Krishani Sinhalage, European Master in Animal Breeding and Genetics
The local Swedish sheep breeds belong to a group of sheep breeds called North European short-tailed sheep breeds. Evaluation of genetic diversity and population structure of local breeds offers crucial metrics to prevent inbreeding depression, genetic erosion, and crossbreeding between locally adapted and exotic sheep breeds. The aim of this thesis was to study genetic diversity and the population structure of 191 sheep belonging to 14 Swedish native sheep breeds using 50K SNP genotype data. The population structure was studied with principal coordinate analysis (PCoA), neighbour-joining (NJ) tree, and Structure analysis.
The genetic diversity was assessed using inbreeding coefficients, average observed heterozygosity, and pairwise FST. The inbreeding level was estimated using 2 measures: inbreeding coefficient (FIS) and runs of homozygosity-based inbreeding (FROH). The population structure analyses using Structure v.2.3.4 showed 12 distinct genetic populations among 14 breeds. Rya sheep showed high genetic admixture within the population. The Roslag sheep were highly varied from the other breeds (PC1). The Tabacktorp sheep had the longest branch length in the NJ tree. The highest average FIS and FROH were reported in Roslag (0.25) and Tabacktorp sheep (0.2), respectively. The highest FST value (0.52) was observed between Roslag and Tabacktorp populations. In conclusion, Roslag was highly varied from other breeds and appeared to be genetically isolated. High genetic drift was observed within the Tabacktorp breed. A high FST indicates high genetic differentiation between Roslag and Tabacktorp breeds. Furthermore, relatively high inbreeding levels in Roslag and Tabacktorp sheep indicate low genetic diversity within populations.