Introduction.
Columnaris disease (CD), caused by Flavobacterium columnare is an emerging disease affecting rainbow trout (Oncorhynchus mykiss ) aquaculture worldwide
. Revealing the genomic basis underlying resistance to CD has important implication for selective breeding of trout and to better understand the genes involves in disease resistance. In a previous study a main QTL associated with resistance was detected on chromosome Omy3 (Fraslin et al., 2022) after a natural outbreak in commercial conditions with mortality phenotypes recorded on 3,054 individuals genotyped for about 28K SNPs. In the present study 45 parents out of 81 were sequenced to further refine the QTL location after alignment to the new reference genome USDA_OmykA_1.1 (Gao et al., 2021).
Materiel and methods
From the initial dataset composed of 3,054 offspring and 81 parents, 45 parents and 5 offspring were selected for whole genome resequencing (WGS) based on the number of offspring per family, survival rate and segregation of the resistance QTL detected in Fraslin et al., (2022). Alignment on the trout reference genome, USDA_OmykA_1.1, was performed with Bowtie2, SNP calling was performed using recommended pipelines with GATK and BCFTools, Genomic imputation from the 18,940 SNPs obtained by genotyping after alignment to the new genome assembly was performed using FImpute V3. The accuracy of imputation was analyzed using data from the 5 offspring that were sequenced. A genome wide associated study (GWAS) was performed using the imputed genotypes and a mixed linear model implemented in the GCTA software.
Results and discussion.
About 24 millions SNPs were called by each software, only the common biallelic SNPs detected by both software were kept resulting in a total of 10,666,323 post quality controls (maf 10%, HWE p> 0.001, coverage 60% and depth between 8x and 30x). Imputation was performed correctly for the 5 individuals, with accuracy ranging from 78% for individuals with no parents in the sequenced dataset to 84% for individuals with both parents in the sequence dataset. The QTL on Omy3 was confirmed with the WGS based GWAS. Other QTLs on Omy5 , 14 and 20 were detected. This study paves the way towards a better understanding of the genetic mechanisms underlying resistance to CD in rainbow trout. Further study is needed to identify positional candidate genes within the QTL and their implication in fish resistance.
Acknowledgment.
The dataset originated from the AQUAimpact project, funded by the European Union’s Horizon 2020 R esearch and I nnovation Programme (grant agreement No 818367). The staff of Savon Taimen Oy and Hanka-Taimen Oy are thanked for their expertise in data collection and fish rearing.
References .
Declercq et al. (2013). Veterinary Research 44, 10.1186/1297-9716-44-27 . Fraslin et al. (2022). Aquaculture 557, 738332. Gao et al. (2021). Genes Genomes Genetics 11, jkab052.