Evaluation of Genomic Inbreeding Rate in Iranian Native Sheep using Dense SNP Markers (600K)

Whereas high levels of inbreeding in domestic animals reduce genetic diversity and increase the probability of animals being homozygous for deleterious alleles. Therefore, the longevity of inbred animals is decreased due to reduced genetic merit. Therefore, in designing breeding programs, preknowledge about the level of inbreeding is essential to control the increase in inbreeding and thus control the inbreeding depression in animals. In this regard, genomic data can be used to estimate inbreeding coefficients. The aim of this study was to investigate the rate of inbreeding using SNP marker data available throughout the genome from the Illumina OvineSNP600K array in Iranian native sheep.

In this study, the genomic inbreeding of 154 samples including 11 Iranian sheep breeds (Kermani, Baluchi, Afshari, Karakul, Sanjabi, SiahKabud, LoriBakhtiari, Shal, Ghezel, Chios, GrayShiraz) was studied. For this purpose, five different methods were used by using Plink software: molecular indices of inbreeding coefficient based on observed and expected heterozygosity (FIS), inbreeding coefficient based on “runs of homozygosity” (FROH), inbreeding coefficient based on genomic relationship matrix (FGRM), inbreeding coefficient Based on the number of observed and expected homozygous genotypes (FHOM) and the correlation between uniting gametes (FUNI).

The average minor allele frequency in Iranian native sheep was 0.268. Also, the mean of observed heterozygosity and expected heterozygosity was 0.341 and 0.360, respectively. The lowest rate of inbreeding according to FIS was related to Baluchi breed and the highest was related to Shal breed.  The highest amount of FROH (0.129) was observed in Kermani breed and the lowest amount (0.019) was observed in Baluchi breed. Also, the highest amount of FGRM, FHOM and FUNI indices was observed in Kermani breed and lowest amount was related to Baluchi breed. The highest ROH coverage was observed on chromosome 26 (20.23%), while the lowest was on chromosome 2 (6.62%).

The genetic diversity of Iranian native sheep was moderate and ranged from 0.315 to 0.354. ROH was found in all breeds, so that the average length of ROH was between 48 to 318 Mb, while the average number of ROH was between 8 to 53. The mean of genomic inbreeding coefficients for the whole population of native sheep were similar (0.05). The results of this study indicate that there is no high level of genomic inbreeding in most of the native sheep populations of Iran.