Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 The Atlantic salmon S-lineage molecule shows a close relationship to the Onmy-SAA molecule. Based on their sequence identity, both molecules seem to have evolved very little following the divergence of these two species [24]. Expression of Atlantic salmon MHC class I genes One of the definitions of a MHC class Ia gene is that it is expressed in most tissues. To investigate the expres- sion patterns of Atlantic salmon MHC class I molecules, blood, foregut, hindgut, head kidney, gills, spleen, liver, eye, tongue, skin, muscle, heart and brain samples were taken from three Atlantic salmon individuals and ana- lyzed for gene expression by quantitative real-time PCR (Figure 4). To evaluate the expression patterns from the heart, blood was included as sample to differentiate between the expression patterns in heart structural tissue. Highest expression for UBA was observed in foregut, hindgut, spleen and gills, while moderate expression was observed in blood and heart. Lowest expression was observed in tongue, liver and brain. Without using an absolute quantification method i.e. including a standard curve, it is not possible to compare different genes for Page 9 of 17 same tissues, however the transcriptional level of other MHC class I genes were low in comparison to UBA with the exception of UGA in blood. In general, the high expression of UBA in comparison to the other MHC class I genes, is also supported by hits found in databases. Various BlastN, BlastX, and TBlastN searches in Genbank [25] and cGRASP [26,27] using UBA sequences hit numerous sequences, while blasting with other U-, S-, or Z-lineage sequences results in generally few hits. We found that ULA had highest expression in tongue, and lower in skin and heart. In contrast to our results, Miller et al [15] found that ULA was only weakly expressed in posterior kidney in un-infected fish, while expression was up-regulated in IHNV-infected liver, brain and eye tissues. They did not detect expression in the heart of un-infected nor infected tissues. UDA showed little variation in expression patterns between the different tissues tested. The remaining nonclassical U-lineage class I genes, UHA1, UHA2 and UGA all showed the highest expression in blood. Expression analysis of the Z-lineage genes showed that ZAA had highest expression in blood, while lower expression in the heart, spleen, gills and hindgut. ZBA Figure 4 Expression analysis of MHC class I genes in Atlantic salmon. Relative expression of Sasa-UBA, Sasa-UDA, Sasa-UGA, Sasa-UHA1, Sasa-UHA2, Sasa-ULA, Sasa-ZAA, Sasa-ZBA, Sasa-ZCA and Sasa-SAA in various tissues of Atlantic salmon using EF1A as reference gene. The Relative expression values for UBA in hindgut and spleen has been truncated and their values are indicated above their respective bars.