Browsing by Subject "3’ RNA sequencing"

Atlantic salmon (Salmo salar) have a complex life history, characterized by a juvenile stage spent in freshwater before migrating to the sea for one to several years and then returning to their natal river to spawn. Sea-age at maturity, which corresponds to the number of years spent at sea, is an important life-history trait influenced by environmental and genetic factors. Variation in sea-age at maturity in Atlantic salmon has been associated with a SNP located in the intron of six6 on chromosome 9 (six6a). This gene is also known to be evolutionary conserved in eye development in vertebrates and has a crucial role in sexual maturation in mammals. In 3-year-old Atlantic salmon, six6a was found to be expressed in the eyes, brain, gills, and testes. In addition, in situ hybridization has shown that six6a is expressed in multiple organ systems in embryos, for example, the eye and brain developing areas. However, quantification of its level of expression has only been carried out on whole individuals so far. Therefore, this thesis aims to quantify the expression level of six6a, and its paralogue, six6b, at different time points (1-9 months post-hatching) and in four different tissues and a body part (brain, eye, gill, hypothalamus, and head) to identify the tissues and developmental stages that are relevant for future functional studies on the association between six6a genotype and variation in sea-age at maturity. Using a 3’ RNA sequencing approach we found that the eyes and hypothalamus had the highest expression level of both paralogues with a higher expression level of six6b. The expression of the two paralogues in gill samples was very low or non-existent and the low level of expression detected in head and whole brain samples could be influenced by the presence of the eyes and the hypothalamus, respectively. Based on these results, the hypothalamus and eyes would be important tissues for further investigation to gain more information on the association between the six6a genotype and variation in sea-age at maturity in Atlantic salmon. In addition, a more in-depth analysis of the transcriptomic data obtained would allow the investigation of the specific roles of each paralogue, for example by studying correlated genes in the different tissues.