Analysis of relatedness and genetic diversity in Swedish sheep breeds using medium density (50K) SNP data

Abstract: The local Swedish sheep breeds belong to a group of sheep breeds known as North European short-tailed sheep breeds. Evaluation of genetic diversity, relatedness, and population structure of local breeds offers crucial metrics to prevent inbreeding depression, genetic erosion, and crossbreeding between locally adapted and exotic sheep breeds since these occurrences can have detrimental effects and ultimately lead to extinction. The aim of this thesis was to study genetic diversity and the population structure of 191 sheep belonging to fourteen Swedish native sheep breeds using medium density (50K) SNP genotype data. The population structure was studied with principal coordinate analysis (PCoA), neighbour-joining (NJ) trees (a, b), and Structure analysis. The genetic diversity was assessed based on the inbreeding coefficients, average observed heterozygosity, minor allele frequency (MAF), polymorphic information content (PIC), and pairwise FST. The level of inbreeding was estimated using two measures: inbreeding coefficient (FIS) and runs of homozygosity-based inbreeding (FROH). Moreover, genetic variants in the melanocortin 1 receptor (MC1R) gene that is responsible for coat colour in sheep were examined using seven Swedish sheep breeds. The population structure analyses using Structure v.2.3.4 showed twelve distinct genetic populations among fourteen 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 (b). The highest average inbreeding level (FIS) was reported in Roslag sheep (0.25), while the highest average FROH was observed in Tabacktorp sheep (0.2). The highest FST value (0.52) was observed between Roslag and Tabacktorp populations. Moreover, two previously discovered mutations in the MC1R gene in sheep were found in this thesis: c.-31 G>A and c.218 T>A. The c.218 T>A mutation was associated with black/brown coat colour in Finull sheep. In conclusion, Roslag was highly varied from other breeds and appeared to be genetically isolated with no genetic admixture. High genetic drift was observed within the Tabacktorp sheep population. A high FST value 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.