Functional genomics studies of Atlantic salmon (Salmo salar) development, and sac fry responses to chronic incremental hyperthermia

Functional genomics techniques, including the 32K cGRASP microarray and real-time quantitative polymerase chain reaction (QPCR), were used to study gene expression in a single Atlantic salmon cohort: 1) during embryonic and early sac fry development; and 2) after sac fry were exposed to chronic incremental hyperthermia (water temperature increased by 1°C every 24 hours, from 7.4 to 21.4°C). The first study focused on the transcript expression of four microarray-identified paralogous γM-crystallin genes as well as four paralogous α-sHSP genes. The four α-sHSPs, as well as cryGM4-like and cryGM3-like, were shown by QPCR as higher expressed at hatch or post-hatch stage relative to eye-up stage (although the degree of induction varied between paralogues). This research provides possible evidence of divergent transcript expression (i.e., regulation) of duplicated genes, suggesting that some of the paralogues studied may have diverged functionally. These results provide insight into the evolutionary relationships between these genes, and may provide evidence of neofunctionalization following GD events. The second study focused on four microarray-identified genes of interest (trypsin-1 precursor, chymotrypsin b, ferritin middle subunit, and ubiquitin) as well as the four paralogous α-sHSP genes. The transcripts encoding trypsin-1 precursor, ferritin middle subunit, and ubiquitin, as well as α-sHSPs 1, 3 and 4, were shown by QPCR as responsive to the incremental hyperthermia conditions. This study identified molecular biomarkers that may be useful for studying adaptation of early life stage salmon under potentially stressful conditions (e.g., warming climate)