Gjerde, B. | Search bioRxiv

bioRxiv2024

Transcriptomic profiling of gill biopsies to define predictive markers for seawater survival in farmed Atlantic salmon

Wild Atlantic salmon migrate to sea following completion of a developmental process known as parr - smolt transformation (PST), which establishes a seawater (SW) tolerant phenotype. Effective imitation of this aspect of anadromous life-history is a crucial aspect of commercial salmon production, with current industry practice being marred by significant losses during transition from the freshwater (FW) to SW phase of production. The natural photoperiodic control of PST can be mimicked by exposing farmed juvenile fish to a reduced duration photoperiod for at least 6 weeks before increasing the photoperiod in the last 1 - 2 months before SW transfer. While it is known that variations in this general protocol affect subsequent SW performance, there is no uniformly accepted industry standard; moreover, reliable prediction of SW performance from fish attributes in the FW phase remains a major challenge. Here we describe an experiment in which we took gill biopsies 1 week prior to SW transfer from 3000 individually tagged fish raised on 3 different photoperiod regimes during the FW phase. Biopsies were subjected to RNA profiling by Illumina sequencing, while individual fish growth and survival was monitored over 300 days in a SW cage environment, run as a common garden experiment. Using a random forest machine learning algorithm, we developed gene expression-based predictive models for initial survival and stunted growth in SW. Stunted growth phenotypes could not be predicted based on gill transcriptomes, but survival the first 40 days in SW could be predicted with moderate accuracy. While several previously identified marker genes contribute to this model, a surprisingly low weighting is ascribed to sodium potassium ATPase subunit genes, contradicting advocacy for their use as SW readiness markers. However, genes with photoperiod-history sensitive regulation were highly enriched among the genes with highest importance in the prediction model. This work opens new avenues for understanding and exploiting developmental changes in gill physiology during smolt development.

genomics↗

bioRxiv2024

Impact of three light smoltification regimes on performance and genetic parameters of traits in Atlantic salmon

2800 Atlantic salmon pre-smolts (50 g on average, the offspring of 53 sires and 100 dams) were individually tagged with PIT-tags and distributed among six circular 1200L tanks with approximately 450 fish per tank. Fish in duplicated tanks were put on three different light regimes, i.e. six weeks on either 8L:16D, 12L:12D or 24L:0D followed by six weeks on 24L:0D. One week prior to their transfer as 1+ smolt to a net cage in the sea in June 2021 their body weight, length, subjectively scored smolt status and fin damage were recorded. Recording of animal traits (body weight, wounds, fin damage, snout damage) were also performed in November 2021 and in April 2022. During the light regimes, fish on the two short day regimes had slower growth compared to fish on continuous light. However, after four (November 2021) and ten (April 2022) months in the sea the effect of light regime on fish size was not significantly different from zero (P>0.05). The fish on the 24L:0D regime showed increased mortality from day two after sea transfer with an accumulated recorded mortality of 8.9% during the two first months while it was only 1.0% and 0.7% for the 12L:12D and the 8L:16D fish, respectively. However, from the third until ten months in the sea recorded mortality was very similar for fish on the three light regimes. The effect of light regime on the recorded welfare traits (fin and snout damage and runts) was not significantly different from zero. For traits measured prior to seawater transfer the difference between fish that survived and those that died during the first two months in the sea were largest in the 24L:0D group indicating a positive effect of the short-day regimes also on the general smolt synchronization (i.e., group level uniformity). Moderate heritability estimates were found for the external smolt indicator traits condition factor, smolt status score and skin silveriness, as well as for snout damage, wounds, runts and body weight, but low estimates fin damage. For survival in the sea heritability on the liability scale was 0.09 after four months in the sea and 0.22 from five to ten months in the sea. The estimated genetic correlations between the same trait of the three different light regimes were moderate to high and thus unimportant genotype by light regime interaction. The genetic correlation of body in June 2021 with survival after two months in the sea was high (0.96), but not significantly different from zero with survival after four months in the sea and survival from five to ten months in the sea. Genetic correlations of survival with the other traits recorded in June 2021, November 2021 and April 2022 were low to medium in magnitude and not significantly different from zero. Therefore, for genetic improvement of survival in the seawater period direct selection for increased survival and growth during the first months is probably a better strategy than to perform indirect selection for smolt indicator traits.

genetics↗