Genetic diversity of Estonian horse breeds and their genetic affinity to northern European and some Asian breeds

EquCab_Finn: A new reference genome assembly for the domestic horse, Finnhorse

Finnhorse is Finland's native and national horse breed and it has genetic affinities to northern European and Asian horses. It has historical importance for agriculture, forest work and transport and as a war horse. Finnhorse has four breeding sections in the studbook and is under conservation and characterisation efforts. We sequenced and annotated the genome of a Finnhorse mare from the working horse section using PacBio and Omni-C data. This genome can complement the existing Thoroughbred reference genome (EquCab 3.0) and facilitate genetic studies of horses from northern Eurasia. We assembled 2.4 Gb of the genome with an N50 scaffold length of 83.8 Mb and the genome annotation resulted in a total of 19 748 protein coding genes of which 1200 were Finnhorse specific. The assembly has high quality and synteny with the current horse reference genome. We manually curated five genes of interest and deposited the final assembly in the European Nucleotide Archive under the accession no. PRJEB71364.

Genetic Differentiation among Livestock Breeds-Values for Fst

(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06-0.12, SNP 0.08-0.15; sheep: microsatellite 0.06-0.10, SNP 0.06-0.17; horses: microsatellite 0.04-0.11, SNP 0.08-0.12; goats: microsatellite 0.04-0.14, SNP 0.08-0.16; pigs: microsatellite 0.06-0.27, SNP 0.15-0.22; chickens: microsatellite 0.05-0.28, SNP 0.08-0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world's livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.

Evaluation of the Conservation Status of the Croatian Posavina Horse Breed Based on Pedigree and Microsatellite Data

Simple Summary

Conservation of local horse breeds as part of animal genetic resources is of national and global importance. Monitoring of local breeds is often fragmentary, i.e., it involves analysis of pedigrees, phenotype, and genetic structure. Using the Croatian Posavina horse as an example, we analyzed the status of the population with regard to available pedigree information, phenotype measures of stallions and mares, and genetic structure based on microsatellites. The generation interval is about eight years, indicating relatively early involvement of animals in reproduction for economic use of the breed. The depth of the pedigree is relatively modest due to a relatively short period of systematic breeding work (two decades). The number of active sire-lines and mare-lines is favorable and forms a good basis for the preservation of the breed. Regarding conformation, the Croatian Posavina horse kept the recognizability of the small-sized horse breed in the coldblooded type, in which there are clear traces of the earlier controlled introduction of the Arabian and other breeds. Its genetic diversity component has been preserved. The above results are a guide for further implementation of effective programs for the conservation of endangered local horse breeds.

Abstract

The Croatian Posavina horse (CPH) is native Croatian breed under a conservation program and under various programs of economic use (ecosystem services, agrotourism, and meat production). The aim of this study was to analyze the status of the CPH population through an analysis of their pedigree (28,483 records), phenotype (292 licensed stallions, 255 mares), and genetic structure (292 licensed stallions). The average generation interval was 8.20 years, and the number of complete generations was 1.66. The effective number of founders and ancestors was 138 and 107, respectively, with a ratio of 1.29, and the genetic conservation index was 4.46. As for the morphometric characteristics, the average withers height of the stallions was 142.79 cm, the chest circumference was 194.28 cm, and the cannon bone circumference was 22.34. In mares, the withers height, chest, and cannon bone circumference were lower (139.71 cm, 190.30 cm, and 20.94 cm, respectively). Genetic microsatellite analysis of the 29 sire-lines showed high genetic diversity, expressed as the mean allele number (7.7), allele richness (4.0), and expected heterozygosity (0.740). There was no evidence of high inbreeding or a genetic bottleneck. The genetic and phenotypic data indicate that the CPH is an important and diverse reservoir of genetic diversity and can be conserved because of its special characteristics (adaptability).

Modern Northern Domestic Horses Carry Mitochondrial DNA Similar to Przewalski’s Horse

Several recent studies have suggested past gene flow between the Przewalski’s horse and modern domestic horse and questioned the wild origin of the Przewalski’s horse. Mitochondrial DNA has placed representatives of the Przewalski’s horse into three among the eighteen haplogroups detected from the modern horse. Of these, two haplogroups have so far been found exclusively in the Przewalski’s horse, while the one shared with the domestic horse includes captive individuals that have uncertain pedigrees. We recently found five domestic horse individuals of North European horse breeds to carry a mitochondrial haplogroup that was previously confined only to the Przewalski’s horse. These individuals were sequenced for 6039 bp of mitochondrial DNA and used, together with domestic and Przewalski’s horse sequences presenting all horse haplogroups, to examine the phylogenetic relationships and to date the divergence time between Przewalski’s and domestic horse clusters within this haplogroup. The divergence was dated to have likely occurred about 13,300–11,400 years ago, which coincides with the time of the Younger Dryas.

Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era

The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.

Maternal and paternal genetic variation in Estonian local horse breeds in the context of geographically adjacent and distant Eurasian breeds

The maternal and paternal genetic variation of horse breeds from the Baltic Sea region, including three local Estonian breeds, was assessed and compared with that of Altai and Yakutian horses. In the mtDNA D‐loop region, 72 haplotypes assigned to 20 haplogroups in the nine breeds were detected. In Estonian local breeds, 38 mtDNA haplotypes were found, and five of them were shared by the three breeds. More than 60% of all identified haplotypes were rare. Compared with the Estonian Native and Estonian Heavy Draught breeds, a higher haplotypic diversity was found in the Tori breed (h = 0.969). Moreover, four haplotypes shared among Finnish and Estonian local horse breeds indicated ancient ancestry, and of these, H30 (haplogroup D3) showed global sharing and genetic links between modern Baltic Sea region and Siberian horses, specifically. The studied breed set showed high variability in maternal inheritance and mixed patterns of the international and native breeds of the Siberian and Baltic regions. No variation was found in paternally inherited markers among horse breeds in the Baltic Sea region.

Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines

The Estonian Native Horse (ENH) is a medium-size pony found mainly in the western islands of Estonia and is well-adapted to the harsh northern climate and poor pastures. The ancestry of the ENH is debated, including alleged claims about direct descendance from the extinct Tarpan. Here we conducted a detailed analysis of the genetic makeup and relationships of the ENH based on the genotypes of 15 autosomal short tandem repeats (STRs), 18 Y chromosomal single nucleotide polymorphisms (SNPs), mitochondrial D-loop sequence and lateral gait allele in DMRT3. The study encompassed 2890 horses of 61 breeds, including 33 ENHs. We show that the expected and observed genetic diversities of the ENH are among the highest within 52 global breeds, and the highest among 8 related Northern European ponies. The genetically closest breeds to the ENH are the Finn Horse, and the geographically more distant primitive Hucul and Konik. ENH matrilines are diverse and relate to draught and Pontic-Caspian breeds. ENH patrilines relate to draught breeds, and to a unique haplogroup not described before. None of the 33 ENHs carried the "gait" mutation, but the mutation was found in 2 Huculs. The study demonstrates that the ENH is a genetically distinct and diverse breed of ancient origin with no notable pressure of selective breeding.

Genetic variability and history of a native Finnish horse breed

Background

The Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and colour, and severe population bottlenecks that are connected with its initial foundation and subsequent changes in agricultural and forestry practices. Here, we used sequences of the mitochondrial control region and genomic single nucleotide polymorphisms (SNPs) to estimate the genetic diversity and differentiation of the four Finnhorse breeding sections: trotters, pony-sized horses, draught horses and riding horses. Furthermore, we estimated inbreeding and effective population sizes over time to infer the history of this breed.

Results

We found a high level of mitochondrial genetic variation and identified 16 of the 18 haplogroups described in present-day horses. Interestingly, one of these detected haplogroups was previously reported only in the Przewalski’s horse. Female effective population sizes were in the thousands, but declines were evident at the times when the breed and its breeding sections were founded. By contrast, nuclear variation and effective population sizes were small (approximately 50). Nevertheless, inbreeding in Finnhorses was lower than in many other horse breeds. Based on nuclear SNP data, genetic differentiation among the four breeding sections was strongest between the draught horses and the three other sections (F_ST = 0.007–0.018), whereas based on mitochondrial DNA data, it was strongest between the trotters and the pony-sized and riding horses (Φ_ST = 0.054–0.068).

Conclusions

The existence of a Przewalski’s horse haplogroup in the Finnhorse provides new insights into the domestication of the horse, and this finding supports previous suggestions of a close relationship between the Finnhorse and eastern primitive breeds. The high level of mitochondrial DNA variation in the Finnhorse supports its domestication from a large number of mares but also reflects that its founding depended on many local landraces. Although inbreeding in Finnhorses was lower than in many other horse breeds, the small nuclear effective population sizes of each of its breeding sections can be considered as a warning sign, which warrants changes in breeding practices.

Electronic supplementary material

The online version of this article (10.1186/s12711-019-0480-8) contains supplementary material, which is available to authorized users.