Genomic and transcriptomic analysis of amoebic gill disease resistance in Atlantic salmon

This work investigated the genetic basis of tolerance against the amoebic gill disease (AGD) in Atlantic salmon by integrating the information obtained from transcriptomics and genomics approaches. First, through whole transcriptome sequencing of 36 animals with different levels of tolerance to infection, we identified genes and genetic pathways with important roles in the host's response to the amoeba. In particular, we found a significant increase in the transcription of genes with functional properties in cell adhesion. Next, following a challenge testing, we genotyped more than 1,300 animals over thousands of genetic markers and performed various analysis and estimation of genetic parameters. Through genome-wide association analysis, we detected significant genetic markers, located on 3 different chromosomes (chromosomes 4, 9 and 13) to be linked to a higher tolerance for this disease. The QTL region on chr. 4 harbours the cadherin gene family. These genes play an important role in target recognition and cell adhesion. The QTL region on chr. 9 also harbours a member of the cadherin gene family, protocadherin Fat 4. The associated genetic markers on ssa13 span a large genomic region that includes interleukin IL18.