Genomic inbreeding estimation and evaluation of runs of homozygosity in Sarabi and Najdi cattle populations.

The present study was carried out to estimate levels of genomic inbreeding based on ROH (FROH) analysis in the two Iranian native cattle populations including Sarabi and Najdi, as well as comparing the FROH estimates with other inbreeding estimates obtained based on the genomic relationship matrix (FGRM), percentage of homozygous SNPs (FHOM) and pedigree information (FPed). To do this, 213 and 211 samples were randomly selected from Sarabi and Najdi populations, respectively. The samples were genotyped using the Illumina BeadChip40K v2 microchip. In addition, 30 samples of Holstein dairy cattle of Iran provided by Animal Breeding Center of Iran, were included in the analysis . Genomic analysis was performed using CFC, Excel, Plink, SNeP programs. A total of 2030 haplo-blocks were identified in the populations. The highest and lowest number of ROH segments (ROHs) was observed within Najdi and Sarabi Population, respectively. Furthermore, ROH length were found to be significantly different among breeds (p < 0.05). Najdi population had the highest number of ROH across different categories of ROH length (4-8Mb, 8-16Mb and >16Mb). Maximum correlation coefficient among the estimated inbreeding coefficients was obtained between FPed and FROH>4Mb (0.592) in the Sarabi population (p < 0.001). The results of this study indicate that presence of inbreeding at least in the five early generations of the studied native populations and the conservation programs must be taken to manage the inbreeding levels in both populations.