Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis

• Published in: Frontiers in Genetics
• Main Authors: Yanez, Jose M., Yoshida, Grazyella M., Parra, Angel, Correa, Katherina, Barria, Agustin, Bassini, Liane N., Christensen, Kris A., Lopez, Maria E., Carvalheiro, Roberto, Lhorente, Jean P., Pulgar, Rodrigo
• Other Authors: Universidade Estadual Paulista (UNESP)
• Format: Article in Journal/Newspaper
• Language: English
• Published: Frontiers Media Sa 2019
• Subjects: coho salmon; rainbow trout; Atlantic salmon; Piscirickettsia salmonis; genome-wide association study; comparative genomics; piscirickettsiosis; British Columbia; Canada; Norway; Salmo salar
• Online Access: http://hdl.handle.net/11449/184618; https://doi.org/10.3389/fgene.2019.00665

U-Inicia grant, from the Vicerrectoria de Investigacion y Desarrollo, Universidad de Chile CONICYT (Government of Chile) Nucleo Milenio INVASAL from Iniciativa Cientifica Milenio (Ministerio de Economia, Fomento y Turismo, Gobierno de Chile) government of Canada through Genome Canada government of Canada through Genome British Columbia government of Canada through Genome Quebec CONICYT (Government of Chile): IT14I10100 Piscirickettsia salmonis is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; Oncorhynchus kisutch), Atlantic salmon (AS; Salmo salar), and rainbow trout (RT; Oncorhynchus mykiss) in several countries, including Norway, Canada, Scotland, Ireland, and Chile. We used Bayesian genome-wide association study analyses to investigate the genetic architecture of resistance to P. salmonis in farmed populations of these species. Resistance to SRS was defined as the number of days to death and as binary survival (BS). A total of 828 CS, 2130 RT, and 2601 AS individuals were phenotyped and then genotyped using double-digest restriction site-associated DNA sequencing and 57K and 50K Affymetrix (R) Axiom (R) single nucleotide polymorphism (SNP) panels, respectively. Both traits of SRS resistance in CS and RT appeared to be under oligogenic control. In AS, there was evidence of polygenic control of SRS resistance. To identify candidate genes associated with resistance, we applied a comparative genomics approach in which we systematically explored the complete set of genes adjacent to SNPs, which explained more than 1% of the genetic variance of resistance in each salmonid species (533 genes in total). Thus, genes were classified based on the following criteria: i) shared function of their protein domains among species, ii) shared orthology among species, iii) proximity to the SNP explaining the highest proportion of the genetic variance, and iv) presence in more than one genomic ...