Genome-wide association study and haplotype characterization of bacterial kidney disease (BKD) resistance in Atlantic salmon (Salmo salar) across two generations

Introduction Bacterial Kidney Disease (BKD) is a disease affecting Atlantic salmon aquaculture. This study aimed to evaluate the genetic architecture of resistance to BKD across two generations of the same genetic line in an Atlantic salmon (Salmo salar) breeding program, characterize favorable haplotypes associated with resistance, and identify candidate genes related to immune response to support future selective breeding strategies. Methods Genome-wide association analyses were conducted for mortality and time-to-death traits across two generations. Heritability was estimated, and haplotype analysis was performed to characterize favorable haplotypes associated with resistance. Candidate genes were proposed based on their immune relevance and proximity to significant SNPs. Results Genome-wide association analyses identified a significant region on chromosome 25 containing 36 significant single nucleotide polymorphisms (SNPs), with p-values as low as 5.94 × 10 -36 . Heritability estimates ranged from low to moderate, from 0.147 ± 0.01 to 0.197 ± 0.01 on average. Haplotype analysis identified a two-SNP haplotype associated with an average reduction in mortality of 17.45% and an increase of approximately 3 days in survival time under challenge conditions. Seven candidate genes were proposed for further validation. Discussion These findings suggest that genomic selection should remain the primary strategy for improving BKD resistance, while marker-assisted selection targeting the identified chromosome 25 region may provide complementary value by capturing a moderate but biologically relevant proportion of the genetic variation associated with disease resistance in Atlantic salmon.