The genetic basis of resistance to complex gill disease in Atlantic salmon (Salmo salar)

Complex gill disease (CGD) of farmed Atlantic salmon ( Salmo salar ) is currently one of the most significant health problems in the global salmon industry. To understand the genetic basis of CGD and investigate the potential of breeding for improved robustness, an experimental CGD challenge test was conducted using a pedigreed population from an Icelandic breeding program. A population consisting of 3120 individuals representing 195 families were subjected to two sequential CGD infections, designed to replicate pathogenic exposure scenarios encountered in commercial Atlantic salmon net pen environments. A standardized 4-hour therapeutic freshwater immersion was administered between challenges to simulate routine mitigation strategies employed in industry to ameliorate disease severity. The animals were then phenotyped to identify severity of gill disease and all survivors of the second CGD challenge test (N = 1,946) were recorded for body weight, gill score (16 gills sides) and were genotyped using a 67K SNP array. In total, 1663 fish successfully passed quality control and underwent parentage analysis, had phenotypic records and were available for further analysis. Genomic analysis indicated that gill severity to CGD infection is influenced by genetic factors, with moderate heritability ( h 2 ) ranging from 0.16 to 0.26. Genome wide analysis identified specific genomic regions on chromosomes 9, 16, and 24 that are tentatively associated with gill damage from CGD. These tentative associations show little evidence for any major quantitative trait loci (QTL), indicating numerous small effect genes determining gill severity to CGD infection, implying that genomic selection may be a valuable approach in a breeding program. Cross-validation results indicate high accuracy (0.74) of prediction of genomic breeding values supporting the use of genomic selection for improving resistance. Breeding for CGD resistance can be effective irrespective of the gill region targeted for phenotyping (left or right), as the trait remains consistent across the gill. Reducing phenotyping to the right or left gill region only can increase efficiencies by minimizing the number of phenotypes while reducing labor and resource costs. Therefore, selective breeding augmented by genomics represent a viable approach to improve gill damage to CGD in a farmed Atlantic salmon.