Genome analysis in local breeds: A case study on Olkuska sheep

Abstract

In the 1980s, Olkuska sheep went through a dramatic decline in population size, which resulted in a rapid increase in the inbreeding level. Implementation of conservation program led to enhancement of the number of flocks and resulted in establishment of flocks in regions far away from the center of origin of the breed. In this study, we analyzed genetic variation within this unique breed to better understand genetic structure and to support enhanced management strategies. The analysis of genetic diversity in Olkuska sheep was performed using two sources of information, pedigree and genomic data. Single nucleotide polymorphisms (SNP) data supported analysis of runs of homozygosity (ROH), inbreeding coefficient FROH, genomic inbreeding FHOM, linkage disequilibrium and observed heterozygosity. On the basis of the pedigree data, inbreeding coefficient (F) and coancestry were calculated. Both sources of information provided similar results in regard to inbreeding level and showed significant differences between the Southern and the Central subpopulations of the breed. The average inbreeding coefficient (F) was 0.102 in the Southern subpopulation and 0.053 in the Central subpopulation. The average FROH in the Southern population was 0.124, and 0.082 in the Central population. The highest number of ROHs were observed on OAR1, OAR2 and OAR3.. Most of ROHs were short (1–10 Mb). The pattern of ROHs detected in the study on Olkuska sheep is similar to other research findings cited in the paper. Significant differences between two subpopulations within the local breed which in the past went through a major decline in numbers, creates the threat of genetic diversity loss. Exchange of individuals between flocks located in the south and in the central Poland is strongly recommended.