Estimation of Effective Population Size and Genomic Inbreeding Coefficients in Baluchi Sheep Using Genome-Wide Single Nucleotide Polymorphisms (SNPs)

The aim of this study was to estimate the effective population size (Ne) and genomic inbreeding coefficients in 96 Baluchi sheep genotyped using Illumina OvineSNP50 BeadChip. Using NEESTIMATOR software, the estimation of contemporary Ne based on heterozygoteexcess and linkage disequilibrium (LD) methods was obtained 15 and 25, respectively. The historical Ne estimated with SNeP software showed a fast decreasing trend over the last 1000 generations. The Ne estimate for the previous 4 generations was ranged from 48 to 75. Three estimates of inbreeding coefficients including genomic relationship matrix (FGRM), excess of homozygosity (FHOM) and correlation between uniting gametes (FUNI) were calculated using GCTA software. The values of FGRM, FHOM and FUNI were calculated the same at 0.017. The average expected and observed heterozygosity using PLINK software were calculated as 0.374 and 0.383, respectively. Our results showed a considerable genetic variation in Baluchi sheep, however the low values of Ne emphasize that measures should be taken to avoid a further reduction in the effective population size. The results of this study provide guidance for future sheep breeding to increase the conservation activities of the native sheep breeds.