The Single Nucleotide Polymorphisms (SNP) Discovery on Transcriptome of Pure Sistani and Cross-Breeding of Sistani and Holstein, Simmental and Monte Billiard Bulls

Breeding between Indus cows and Taurus cows in the Sistan region of Iran has been done in recent years through the use of liquid sperm, frozen sperm, or foreign bulls. There are few studies in Iran on the effects of interbreeding programs on Sistani cattle. The present study was performed to identify mononucleotide polymorphisms (SNPs) based on RNA-Seq data in purebred Sistani cows and its crosses with three foreign breeds of Holstein, Simmental, and MonteBilliarde cows.

In this study, RNA-Seq data were used for pure Sistani, Sistani and Holstein, Sistani and Montebeliarde, Sistani and Simmental cattle. For this purpose, first of the tail vein of purebred cattle mixed with Holstein, Simmental, and MonteBilliarde. (4 treatments and for each treatment two biological replications) in the same environmental, nutritional, and managerial conditions located in the breeding center of Sistani cattle in Zabol. blood was drawn.

SNP discovery analysis was performed on transcriptome using SAMtools software package, which led to the discovery of 152496, 177042, 134285, and 163362 SNPs in pure Sistani breeds and its crosses with three foreign breeds of Holstein, Simmental, and Montebeliarde bulls. In this study, there was no direct relationship between the number of SNPs identified and the length of chromosomes. Also, 12 types of SNPs were identified, of which four types were transition and eight types were transversion. The most common known SNPs were transition which was 71.84% in pure Sistani, 72.65% in Sistani and Holstein, 72.60% in Sistani and Simmental, and 71.94% in Sistani and MonteBilliarde.

Overall, the results of this study confirmed that RNA-Seq technology is an effective, economical, and efficient method for identifying SNP loci. Factors influencing RNA-Seq evaluation are such as the number of samples.