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ABSTRACT: Functional Genomic Characterization of Viral Nervous Necrosis Disease resistance in farmed European seabass

PROVIDER: PRJNA1122486 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29355800.fastq.gz	Fastqsanger.gz
	SRR29355900.fastq.gz	Fastqsanger.gz
	SRR29356000.fastq.gz	Fastqsanger.gz
	SRR29356100.fastq.gz	Fastqsanger.gz
	SRR29356200.fastq.gz	Fastqsanger.gz

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Project description:I this study we aimed to functionally characterize the genomic background of viral nervous necrosis resistance in farmed European seabass. Offspring from a cross of 25 males and 25 females were challenged with nervous necrosis virus and their response to the infection were recorded as days to death or binary survival (dead or alive) for a period of about 26 days. A total of 1796 European seabass fish including 50 parents (25 dams and 25 sires) and 1746 juvenile offspring were genotyped on an MedFish Axiom Affymetrix SNP array for 29,888 SNP markers. A section of this fish, 50 parents and 40 offspring were whole genome sequenced at a coverage of 15X. Genotypes of 8.4M variants (SNPs and Indels) were called from whole genome sequence data using BCFTools software after the sequence data had been aligned to European seabass reference genome (GCA_905237075.1) by the BWA aligner. The whole genome sequence genotypes of the 90 samples were utilized as the reference used to impute all the offspring (1706 fish) from SNP array genotype dataset to whole genome variant genotypes of 8.4M variants (SNPs and Indels) using Fimpute3 software with the pedigree relationships (reconstructed using APIS package in R) between the animals supplied to the software. The whole genome data generated from this imputation together with phenotype data of survival and days to death were then used for WGS genome-wide association study analysis. These genotypes were further utilized in a targeted expression quantitative loci analysis for the candidate genes located in the genomic region identified as associated with nervous necrosis resistance in this study.

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