GENOME-WIDE ASSOCIATION STUDY (GWAS) ON RESISTANCE TO SALMON RICKETTSIAL SYNDROME (SRS) IN RAINBOW TROUT USING GENOTYPES IMPUTED FROM WHOLE-GENOME SEQUENCING

Rainbow trout (Oncorhynchus mykiss) production in Chile faces significant challenges from Salmonid Rickettsial Syndrome (SRS), caused by the bacterium Piscirickettsia salmonis. In 2022, SRS was responsible for 49.4% of trout mortality. Traditional control methods, such as vaccines and antibiotics, have been largely ineffective. However, rainbow trout show moderate heritability for resistance to P. salmonis (0.34-0.44), suggesting that genetic selection could be a viable alternative.

Genome-wide association studies (GWAS) are instrumental in linking genetic variations to crucial traits phenotypes, such as disease resistance in fish. The integration of Whole Genome Sequencing (WGS) data enhances the precision and statistical power of association mapping. In this research, we employed GWAS to investigate resistance to the facultative intracellular bacterium P. salmonis, which affects farmed rainbow trout, using imputed sequence-level genotypes to identify candidate genes linked to resistance.

In this study, 2,130 rainbow trout were exposed to SRS under controlled conditions and genotyped with 57K single nucleotide polymorphism (SNP) panel. Genotype imputation for all genotyped animals was conducted using WGS data from 102 individuals, provided 488,979 imputed variants for analysis, table 1.

The GWAS identified significant quantitative trait loci (QTL) associated with resistance on chromosomes Omy03, Omy13, Omy25, Omy26, and Omy27 for time to death (TD), and Omy03, Omy26, and Omy27 for binary survival (BS). Additionally, 24 candidate genes linked to resistance were discovered, primarily involved in processes such as phagocytosis, immune response, inflammation, oxidative stress, lipid metabolism, and apoptosis. These findings advance our understanding of the genetic mechanisms underlying resistance to P. salmonis in rainbow trout and support future genetic selection efforts.