, and validate state-of-the-art approaches for applying these findings to industry breeding programs.
Keywords
Selective breeding;
Genetic;
Disease;
Fish;
Genomic sequencing;
Fish health;
Salmon;
Marine Region
76
Not associated to marine areas
0
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