Atlantic cod families from year 2009 of the Norwegian national cod breeding program were challenged for viral nervous necrosis and vibriosis. Mortality was recorded. Around 1600 offspring and their parents were genotyped at 10,913 SNP loci, covering 2,285 scaffolds/contigs in the  reference genome, which accounts for 71.3% of total sequence length. Genomic enabled breeding values (GEBV) were estimated. A 10-folds cross-validation shows that the correlations of the survival states and corresponding GEBV were 0.085 for vibriosis and 0.55 for VNN. Whole genome resequencing of 111 parents was performed to an approximately 12x coverage per individual. Variant calling in the sequence of a subset of parents showed that all 12K SNP array SNPs were called and had matching genotypes. Imputation with Beagle and LDMIP software will enable inference of sequence data for all the challenge tested fish and the resulting improvement in accuracy will be investigated.


Xijiang Yu, Theo HE Meuwissen, Matthew Baranski, Anna K Sonesson

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Genetic Improvement Programs: Selection using molecular information, , 085, 2014
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