Mitochondrial Diversity and Phylogenetic Relationship of Eight Native Bulgarian Sheep Breeds.

The geographical, geomorphological, and climatic characteristics of Bulgaria are particularly favorable for animal breeding and, above all, for pastoral farming and sheep breeding. These conditions created prerequisites for the creation of about 30 unique local breeds of sheep. In this study we investigated the genetic diversity of eight of the most popular Bulgarian native breeds, based on the sequence analysis of a part of the mitochondrial D-loop region. An almost entire mitochondrial DNA (mtDNA) D-loop region (1180 bp) was amplified and sequenced. The obtained results showed the presence of a large number of haplotypes-225, belonging to two main haplogroups. The majority of samples showed a high prevalence of the European haplogroup B (95.2%) while the remaining individuals were assigned to haplogroup A (4.8%). None of the other reported mitochondrial haplogroups were observed. The number of polymorphic sites, nucleotide and haplotype diversity was high (240, 0.01237, and 0.9968, respectively), which is evidence for multiple maternal origins in all populations. The Tajima D-test value in all the study populations was -1.905 (p < 0.05), indicating that the abundance of rare alleles was most likely due to population expansion after a recent bottleneck. The Median joining network showed that almost all haplotypes belonging to haplogroup B formed a star-like network, which revealed a weak genetic differentiation and a large gene flow between the Bulgarian native breeds.

Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives - Danubian horse and Serbian Nonius.

From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses.The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds - the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O'P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O'P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations.In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.

Genetic Diversity and Structure of the Main Danubian Horse Paternal Genealogical Lineages Based on Microsatellite Genotyping.

The Danubian horse, together with the Pleven and the Eastern Bulgarian horse breeds, is one of the modern breeds in Bulgaria. The objective of this study was to compare the genetic structure and genetic diversity of six paternal genealogical lineages of the Danubian horse breed (Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar). In total, 166 individuals from the six genealogical lines were investigated, based on 15 STR markers (short tandem repeats, also known as microsatellites). In total, 184 alleles were found in the six populations, using 15 microsatellite loci. The mean number of alleles, the effective number of alleles, and the polymorphic information content (PIC) values per locus were 12.28, 9.48, and 0.73, respectively. In a comparison of the allelic diversity among sire lineages, the highest genetic diversity (Na) was observed in Lider and Kalifa (14.60 ± 0.21), while the lowest value of this parameter was observed in the Zdravko lineage 4.20 ± 0.35. The largest genetic diversity was found in loci HMS3 and HMS7, with 13 alleles, and the smallest polymorphism was noted for the locus ASB17, with 10 alleles. The level of observed heterozygosity was in the range of 0.65 ± 0.069 for the Zdravko lineage to 0.93 ± 0.01 for the Torpedo lineage. The expected heterozygosity level range was from 0.57 ± 0.048 to 0.91 ± 0.01 for all horse lineages. Structure analysis revealed three main gene pools in the study population. The first pool included the Zdravko lineage; the second had the NONIUS XVII-30, Torpedo, Lider, and Kalifa lineages; and the third defined the Hrabar lineage, which was significantly differentiated from the other genealogical lineages.

The Sequence Analysis of Mitochondrial DNA Revealed Some Major Centers of Horse Domestications: The Archaeologist's Cut.

The question about the time and the place of horse domestication, a process which had a profound impact on the progress of mankind, is disputable. According to the most widely accepted hypothesis, the earliest domestication of the horse happened in the western parts of the Eurasian steppes, between the Northern Black Sea region and present-day Kazakhstan and Turkmenistan. It seems that it occurred not earlier than the first half and most probably during the middle (even the last third) of the fourth millennium BC (from ∼ 5.5 kya). The next steps of large-scale horse breeding occurred almost simultaneously in Eurasia and North Africa due to the development of the social structure of human communities. On the other hand, the morphological differences between wild and domestic animals are rather vague and the genetic introgression between them is speculative. In this review, we have tried to gather all available scientific data on the existing possible hypotheses for the earliest domestication of the horse, as well as to highlight some data on the most plausible ones. This is due to the frequency of some significant data on the frequency of strictly defined mitotypes in different historical periods of human civilizations existing in the same periods.

Sequence analysis of the mitochondrial D-loop region throws a new light on the origin of Hungarian Nonius, Danubian Horse and Serbian Nonius.

The objective of our study was to investigate the genetic structure of yet uninvestigated populations of three closely related horse breeds - the Danubian Horse, the Hungarian Nonius and the Serbian Nonius - in order to clarify their origin and genetic diversity. A 640-bp-long fragment of the mtDNA D-loop region was amplified and sequenced. The results showed that the investigated breeds have different genetic profiles although they share some common characteristics. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fall into the M, L, G, and O'P lineages, which is indicative of the genetic profile of the ancestral mares that had probably been used at the initial stages of the formation of the breeds. The population of the Danubian Horse is characterised by a high prevalence of the Anatolian specific haplogroup G (45%), followed by the Western Eurasian specific haplogroups L and M (both about 21%). In the Hungarian Nonius breed we found the highest frequency of the Western Eurasian haplogroup M (44%), followed by the Middle Eastern O'P (26%) and the Central Asian specific E (13%) and G (13%). The Serbian Nonius showed a distinct genetic profile, characterised by a high prevalence of the rare European haplogroup D (67%), followed by the Central Asian specific haplogroup G (17%). The high percentage of haplogroups shared especially between the Danubian and the Hungarian Nonius indicates the possibility of a common origin of the two breeds. In contrast, the Serbian Nonius showed a specific genetic profile, which can be explained by a different and independent origin.