Investigating the genetic diversity of Iranian native and Holstein cattle breeds using genomic data

In this study, genomic data of 590 cattle were used including native breeds of Sarabi, Kermani, Kurdi, Talashi, Sistani, Najdi, Mazandarani and Pars, crossbred from northwest of Iran, Holstein populations from Iran, France and Ireland. Quality control and data filtration were performed using Plink 1.9 software. After this quality control, individuals and SNPs with call rate below 0.95%, SNP makers with minor allele frequency (MAF) > 0.01%, divergence from Hardy-Weinberg Equilibrium were excluded. This procedure yielded 509 individuals with 13512 SNP marker. Then filtered data were used to genetic diversity and clustering analysis. Identification of genetic groups were performed using PCA analysis data by GenABEL software. PCA and ADMIXTURE analysis showed that studied populations are in 4 separate categories including purebred Sarabi population in the first group, crossbred from northwest of Iran in the second group, purebred Holstein populations in the third group and native breeds of Iran were in the fourth group. Further details of demographic differentiation were identified by Weir and Cockerham's fixation index. The range of differentiation in the present study varied from 0.180 between Sistani and Kurdish breeds to 0.007 to 0.004 between the Iran Holstein breed and Ireland with France Holstein breeds. The results showed that the highest difference between indigenous and Holstein breeds related to Sistani breed that had the highest difference with different Holstein breeds (0.128 to 0.138). With slight differences from other Iranian indigenous breeds, the Kurdish and Mazandaran breeds had the smallest genetic differences with the studied Holstein populations.