An Overview of Ten Italian Horse Breeds through Mitochondrial DNA

Discrepancies between Genetic and Visual Coat Color Assignment in Sarcidano Horse

This study aimed to evaluate the discrepancies between genetic and visual coat color assignment in the Sarcidano Horse and to elucidate potential reasons. Individual DNA from 90 Sarcidano Horses was used for genetic assignment of coat color to explore the correspondence with individual forms containing phenotypical traits. The MC1R exon 1 and ASIP exon 3 have been genotyped and sequenced to obtain a picture of the coat color distribution in this breed. Surprisingly, once we compared the genetic results with the individual forms reporting the phenotypic data for each subject, a certain degree of non-correspondence between the phenotypic and genetic data in relation to coat color emerged. From the genetic analysis, Chestnuts (n = 58) resulted the most common Sarcidano Horse (n = 58), followed by a quite large number of Blacks (n = 28) and a very small number of Bays (n = 4), whereas phenotypic distribution resulted in 38 Chestnuts, 40 Bays, only 2 Blacks, and 10 Grays (without the possibility of recognizing the true color they carried). Chestnut resulted a very representative coat color, while many horses that visually identified as Bays were genetically Blacks. This discrepancy, that could be due to a variety of individual and external factors, including age, time of year, living situation and dietary condition, suggesting the importance of accurate coat color identification to ensure adequate features registration and reliable prediction of offspring's coat color.

Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia

The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and Seglawi) from the previous study for phylogenetic comparison. The whole mitochondrial genome sequencing resulted in intra and inter mtDNA variations between the studied horses. Interestingly, the Hamdani horse has nucleotide substitutions similar to those of the Hadban horse, which is reflected in the phylogenetic tree as a significantly close relationship. This type of study provides a better understanding of mitogenome structure and conservation of livestock species genetic data.

Y-Chromosome Haplotype Report among Eight Italian Horse Breeds

Horse domestication and breed selection processes have profoundly influenced the development and transformation of human society and civilization over time. Therefore, their origin and history have always attracted much attention. In Italy, several local breeds have won prestigious awards thanks to their unique traits and socio-cultural peculiarities. Here, for the first time, we report the genetic variation of three loci of the male-specific region of the Y chromosome (MSY) of four local breeds and another one (Lipizzan, UNESCO) well-represented in the Italian Peninsula. The analysis also includes data from three Sardinian breeds and another forty-eight Eurasian and Mediterranean horse breeds retrieved from GenBank for comparison. Three haplotypes (HT1, HT2, and HT3) were found in Italian stallions, with different spatial distributions between breeds. HT1 (the ancestral haplotype) was frequent, especially in Bardigiano and Monterufolino, HT2 (Neapolitan/Oriental wave) was found in almost all local breeds, and HT3 (Thoroughbred wave) was detected in Maremmano and two Sardinian breeds (Sardinian Anglo-Arab and Sarcidano). This differential distribution is due to three paternal introgressions of imported stallions from foreign countries to improve local herds; however, further genetic analyses are essential to reconstruct the genetic history of native horse breeds, evaluate the impact of selection events, and enable conservation strategies.

Genetic History of the Altai Breed Horses: From Ancient Times to Modernity

This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.

Mitochondrial DNA D-loop hyper-variable region 1 variability in Kurdish horse breed

BACKGROUND

Kurdish horse is one of the most valuable horse genetic resources in the Middle East.

OBJECTIVES

To assess the genetic diversity of Kurdish horses, Mitochondrial DNA D-loop hyper-variable region1 (HVR1) was sequenced in 29 non-related Kurdish horses which were sampled from diverse geographic regions of Iran.

METHODS

Total DNA was extracted from the collected blood samples by modified salting out method. The HVR1 was amplified by PCR and then sequenced using ABI PRISM BigDyeTM Terminator Cycle Sequencing Ready Reaction Kit. Consequently, the sequences were trimmed to 294 bp using BIOEDIT to become comparable with other reported HVR1 sequences in GeneBank. Sequence alignment was performed using CLUSTALW package. Haplotype and nucleotide diversity were estimated using DNASP5.10 and phylogenetic tree was constructed by neighbour joining method.

RESULTS

Fourteen different haplotypes and 22 polymorphic sites were detected. Haplotype diversity, nucleotide diversity and Tajima D values were 0.901 ± 0.001, 0.01153 ± 0.0020 and -1.378, respectively. Kurdish horse showed a high haplotype and low nucleotide diversity. The compositional frequency of consensus sequences for base A was the highest (29.93%) compared to other three nucleotides (C = 28.91%, T = 26.53% and G = 14.63%). As expected, all of the detected Kurdish horse haplotypes belonged to haplogroup K (i.e., Kurdish horses).

CONCLUSIONS

According to the phylogenetic analysis, Kurdish horses were genetically more closely related to Tibetan, Chinese, Bulgarian and Iranian native horse breeds, compared to other Asian horse breeds, but some traces of European horse breeds were detected in their maternal lines.

Phylogeographic and population genetic structure of hound-like native dogs of the Mediterranean Basin

The dog was probably the first domesticated animal. Despite extensive archaeological and genetic investigations, the origin and the evolution of the extant dogs are still being debated. Dog breeds that have over time been selected for hunting share common ancestral traits. This study represents the first comprehensive attempt to survey at the genomic and mitochondrial level eight hound-like dogs breeds indigenous to the Mediterranean Basin to determine if they share common ancient origins. Results from the microsatellite analysis indicate that all the dog populations have a low inbreeding value.The Kelb tal-Fenek has a high divergence from the current Egyptian street population, however there is not enough evidence from this study to exclude completely the potential of an ancient common relationship. Overall, the mitochondrial results indicate high frequencies of haplogroups A and B and a low representation of haplogroup C, while only one Egyptian dog could be assigned to haplogroup D. Results reveal identities and shared clades, suggesting the conservation of ancient European mitotypes in the Mediterranean hound-like breeds, especially in the Egyptian population. Although none of the dog populations/breeds participating in this study indicate to be direct descendants of the Egyptian dogs, they still have a very close morphologically resemblance to those iconic Egyptian dogs often depicted in ancient art forms and share some genetic links with the current Egyptian population. Further research is required with other markers such us complete mitogenomes and SNP panels to confirm the complex history of the Mediterranean dogs involved in this study.

Exploring the Italian equine gene pool via high-throughput genotyping

Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed. Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness.

Unlocking Horse Y Chromosome Diversity

The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.

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.

Вариабельность последовательности D-петли митохондриальной ДНК у лошадей забайкальской породы

The Zabaikalskaya horse is an indigenous breed of horses from Siberia with diverse use. It is characterized by endurance and good adaptability to year-round herd maintenance in the harsh conditions of the Baikal steppes. To determine the genetic characteristics of the maternal lineage of the Zabaikalskaya horse breed based on mitochondrial DNA polymorphisms, we collected hair samples from 31 horses belonging to breeding farms in the Trans-Baikal Territory. Analysis of the 530 bp sequence of the mtDNA D-loop was performed using the maximum composite likelihood (MCL) model in combination with bootstrap analysis. When studying the polymorphism of the hypervariable region of the mtDNA D- loop in Zabaikalskaya horses, we identif ied 31 haplotypes representing 8 haplogroups: B, C, G, H, L, M, Q and R according to modern classif ication. The sequenced fragment of the D-loop from nucleotide position 15471 to 16000 contained 17 polymorphic sites, mainly represented by the A→G, G→A and T→C transitions. The haplogroups Q (25.81 %), B (19.35 %), G (16.13 %) and H (12.90 %) were prevailing in the mtDNA structure of this breed. Genetic analysis of the mitochondrial genome of the Zabaikalskaya horse revealed a high level of diversity of haplotypes and haplogroups, which are typical for the horse populations of Eurasia.

Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse

Maternal lineages are important for the breeding decision in the Holstein horse breed. To investigate the genetic diversity of the maternal lineages and the relationships between founder mares, the maternal inherited mitochondrial genome (except the repetitive part of the non-coding region) of 271 mares representing 75 lineages was sequenced. The sequencing predominantly revealed complete homology in the nucleotide sequences between mares from one lineage with exceptions in 13 lineages, where differences in one to three positions are probably caused by de novo mutations or alternate fixation of heteroplasmy. We found 78 distinct haplotypes that have not yet been described in other breeds. Six of these occurred in two or three different lineages indicating a common ancestry. Haplotypes can be divided into eight clusters with all mares from one lineage belonging to the same cluster. Within a cluster, the average number of pairwise differences ranged from zero to 16.49 suggesting close maternal relationships between these mares. The results showed that the current breeding population originated from at least eight ancestral founder mares.

Polymorphisms at Myostatin Gene (MSTN) and the Associations with Sport Performances in Anglo-Arabian Racehorses

One hundred and eighty Anglo-Arabian horses running 1239 races were sampled for the present study. DNA was extracted from the blood and myostatin gene, MSTN, was genotyped. Moreover, prizes won and places were achieved for the 1239 races to perform association analyses between the different genotypes and sport traits. Two SNPs already reported in previous studies regarding the Thoroughbred breed, rs69472472 and rs397152648, were revealed as polymorphic. The linkage disequilibrium analysis investigating the haplotype structure of MSTN did not evidence any association block. Polymorphism at SNP rs397152648, previously known as g.66493737 T>C, significantly influenced sport traits, with heterozygous horses TC showing better results than homozygotes TT. The portion of variance due to the random effect of the individual animal, and the other phenotypic effects of sex, percentage of Arabian blood and race distance, computed together with the genotype at MSTN in the statistical models, exerted a significant influence. Hence, this information is useful to improve knowledge of the genetic profile of Anglo-Arabian horses and a possible selection for better sport performance.

Cost-effective horse breeding in the Republic of Bashkortostan, Russia

Background and Aim:

There is a lack of reliable data in agribusiness regarding the economic efficiency of horse breeding, and this limits its further development. The purpose of this study was to create rational parameters for the development of productive horse breeding as an effective agricultural business, in particular, in relation to farms.

Materials and Methods:

The methods of investigation used were induction and deduction, as well as analytical, statistical, and economic-mathematical analysis. We also used the dynamics of time series, CVP analysis, direct costing, and microeconomic analysis. Data were taken from the Russian Federation’s official statistics on animal husbandry as well as closed (commercial) data of agricultural enterprises from our study region.

Results:

Horse ownership in the Republic of Bashkortostan is higher than in the rest of Russia with about 9% of the total number of horses in Russia. We found that landowners need one hectare of arable land to ensure profit and that the highest economic income occurs on farms specializing in kumis production. The production of kumis under intensive farming is less profitable than with free-range horses kept in pastures. Family farms need a large amount of arable land with natural foliage to balance space and profit.

Conclusion:

Successful implementation of these parameters will make it possible to turn agriculture into successful horse breeding businesses. The expected volume of agricultural production may be approximately 9-11 thousand US dollars per employee.

Comprehensive analysis of mitochondrial and nuclear DNA variations in patients affected by hemoglobinopathies: A pilot study

The hemoglobin disorders are the most common single gene disorders in the world. Previous studies have suggested that they are deeply geographically structured and a variety of genetic determinants influences different clinical phenotypes between patients inheriting identical β-globin gene mutations. In order to get new insights into the heterogeneity of hemoglobin disorders, we investigated the molecular variations on nuclear genes (i.e. HBB, HBG2, BCL11A, HBS1L and MYB) and mitochondrial DNA control region. This pilot study was carried out on 53 patients belonging to different continents and molecularly classified in 4 subgroup: β-thalassemia (β+/β+, β0/β0 and β+/β0)(15), sickle cell disease (HbS/HbS)(20), sickle cell/β-thalassemia (HbS/β+ or HBS/β0)(10), and non-thalassemic compound heterozygous (HbS/HbC, HbO-Arab/HbC)(8). This comprehensive phylogenetic analysis provided a clear separation between African and European patients either in nuclear or mitochondrial variations. Notably, informing on the phylogeographic structure of affected individuals, this accurate genetic stratification, could help to optimize the diagnostic algorithm for patients with uncertain or unknown origin.

A Genetic Window on Sardinian Native Horse Breeds through Uniparental Molecular Systems

Simple Summary

The horse is a mammalian species showing a high variation among maternal lineages but a limited variability in the paternal inheritance. The female phylogenetic history is commonly investigated by analyzing the maternally transmitted mitochondrial DNA (mtDNA), while the male perspective is provided by the paternally inherited portion of the Y chromosome (NRY). Here we explored the variation of both non-recombining genetic systems in three horse breeds present in Sardinia: Giara, Sarcidano, and Sardinian Anglo-Arab. The analysis of 34 stallions revealed three differentially distributed NRY types: (i) the first and most ancestral one is typical of Sarcidano; (ii) the second is well represented in Giara and seems to derive from Neapolitan/Oriental stallions; (iii) the third confirms the Thoroughbred influence in the Sardinian Anglo-Arab breed. By extending the analysis to 178 mtDNAs, we observed a common maternal origin for Giara and Sarcidano. Contrarily, the outlier behavior of the Sardinian Anglo-Arab is due to its higher mitochondrial variability, testifying for multiple maternal lineages in its current population. Our preliminary findings highlight the importance of a parallel molecular screening of NRYs and mtDNAs to reconstruct both paternal and maternal phylogenetic histories and to fully evaluate the extent of autochthonous genetic resources in the island.

Abstract

Sardinia, an island located to the west of Italy in the Mediterranean Sea, boasts three native horse breeds: Giara, Sarcidano, and Sardinian Anglo-Arab. Here, we have investigated for the first time three loci of the non-recombining region of the Y chromosome (NRY) in 34 stallions from these breeds and performed a phylogenetic analysis of the maternal relationships among 178 previously published mitochondrial control regions. We found that the current NRY diversity of Sardinian horse breeds is linked to three haplotypes (HT), all identified within Sarcidano. Each breed showed a typical HT: HT1 (ancestral) was the most represented in Sarcidano, HT2 (Neapolitan/Oriental wave) in Giara, and HT3 (Thoroughbred wave) in Sardinian Anglo-Arab. The specificity of each haplotype suggests the influence of independent breeding strategies and the effect of genetic drift in each Sardinian population. The female counterpart, extended to 178 horses, showed a low genetic variability and a common maternal origin for Giara and Sarcidano. The higher variability of the Sardinian Anglo-Arab indicates multiple mare lineages in its current population. Further genetic analyses will be crucial to understand the paternal history of male horses, preserve the endangered mares’ and stallions’ lineages, and improve the enhancement of autochthonous genetic resources on this island.

Elo Method and Race Traits: A New Integrated System for Sport Horse Genetic Evaluation

Simple Summary

The current selection of the Sardinian Anglo-Arab horse (SAA) for racing is not based on any scientific method because the breeders decide only on their knowledge of pedigree and on the comparison of racing results. The comparison between competitors is a common situation in sports and games, and it might cause problems in horse performance evaluation. To overcome this problem in the game of chess, Elo suggested using a method based on winning chances. Elo’s system assumed that ranking probability for two competitors could be estimated from their rating difference. Even in horse races, the ranking of each horse, and consequently its earnings, depends on the level of its competitors. A genetic index based on Elo’s rating can clearly show the value of each animal. The strength of this method is that it allows evaluation of a horse by considering various different traits such as wins, placings, earnings over the entire career altogether.

Abstract

This first survey on Sardinian Anglo-Arab horse (SAA) race traits highlights important aspects for the breeding purpose of this population. The heritability of the race traits were estimated through a trivariate model; the estimates were 0.39, 0.33, and 0.30 for the number of placings, total earnings and Elo rating, respectively. The genetic progress could be improved by using an MT genetic evaluation of stallions and mares, combining information from competition traits.

Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse

The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In the current population, pedigree completeness was observed to be close to 100%, while the inbreeding coefficient and the average relatedness were lower than 3%. The ratio of effective founders/numbers of ancestors was 3.68 for the whole pedigree. The effective population size (N_e) computed by an individual increase in inbreeding (N_{e_1}) was 456.86, the N_e on equivalent generations (N_{e_2}) was 184.75, and this value slightly increased to 209.31 when computed by log-regression on equivalent generations (N_{e_3}). These results suggest the presence of crossbreeding and bottleneck phenomena, and they were compared with other Italian horses (reported in bibliography) to present the SAA among the Italian horse breeds scenario. Furthermore, the noteworthy mitochondrial variability reflects the use of a considerable number of founder mares; the contribution of L lineage was very important, probably because of the re-colonization from the Iberian Peninsula after the Last Glacial Maximum.

Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria

Poultry are the most widely distributed type of livestock in Nigeria. Indigenous chickens are extremely common throughout the country. Indeed, approximately 83 million chickens are raised in extensive systems and 60 million in semi-intensive systems. To provide the first comprehensive overview of the maternal lineages in Southwest Nigeria, we analyzed 96 mitochondrial DNA control region sequences from 2 indigenous chicken ecotypes: Fulani and Yoruba. All samples belonged to the most frequent haplogroup (E) in Africa and Europe and showed noticeably low haplotype diversity. Although only 11 different haplotypes were detected, with 2 of them never found before in Nigeria, the presence of unique sequences among our indigenous samples testified to their status as an important genetic resource to be preserved. Furthermore, a total of 7,868 published sequences were included in the comparative analysis, which revealed an east-west geographic pattern of haplogroup distribution and led to the conclusion that the gene flow from Southeastern Asia mainly involved one mitochondrial clade. Moreover, owing to the extensive genetic intermixing among Nigerian chickens, conservation efforts are required to safeguard the extant mitochondrial variability in these indigenous ecotypes and establish future improvement and selection programs.

Mitochondrial DNA variation in the Italian Heavy Draught Horse

Background

In the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook.

Methodology

To provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds.

Results

Among the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.

Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records

* Correspondence: andrea [...].

Genetic Parameters and Inbreeding Effect of Morphological Traits in Sardinian Anglo Arab Horse

The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses (27,052 females and 16,572 males) was provided by the Agricultural Research Agency of Sardinia (AGRIS). Cannon bone circumference (BC), chest girth (CG), shoulder length (SL), and withers height (WH) were measured on 6033 SAA horses born in Sardinia between 1967 and 2005; beside the measurements, an overall score (OS) was taken comparing the morphology of each horse to an "ideal type" that is scored out of 100. The mean value is 20.5 cm for BC, 185.9 cm for CG, 67.6 cm for SL, 160.8 cm for WH, and 73.2 for the OS. The heritability estimates ranged from 0.78 to 0.23. The results allow to foresee high genetic progress through the breeding programs. The most affected trait by the inbreeding rate seems to only be the withers height.

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.

Analysis of founders and performance test effects on an autochthonous horse population through pedigree analysis: structure, genetic variability and inbreeding

The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the 'Endog v 4.8' program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the most important one was the population of the 12 368 Maremmano horses officially registered in the National Studbook. The pedigree completeness of this population was very good because it was more than 90% at the third parental generation and more than 70% at the fifth generation; the pedigree traced back to a maximum of 10.50 generations with an average of 3.30 complete generations and 5.70 equivalent complete generations. The average generation interval was 10.65±4.72 years, with stallions used for longer periods than mares. The intervals ranged from 10.15±4.45 (mother-daughter) to 10.99±4.93 (father-daughter). The effective number of founders (f e) was 74 and the effective number of ancestors (f a) was 30 so that the ratio f e/f a was 2.47. The founder genome equivalents (f g) was 13.72 with a ratio f g/f e equal to 0.18. The mean of the genetic conservation index was 5.55±3.37, and it ranged from 0.81 to 21.32. The average inbreeding coefficient was 2.94%, with an increase of 0.1%/year, and the average relatedness coefficient was 5.52%. The effective population size (N e) computed by an individual increase in inbreeding was 68.1±13.00; the N e on equivalent generations was 42.00, and this value slightly increased to 42.20 when computed by Log regression on equivalent generations. The analysis confirmed the presence of seven traditional male lines. The percentage of Thoroughbred blood in the foals born in 2015 was 20.30% and has increased 0.21%/year since 1980; in particular, it increased more than twice (0.51%/year) until 1993 and afterwards slightly fluctuated. The pedigree analysis confirmed the completeness of genealogical information and the traditional importance that breeders gave to the male lines; although the genetic diversity of Maremmano seemed to be not endangered by the selection program, some effects on the population structure were found and a more scientific approach to genetic conservation should be incorporated in the selection plans.

Genetic Diversity and Structure of Iranian Horses' Population Based on Mitochondrial Markers

The source and history of horse domestication have been studied for decades in biology and archeology. The aim of this study was to evaluate the genetic structure and the genetic relationship between six breeds of native horses using mitochondrial D-loop region. Blood samples were collected from 96 horses. Total DNA was extracted, and 430 bp of D-Loop region (hyper variable) was amplified and sequenced using Sanger sequencing methods. The analysis of data led to identify 48 polymorphic sites that create 52 haplotypes. The plotted phylogenic tree for haplotypes of Iranian native horses is placed in the 11 haplogroups including A, B, C, E, G, I, L, M, N, P, and Q. Genetic and haplotype diversity values obtained were 0.0233 and 0.980, respectively. Nucleotide diversity (Pi) was observed between 0.0172 and 0.0242 in populations. In addition, the average number of nucleotide differences (k) ranged from 6.0 (Darehshori or Qashqai horse [DAH]) to 8.5 (Kord horse [KOH]) with an average value of 7.8. The highest and lowest genetic differentiates were observed between KOH and DAH (Fst = 0.193) and between North West native horse and horse riding club in North West (Fst = 0.003), respectively. Tajima D of 0.441 was obtained for all samples which was not significant (P > .01). The results indicate high genetic variety and numerous maternal lines in native horses of Iran.

Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin

BACKGROUND

Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin.

METHODOLOGY

The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison.

CONCLUSION

The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.

Genetic analysis of maternal and paternal lineages in Kabardian horses by uniparental molecular markers

Studies of mitochondrial DNA (mtDNA) as well as the non-recombining part of the Y chromosome help to understand the origin and distribution of maternal and paternal lineages. The Kabardian horse from Northern Caucasia which is well-known for strength, stamina and endurance in distance riding has a large gap in its breeding documentation especially in the recent past. A 309 bp fragment of the mitochondrial D-loop (156 Kabardian horses) and six mutations in Y chromosome (49 Kabardian stallions), respectively, were analyzed to get a better insight into breeding history, phylogenetic relationship to related breeds, maternal and paternal diversity and genetic structure. We found a high mitochondrial diversity represented by 64 D-loop haplotypes out of 14 haplogroups. The most frequent haplogroups were G (19.5%), L (12.3%), Q (11.7%), and B (11.0%). Although these four haplogroups are also frequently found in Asian riding horses (e.g. Buryat, Kirghiz, Mongolian, Transbaikalian, Tuvinian) the percentage of the particular haplogroups varies sometimes remarkable. In contrast, the obtained haplogroup pattern from Kabardian horse was more similar to that of breeds reared in the Middle East. No specific haplotype cluster was observed in the phylogenetic tree for Kabardian horses. On Kabardian Y chromosome, two mutations were found leading to three haplotypes with a percentage of 36.7% (haplotype HT1), 38.8% (haplotype HT2) and 24.5% (haplotype HT3), respectively. The high mitochondrial and also remarkable paternal diversity of the Kabardian horse is caused by its long history with a widely spread maternal origin and the introduction of Arabian as well as Thoroughbred influenced stallions for improvement. This high genetic diversity provides a good situation for the ongoing breed development and performance selection as well as avoiding inbreeding.

Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing

Background

The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks.

Methods

To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed.

Results

One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (H_d = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (H_d = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected.

Discussion

Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while.

Mitochondrial DNA genetic variations among four horse populations in Egypt

Horses are one of the early domesticated animals in the world that changed societies and civilizations on a continent-wide scale. Due to the rare information about the genetic characterization of different horse populations in Egypt, this study aimed to identify the genetic biodiversity and relationships between four horse populations reared in Egypt. Genomic DNA was extracted and mtDNA region was amplified using polymerase chain reaction (PCR). The alignment of 384-bp amplified fragments showed the presence of 41 polymorphic sites resulting in 29 haplotypes which their sequences were submitted to GenBank under the accession numbers: KX909898-KX909926. The phylogeny tree for tested horses declared the presence of mixing maternal lineages between the four tested populations but still there are some separated lineages especially for Arabian and Thoroughbred horses. The sequences of 72 tested sequences were aligned with 13 published sequences as references, 11 of them for different Equus caballus whereas the other two reference sequences for Equus burchellii and Equus asinus. The results showed that all tested horses from the four populations are grouped with reference sequences of Equus caballus and separated from the other two reference sequences of Equus burchellii and Equus asinus. It is concluded that sequence analysis of mtDNA control region is still the most informative tool for the identification of genetic biodiversity and phylogeny of different horse breeds and populations. The horse populations reared in Egypt possess low genetic diversity and all of them are belonged to Equus caballus breed.

Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation

The Polish Primitive Horse (PPH, Konik) is a Polish native horse breed managed through a conservation program mainly due to its characteristic phenotype of a primitive horse. One of the most important goals of PPH breeding strategy is the preservation and equal development of all existing maternal lines. However, until now there was no investigation into the real genetic diversity of 16 recognized PPH dam lines using mtDNA sequence variation. Herein, we describe the phylogenetic relationships between the PPH maternal lines based upon partial mtDNA D-loop sequencing of 173 individuals. Altogether, 19 mtDNA haplotypes were detected in the PPH population. Five haplotypes were putatively novel while the remaining 14 showed the 100% homology with sequences deposited in the GenBank database, represented by both modern and primitive horse breeds. Generally, comparisons found the haplotypes conformed to 10 different recognized mtDNA haplogroups (A, B, E, G, J, M, N, P, Q and R). A multi-breed analysis has indicated the phylogenetic similarity of PPH and other indigenous horse breeds derived from various geographical regions (e.g., Iberian Peninsula, Eastern Europe and Siberia) which may support the hypothesis that within the PPH breed numerous ancestral haplotypes (found all over the world) are still present. Only in the case of five maternal lines (Bona, Dzina I, Geneza, Popielica and Zaza) was the segregation of one specific mtDNA haplotype observed. The 11 remaining lines showed a higher degree of mtDNA haplotype variability (2-5 haplotypes segregating in each line). This study has revealed relatively high maternal genetic diversity in the small, indigenous PPH breed (19 haplotypes, overall HapD = 0.92). However, only some traditionally distinguished maternal lines can be treated as genetically pure. The rest show evidence of numerous mistakes recorded in the official PPH pedigrees. This study has proved the importance of maternal genetic diversity monitoring based upon the application of molecular mtDNA markers and can be useful for proper management of the PPH conservation program in the future.