Investigating the Function of Predicted Proteins from RNA-Seq Data in Holstein and Cholistani Cattle Breeds

This study was performed to determine the digital expression profile of different genes expressed in Holstein and Cholistani breeds as well as to evaluate the performance of predicted proteins derived from differentially expressed genes between these two breeds using RNA-Seq data. For this purpose, the whole mRNA sequence for a blood sample of American Holstein and Pakistani Cholistani cattle populations was obtained and by sequencing and locating RNA-Seq reads on the bovine reference genome and determining the digital expression profile, the differentially expressed genes were obtained. The results of this study showed that there were 24616 genes and 26716 isoforms on the transcriptome of these two breeds, out of which, 41 genes were identified with substantial and significant differential expression (P <0.000015). It was also found that approximately one-third of genes whose functions is altered accros two breeds, encode hydrolase enzymes, five of the predicted proteins, FOS Fos proto-oncogene proteins, AP-1 transcription factor subunit, the vhl-elonginc-elonginb structure, transcription factor FosB/ JunD bZIP domain, T yeast U2AF complex pseudomonas aeruginosa transcriptional regulator PA2196 and zif268 zinc finger-dna complex that are involved in transcriptional regulation and RNA editing. Investigation of network interactions between predicted proteins from differentially expressed genes showed that predicted proteins are involved in different pathways such as TNF signaling pathway, Salmonella infection, MAPK signaling pathway and rheumatoid arthritis. Overall, these two breeds were found to be well-adapted to environmental conditions due to different environmental conditions and evolutionary distance and this coordination at the molecular level of the expression of specific genes was found in this study. One of the reasons supporting this is the greater role of the immune system in the Cholistani breed due to its higher exposition to contamination than the Holstein breed that led the expression of bactericidal proteins (Cathelicidin 1) was up regulaged, as a result, the activity of the immune system might be improved. The study also found that the IL1B gene had the highest degree of gene-drug interaction with Canakinumab drug.The results of this study indicate that in breed comparisons, a close look at the activity of proteins produced by different genes could better explain breed differences at the molecular level.