Detection of selection signature in Esme sheep breed

Objective: Natural and artificial selection processes cause specific changes in the genome of animals and create selection signatures. In recent years, developments in molecular genetic techniques and bioinformatics have made it possible to identify selection signatures in livestock populations. In this study, it was aimed to identify genomic regions and genes that may be under selection in the Esme population. Material and Methods: 50 K SNP chip data from 527 Esme sheep were analyzed by integrated haplotype score (iHS) approach. The integrated haplotype score (iHS) analysis used two different approaches to assign ancestral alleles. The traits that are or could be related to the selection signatures detected in the Esme sheep population were attempted to be explained using three different approaches: comprehensive literature review of candidate genes, QTL overlap of genomic regions, and enrichment analysis of genes. Results: The first approach identified 32 genomic regions (99 SNPs) and 259 genes distributed across 7 chromosomes (OAR1, 2, 9, 11, 12, 23, and 25). In the second approach, 32 genomic regions (98 SNPs) and 255 genes were identified on the same chromosomes. The literature review found that approximately 62% of mutations in genes defined as under selection could be related to reproduction, production, meat, and carcass traits, and approximately 21.5% could be related to health traits. Gene regions under selection were found to overlap most frequently with QTLs related to meat and carcass traits (37.14%). Enrichment analysis revealed that the genes under selection were enriched in biological processes, molecular functions, WikiPathway and KEGG pathways that could be related to production, reproduction, meat and carcass traits, and most importantly, health. Conclusion: These results suggest that the breeding programs implemented increase the frequency of mutations related to meat and carcass traits, production, and reproduction in the population. However, mutations related to health traits important for adaptation to ecological conditions have also been shown to be subject to selection. As a result, there is evidence that genetic improvements in target traits have been achieved in population-based breeding programs, and candidate genes have been identified for use in future breeding programs supported by molecular markers. In addition, evidence was obtained that genetic improvement for target traits was achieved in breeding programs conducted in the population, and candidate genes were identified that can be used in future breeding programs supported by molecular markers.