The Single Nucleotide Polymorphisms (SNP) discovery and calling on genes deferentially expressed between Holstein (Bos taurus) and Cholistani (Bos indicus) cattle populations

In the present study, the single-nucleotide polymorphisms and their transcriptome covereage on differential gene expressions were investigated between Holstein and cholistani population. Thus, the transcriptomes (mRNA Sequence) for a US Holstein and a Pakistanian Colistani cow population were assembled by aligning and mapping the RNA-Seq reads on bovine reference genome. Then differential gene expression analysis was performed. Finally 24616 genes and 26 716 isoforms on the transcriptome of these two populations were found among 41 genes that were showed significantly different expression. (P.value < 0,000015).Analysis of the gene ontology (GO) and routes indicated that they are involved in, 20 pathways A large number of genes in the pathways leading to immune response, leading to translate the electron transfer resistance to thermal stress and disease. A total of 53 478 and 145443 were SNP discovered in the genome of which 154 SNP in Cholistani population and 24 SNP in Holstein population were among 41 genes were significant In 18 genes, no SNP was observed. 23 genes had at least one SNP in each of the populations. The number of SNP in the cholistani breed was almost 5 times expresstion higher than the Holstein breed. These genes also had a high expression in the cholistani popularion breed. This can be one of the causes of differences in gene expression between two populations in this study.