Opportunities for improving feed efficiency and spinal health in New Zealand farmed Chinook salmon (Oncorhynchus tshawytscha) using genomic information

Chinook salmon (Oncorhynchus tshawytscha) is an important aquaculture species in New Zealand and selective breeding since the 1990s has resulted in significant gains in growth related traits. However, feed conversion ratio (FCR) remains highly variable in this species and higher than in other farmed salmonids. Some farmed Chinook salmon are also susceptible to late onset spinal curvature, which further reduces production efficiency. Therefore, the objective of this study was to determine the potential for selecting for improved FCR and reduced spinal curvature while also improving growth. For the evaluation, 82 pedigree families were obtained from two commercial breeding programmes and genotyped using genotyping-by-sequencing to generate a genomic relatedness matrix. Genotyped and tagged juveniles were reared together for 12 months in seawater trial tanks up to ∼2.0 Kg. Multiple assessments of weight, condition factor (CF), feed intake (FI), FCR and skeletal deformity were completed and analysed to estimate genetic parameters (heritability, phenotypic and genetic correlations). High heritabilities were estimated for weight and CF and moderate for spinal curvature. Growth, feed intake and FCR traits had low to moderate heritabilities and demonstrated potential for improvement through selection. Genetic correlations suggested some progress in FCR would be made through selection for growth, but larger gains will be achieved by quantifying FI. An unfavourable genetic correlation was uncovered between CF and spinal curvature and this should be considered when developing breeding goals for commercial broodstock selection.