Genomic diversity characteristics of sheep populations in the Czech Republic, Slovakia, Serbia and Montenegro

Monitoring the genetic diversity in livestock is a critical component for sustainable management of small and endangered breeds. In this paper we follow up the two most often used metrics of genetic diversity, the average inbreeding coefficients (F) and the effective population (Ne) size in 16 sheep breeds from four countries. The analysis was based on single nucleotide polymorphism (SNP) markers, with about 35 to 49 thousand SNPs and 19 to 98 individuals after quality control. The runs of homozygosity (ROH) method with the cgaTOH software was used to estimate FROH, for three different time points in the past (3, 6 and 12 generations before present). Three methods were implemented to estimate Ne, using the NeEstimator v2, GONE and CurrentNe software for different time spans in the past. The average FROH ranged between 0.001 and 0.035 for 3 generations, 0.003 and 0.059 for 6 generations, 0.005 and 0.074 for 12 generations in the past. The wide range of inbreeding coefficients might be a consequence of different population sizes and breed management strategies in the respective countries. The results for Ne ranged from 7 to 352 for NeEstimator, 25 to 303 for GONE, and 15 to 542 for CurrentNe. Overall, the software showed comparable results for 10 out of 16 breeds, and significantly different results for at least one software for at least one of the methods for 6 out of 16 breeds. These differences show a degree of uncertainty in Ne estimations for certain breeds. Overall, we suggest the continued monitoring of sheep breeds, ideally by routine genotyping in all populations. This monitoring is especially important for small breeds with a greater decline in genetic diversity.