Genetic diversity of domestic sheep

Domestic sheep are raised for meat, milk and fibre production and are found all around the world in many types of environments. Sheep have been shown to be genetically diverse but this genetic diversity has not been fully described: there are still many sheep populations which have not yet been studied. The purpose of this thesis was to study genetic diversity in Swedish and French sheep breeds using high density marker arrays. Additional methods, including genotyping of microsatellite markers, and endogenous retroviruses and pedigree information were used to study Swedish sheep populations. Inbreeding and heterozygosity estimated in Gute sheep using the pedigree of the entire registered Swedish population and additionally microsatellite genotypes and pedigree from a sample of the population (N=94) indicated a breeding program with the purpose of reducing inbreeding. Studying genetic relationships among breeds by genotyping endogenous retroviruses indicated Klövsjö, Värmland, Finewool, Gute and Roslag sheep breeds had characteristics of primitive breeds (absence of retroviruses or presence of the specific retrovirus event enJSRV-7) although Finewool, Gute and Roslag sheep breeds had moderate frequencies of enJSRV-18 which is indicative of more modern sheep breeds. Studying variants in two coat colour genes, ASIP and MC1R, and their association with black coat colour revealed different selection histories in five Swedish sheep breeds studied. Studying the population structure of Dalapäls, Fjällnäs, Gotland, Gute and Klövsjö sheep, using high density SNP genotyping revealed that these breeds are genetically distinct breeds. When comparing with other European breeds and south west Asian breeds, they grouped with other north European short-tailed sheep breeds and they had generally accumulated more drift than breeds from other geographical areas. Studying 27 French breeds with high density genotypes revealed that French sheep populations harbour much of European sheep diversity in a small geographic area. Selective sweeps identified: selection hotspots, selection targets in many species; introgression of an adaptive allele; and allelic heterogeneity, which was confirmed with targeted resequencing of a coat colour gene, MC1R, in breeds under selection

Shared Ancestry and Signatures of Recent Selection in Gotland Sheep

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (similar to 50%), Karakul (similar to 30%), Romanov (similar to 20%), and Fjallnas (similar to 10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation F-ST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the F-ST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep

Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes

Background: Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree. Results: The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they’ve been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree. Conclusions: We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep

A chromosome-level assembly of the Atlantic herring : detection of a supergene and other signals of selection

The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation

Firefly: The Case for a Holistic Understanding of the Global Structure and Dynamics of the Sun and the Heliosphere

This white paper is on the HMCS Firefly mission concept study. Firefly focuses on the global structure and dynamics of the Sun's interior, the generation of solar magnetic fields, the deciphering of the solar cycle, the conditions leading to the explosive activity, and the structure and dynamics of the corona as it drives the heliosphere