A comparative study of transcriptome coverage and single nucleotide polymorphisms ‎of mtDNA in Holstein (Bos taurus) vs. Cholistani (Bos indicus)‎

This research aimed to investigate the reasons for the difference of gene expression between two subspecies of Holstein and Cholistani cattle and the importance of mitochondrial genes of these two breeds, the genes under study were COX1, COX2, COX3, ND1and ND2, which are involved in essential processes such as energy metabolism, resistance to biological and non-biological stresses, as well as disease resistance. In this study, RNA-Seq data were used, including 40 samples from the University of Wisconsin Dairy Cattle Center (Bos taurus) and 45 Cholistani cows (Bos indicus) of Gujaratpir farm in Bahawalpur, Punjab, Pakistan. IGB software was used to investigate the level of transcriptome coverage and genetic differences, which included polymorphic, deletion and addition and binding regions. MEGA6 and DnaSPV.5 softwares were also used to determine the location of polymorphic areas as well as to calculate the percentage of different types of transitional and transversional replacements of nucleotides and to align sequences. The results showed that the COX1 gene, with a length of 1542 bp, had the highest level of transcriptome coverage in the mitochondrial genome and the lowest level of transcriptome coverage was related to the ND1 gene. Among mitochondrial genes, the COX1 gene showed the highest deletions and additions, which were higher in Holstein than Cholistani breeds. The number of polymorphic regions in the COX1 locus (19 areas) was higher than other genes. The results also showed that the percentage of transitional substitution is higher than transversional substitution which is the reason for the stability of changes during different generations. Therefore, possible reasons for differences in mtDNA gene expression may be due to differences in deletion and addition processes, transcriptome coverage, and polymorphic regions.