Multi-trait GWAS for growth under contrasting thermal rearing conditions in rainbow trout (Oncorhynchus mykiss)

Thermal variability significantly impacts fish performance, and current breeding objectives may soon be suboptimal due to climate change. Growth is a critical trait for aquaculture profitability. Understanding the genomic differences in growth under varying water temperatures is essential to predict climate change's impact on cold water species production. This study examined a rainbow trout population grown under low (~ 7 °C) and high (~ 22 °C) non-lethal temperatures. The objectives were to: (i) explore the genetic architecture of growth under upper and lower temperature (UT and LT) conditions using multi-trait genome-wide association, and (ii) identify candidate genes and biological processes related to growth in these conditions through a gene-based meta-analysis approach. The results revealed: (i) significant genetic variation for body weight, body length, and average daily gain at both LT and UT conditions, with genomic heritabilities ranging from 0.19 ± 0.06 to 0.32 ± 0.05 and 0.16 ± 0.05 to 0.39 ± 0.08, respectively; (ii) distinct genetic architectures and genes associated with UT and LT growth, with SNP effect correlations from r = 0.06 to 0.22; (iii) shared biological functions for growth at UT and LT, involving cardiovascular function maintenance and cell communication. Cytoskeleton-related functions were predominant in growth at LT, while DNA repair functions were more significant at UT. Notably, sema6ba emerges as a potential candidate gene involved in growth-related traits across contrasting thermal environments in rainbow trout, given its strong association under both low and high temperature conditions.