Primitive Breeds Research Articles

Free‐ranging cattle and the return of the wolf: behavioral responses and implications for conservation management

Over the last decades, wolves have considerably expanded their distribution in Europe. Their range expansion even led to recolonizing densely human‐populated countries such as Belgium and the Netherlands. The few available studies on the effects of returning wolves in these landscapes focus primarily on the behavioral responses of wild ungulates, such as deer. While livestock in intensive farming practices can be protected against wolves, free‐ranging cattle in nature areas often have to protect themselves. How these cattle respond to the returned wolves is thus far unclear, yet highly relevant for conservation management. There is very little information about how free‐ranging cattle respond to the re‐appearance of wolves in terms of anti‐predator behavior and ability to defend themselves. In June 2022, a newly established wolf pair was located in a natural area in Drenthe. This natural area is grazed year‐round by free‐ranging Galloway cattle, a small and hornless primitive breed commonly used in conservation management. Here, we reported on the behavioral responses of the herd following two wolf attacks that occurred at nighttime in April 2023, the first caught on wildlife cameras in the Netherlands. During these events, the Galloways showed a clear behavioral response: they became active, restless and vigilant, and showed grouping behavior, presumably to protect the calves. Chasing behavior towards the attacking wolf was even exhibited by some individuals. The reported attacks did not result in killed or injured cattle. These two well‐documented wolf–cattle interactions show promising information as they highlight anti‐predator behaviors from an unexperienced cattle breed, all within a year of the wolves' return. We broadly discuss the relevance of these findings for grazing management, including selection for breeds, anti‐predator behaviors, and impact of herd structure and size, and we provide avenues for future research to address current knowledge gaps.

Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)

AbstractThe rapid expansion of wild pigs (Sus scrofa) throughout the United States has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the possession or transport of wild pigs. However, genetic and phenotypic similarities between domestic pigs and invasive wild pigs—which overwhelmingly represent domestic pig and wild boar hybrids—pose a challenge for the enforcement of such regulations. We sought to exploit wild boar ancestry as a common attribute among the vast majority of invasive wild pigs as a means of genetically differentiating wild pigs from breeds of domestic pig found within the United States. We organized reference high‐density single nucleotide polymorphism genotypes (1039 samples from 33 domestic breeds and 382 samples from 16 wild boar populations) into five genetically cohesive reference groups: mixed‐commercial breeds, Durocs, heritage breeds, primitive breeds, and wild boar. Building upon well‐established genetic clustering approaches, we structured the test statistic to describe the difference in the likelihood of a given genotype's ancestry vectors (sensu genetic clustering analysis) if derived strictly from the four described domestic pig reference groups versus allowing for admixture from the wild boar group. By fitting statistical distributions to test statistics of reference domestic pigs, we characterized the distribution of the null hypothesis that a given genotype descends strictly from domestic pig reference groups. We tested the approach with simulated genotypes and empirical data from an additional 29 breeds of domestic pig represented by 435 unique genotypes; all associated test statistics for simulated and empirical domestic pig challenge sets fell within the distribution of reference domestic pigs. We then evaluated 6566 invasive wild pigs sampled across the contiguous United States, of which 63% exceeded the maximum threshold for domestic pigs and could be statistically classified as possessing wild boar ancestry. This approach provides a scientific foundation to enforce regulations prohibiting the possession of this destructive invasive species. Further, this computationally efficient and generalizable approach could be readily adapted to quantify gene flow among ecological systems of conservation or management concern.

The genome-wide relationships of the critically endangered Quadricorna sheep in the Mediterranean region.

Livestock European diffusion followed different human migration waves from the Fertile Crescent. In sheep, at least two diffusion waves have shaped the current breeds' biodiversity generating a complex genetic pattern composed by either primitive or fine-wool selected breeds. Nowadays most of the sheep European breeds derive from the second wave which is supposed to have largely replaced oldest genetic signatures, with the exception of several primitive breeds confined on the very edge of Northern Europe. Despite this, some populations also in the Mediterranean region are characterised by the presence of phenotypic traits considered ancestral such as the policeraty, large horns in the ram, short tail, and a moulting fleece. Italy is home of a large number of local breeds, albeit some are already extinct, others are listed as critically endangered, and among these there is the Quadricorna breed which is a four-horned sheep characterised by several traits considered as ancestral. In this context we genotyped 47 individuals belonging to the Quadricorna sheep breed, a relict and endangered breed, from Central and Southern Italy. In doing so we used the Illumina OvineSNP50K array in order to explore its genetic diversity and to compare it with other 41 breeds from the Mediterranean region and Middle-East, with the specific aim to reconstruct its origin. After retaining 32,862 SNPs following data filtering, the overall genomic architecture has been explored by using genetic diversity indices, Principal Component Analysis (PCA) and admixture analysis, while the genetic relationships and migration events have been inferred using a neighbor-joining tree based on Reynolds' distances and by the maximum likelihood tree as implemented in treemix. The Quadricorna breed exhibit genetic diversity indices comparable with those of most of the other analysed breeds, however, the two populations showed opposing patterns of genetic diversity suggesting different levels of genomic inbreeding and drift (FIS and FROH). In general, all the performed genome-wide analyses returned complementary results, indicating a westward longitudinal cline compatible with human migrations from the Middle-East and several additional genetic footprints which might mirror more recent historical events. Interestingly, among the Italian breeds, the original Quadricorna (QUAD_SA) first separated showing its own ancestral component. In addition, the admixture analysis does not suggest any signal of recent gene exchange with other Italian local breeds, highlighting a rather ancestral purity of this population. On the other hand, both the neighbor-joining tree and the treemix analysis seem to suggest a proximity of the Quadricorna populations to breeds of South-Eastern Mediterranean origin. Although our results do not support a robust link between the genetics of the first wave and the presence of primitive traits, the observed genetic uniqueness together with the inferred phylogeograpic reconstruction would suggest an ancient presence of the Quadricorna breed in the Italian Peninsula. Because of this singularity, urgent conservation actions are needed in order to keep the breed and all related cultural products alive.

The ancestral origin of the critically endangered Quadricorna sheep as revealed by genome-wide analysis.

Livestock European diffusion followed different human migration waves from the Fertile Crescent. In sheep, at least two diffusion waves have shaped the current breeds’ biodiversity generating a complex genetic pattern composed by either primitive or fine-wool selected breeds. Among primitive breeds, aside from sharing common ancestral genomic components, they also show several traits such as the policeraty, large horns in the ram, short tail, and a moulting fleece, considered as ancestral. Although most of the primitive breeds characterized by these traits are confined on the very edge of Northern Europe, several residual populations are also scattered in the Mediterranean region. In fact, although in Italy a large number of local breeds are already extinct, others are listed as critically endangered, and among these there is the Quadricorna breed which is a four-horned sheep characterized by several ancestral traits. In this context we genotyped 47 individuals belonging to the Quadricorna sheep breed, a relict and endangered breed, from Central and Southern Italy. In doing so we used the Illumina OvineSNP50K array in order to explore its genetic diversity and to compare it with other 33 primitive traits-related, Mediterranean and Middle-East breeds, with the specific aim to reconstruct its origin. After retaining 35,680 SNPs following data filtering, the overall genomic architecture has been explored by using genetic diversity indices, Principal Component Analysis (PCA) and admixture analysis, while the genetic relationships and migration events have been inferred using a neighbor-joining tree based on Reynolds’ distances and by the maximum likelihood tree as implemented in treemix. Multiple convergent evidence from all our population genetics analyses, indicated that the two Quadricorna populations differ from all the other Italian breeds, while they resulted to be very close to the Middle Eastern and primitive European breeds. In addition, the genetic diversity indices highlighted values comparable with those of most of the other analyzed breeds, despite the two populations exhibit slightly different genetic indices suggesting different levels of genomic inbreeding and drift (FIS and FROH). The admixture analysis does not suggest any signal of recent gene exchange with other Italian local breeds, highlighting a rather ancestral purity of the two populations, while on the other hand the treemix analysis seems to suggest an ancient admixture with other primitive European breeds. Finally, all these evidences seem to trace back the residual Quadricorna sheep to an early Neolithic spread, probably following a Mediterranean route and that urgent conservation actions are needed in order to keep the breed and all related cultural products alive.

Aluminum tolerance and micronutrient content in the grain of oat cultivars with different levels of breeding improvement from the VIR collection

Background. Soil toxicity of Al is associated with severe changes in plant root morphology that limit the uptake of water and mineral nutrients. Long-term exposure to Al results in deficiencies in some important nutrients, such as phosphorus, calcium, magnesium, potassium, and iron. Thus, the joint study of plant resistance to the effects of Al and the accumulation of micronutrients in the oat grain is relevant.Materials and methods. Thirty oat accessions of Russian and French origin from the VIR collection served as the research material. They were represented by cultivars with different levels of breeding improvement: landraces (early 1920s), cultivars developed by primitive breeding (1920–1930s), and modern improved cultivars.Results. Oat cultivars with different breeding improvement levels demonstrated significant differences in the content of micronutrients and aluminum tolerance. Among the studied accessions, landraces and modern improved cultivars showed a tendency towards medium or high Al tolerance, the group of primitive cultivars from Russia had the lowest Al tolerance, while primitive cultivars from France demonstrated the highest average resistance (0.5–1.9).Conclusion. The content of Fe and Zn was influenced by the geographic origin of genotypes. The concentrations of different micronutrients positively correlated with each other. Strong correlations were recorded between the contents of Zn and Fe (r = 0.81), and between Zn and Mg (r = 0.75). There was a positive correlation between the content of micronutrients and the resistance to crown rust (0.38 to 0.50). High content of the studied set of micronutrients was registered in such improved cultivars from France as the naked ‘Avoine Nue Renne’, ‘Chantilly’, ‘Negrita’ and ‘Noire de Michamps’, plus the Russian improved naked cultivar ‘Gavrosh’. Among them, ‘Chantilly’ was distinguished for its yield, and the naked ‘Gavrosh ‘for its high tolerance to aluminum.

Konik, Tarpan, European wild horse: An origin story with conservation implications

Horses are gaining importance in European nature conservation management, for which usually so-called primitive breeds are favored due to their claimed robustness. An increasingly popular breed, the Konik horse, is often said to be the direct descendent of the alleged European wild horse, the Tarpan. However, both the direct descent of the Konik from European wild horses and the existence of the Tarpan as a wild species are highly debated. In this review, we scrutinized both contemporary research and historical sources and suggest that the Tarpan and the Konik as its direct descendent are manmade myths that hinder effective conservation management. We did not find evidence that the Tarpan was a wild horse rather than a feral horse. We did not find any evidence either for a closer connection between the Konik and any extinct wild horse than between other domestic breeds and wild horses. We discuss three perspectives on why the myth has become widely accepted and survived to this day: a historical-political, a biological-ecological, and an emotional perspective. It seems that the origin story of the Konik and its connection to the Tarpan was shaped by personal and political interests, including nationalistic ideas. These as well as general human emotions towards horses have influenced researchers and laypeople to keep the myth alive, which has been possibly negatively impacting contemporary nature conservation. Indeed, today’s Koniks originated from a small founder population of only six male lines that were selected according to their phenotypic traits, with the aim to rebreed the ‘wild Tarpan’. Strict breeding practices have led to high inbreeding levels in recent Konik populations, which may undermine nature conservation purposes. Therefore, we suggest that mythologized origin stories should not be an argument for selecting breeds of grazers for nature conservation.

Thermal features, ambient temperature and hair coat lengths: Limitations of infrared imaging in pregnant primitive breed mares within a year.

Infrared thermography is a non‐invasive technique which allows to distinguish between pregnant and non‐pregnant animals. Detecting accurate body surface temperatures can be challenging due to external factors altering thermograph measurements. This study aimed to determine the associations between the ambient temperature, the hair coat features and the temperatures of mares' abdomens. It compared pregnant and non‐pregnant mares throughout 11 months. The research was carried out on 40 Konik Polski mares, which were divided into pregnant and non‐pregnant groups. The temperature (Tmax, maximal; Taver, average; Tmin, minimal) of the mares' abdomen was evaluated in two regions of interest: the whole area of the lateral surface of the mares' abdomen (Px1) and the flank area of the lateral surface of mares' abdomen (Px2). During the increasing period, the slopes in the linear regression equation did not differ significantly for ambient (Tamb) and surface temperatures in both groups. In the decreasing period, the slopes did not differ significantly for Tamb and Tmax in the non‐pregnant group. They also did not differ for Tamb and Taver in Px1 and Tamb and Tmin in Px1 in both pregnant and non‐pregnant groups respectively. Other slopes varied significantly (p < .001). There was no evidence of parallel changes in hair coat features and measured temperatures. The flank area appears more suitable for thermal imaging in pregnant mares due to the seasonal fluctuations in hair coat lengths.

Owner-Reported Attachment and Behavior Characteristics of New Guinea Singing Dogs Living as Companion Animals

ABSTRACT Domestic dogs are terrific companions in a variety of contexts. However, not all dogs have followed the same trajectory regarding domestication. In fact, little is known about how some dogs, including New Guinea singing dogs (NGSDs), fare as companion animals. The majority of NGSDs in the United States and Canada live as companion animals, yet observational studies of NGSDs have been limited to those living in zoos and in the wild. To learn more about NGSDs kept as companion animals, we compared housing and husbandry practices for NGSDs (n = 55) with those of dogs belonging to five primitive Fédération Cynologique Internationale (FCI) subgroups (n = 1,101). We also compared behavioral traits of NGSDs and dogs belonging to the FCI subgroups using the Canine Behavioral Assessment and Research Questionnaire (C-BARQ), and their relationships with their owners using the Lexington Attachment to Pets Scale (LAPS). NGSDs differed from dogs belonging to some FCI subgroups on several C-BARQ measures. For instance, NGSDs showed greater fear than dogs in some subgroups and were more likely to urinate on objects than dogs in all subgroups. The latter finding might explain why a higher percentage of NGSDs than primitive breed dogs were housed outdoors. Nonetheless, NGSD owners scored just as highly on the LAPS as owners of other primitive dogs. Our findings suggest that NGSD owners may adapt their expectations and husbandry strategies to account for some of the behavioral differences between NGSDs and other dogs.

Eye contact and sociability data suggests that Australian dingoes were never domesticated.

Dogs were the first animal to become domesticated by humans, and they represent a classic model system for unraveling the processes of domestication. We compare Australian dingo eye contact and socialization with Basenji and German Shepherd dog (GSD) breeds. Australian dingoes arrived in Australia 5,000–8,000 BP, and there is debate whether they were domesticated before their arrival. The Basenji represents a primitive breed that diverged from the remaining breeds early in the domestication process, while GSDs are a breed dog selected from existing domestic dogs in the late 1800s. We conducted a 4-phase study with unfamiliar and familiar investigators either sitting passively or actively calling each canid. We found 75% of dingoes made eye contact in each phase. In contrast, 86% of Basenjis and 96% of GSDs made eye contact. Dingoes also exhibited shorter eye-gaze duration than breed dogs and did not respond to their name being called actively. Sociability, quantified as a canid coming within 1 m of the experimenter, was lowest for dingoes and highest for GSDs. For sociability duration, dingoes spent less time within 1 m of the experimenter than either breed dog. When compared with previous studies, these data show that the dingo is behaviorally intermediate between wild wolves and Basenji dogs and suggest that it was not domesticated before it arrived in Australia. However, it remains possible that the accumulation of mutations since colonization has obscured historical behaviors, and dingoes now exist in a feralized retamed cycle. Additional morphological and genetic data are required to resolve this conundrum.

Evaluation of open-pollinated offspring in Cyclamen persicum using vegetative phenology models in a primitive breeding population

Abstract Cyclamen is commercially cultivated to produce the pot and garden flowering plants by sowing the seeds, and the number of leaves is an important trait for the beginning of the initiations of flower buds and flowering. The yield potential is affected by the life cycle of a plant and the plant breeders can have good decisions making with the prediction of plant phenology. In this study, a polynomial function was proposed for modeling behavior of cyclamen offspring during the vegetative growth. This modeling is based on information on environmental changes and plant morphology up to the flowering stage. For this purpose, 30 pots (individuals) from a 121-individual population, which were the same in the size, were considered for sampling of data. The data were recorded as time series that include temperature (°C), relative humidity (%), leaf width (mm) and number of leaves. The output of this model is the number of leaves and the recorded inputs are the time (growth cycle; days), temperature, relative humidity and leaf width. Using the Quantum-behaved Particle Swarm Optimization (QPSO) algorithm, the constant coefficients of the proposed function (linear model) was calculated to match the input and output values to each other. To illustrate the robustness and efficiency of model, the growth rates of all individuals were compared using this proposed model. The result of root mean square error (RMSE), mean absolute error (MAE), and coefficient of determination (R 2 ) between the estimated and observed values for each individual showed that 63% of the tested open-pollinated (OP) population is marketable. Therefore, phenology model could be a good estimation of the vigor of the OP population for commercial production. It should be noted that in obtaining the model, only five individuals were used randomly as training data, and the obtained model was fitted to the others as test dataset without changing the coefficients. Furthermore, a Gaussian model of the whole dataset showed that the OP seeds of cyclamen could be utilized to produce the potted flowering cyclamen without any worry about non-uniformity of harvest for the market if the optimum temperature would be adjusted.

Variability of ACOX1 Gene Polymorphisms across Different Horse Breeds with Regard to Selection Pressure.

Simple SummaryThe genetic mechanisms occurring in organisms are shaped by selection pressure. Features that ought to be useful under given conditions leave their marks on the genome in the form of mutations, thereby creating different alleles. In this study, five different horse breeds were examined to find the connection between an individual’s lifestyle and the presence of the peroxisomal acyl-coenzyme A oxidase 1 (ACOX1) gene, which is necessary for some metabolic pathways. Results indicated that different ACOX1 gene alleles play various roles in primitive breeds and domesticated horses. This led to the conclusion that the DNA profile can be rated on the basis of adaptation to living conditions, opening the gate for further investigation.The ACOX1 gene encodes peroxisomal acyl-coenzyme A oxidase 1, the first enzyme in the fatty acid β-oxidation pathway, which could be significant for organisms exposed to long periods of starvation and harsh living conditions. We hypothesized that variations within ACOX1, revealed by RNA Sequencing (RNA-Seq), might be based on adaptation to living conditions and had resulted from selection pressure. There were five different horse breeds used in this study, representing various utility types: Arabian, Thoroughbred, Polish Konik, draft horses, and Hucul. The single-nucleotide polymorphism (SNP) located in the ACOX1 (rs782885985) was used as a marker and was identified using the PCR restriction fragment length polymorphism method (PCR-RFLP). Results indicated extremely different genotype and allele distributions of the ACOX1 gene across breeds. A predominance of the G allele was exhibited in horses that had adapted to difficult environmental conditions, namely, Polish Konik and Huculs, which are considered to be primitive breeds. The prevalence of the T allele in Thoroughbreds indicated that ACOX1 is significant in energy metabolism during flat racing.

Breed-related differences in the preference for inanimate objects between chicks of laying hens

Our previous study showed significant behavioural differences between breeds of laying hens. Birds differed in their excitability, reactivity, decision-making speed, behavioural strategy, and interest in elements of the surroundings. The results of our investigations and studies conducted by other authors raised a question of potential differences between chicks of different breeds in their preference for objects mimicking a member of their social group or a potential predator. Theoretically, the answer to the question was provided tens of years ago; however, new insight into this problem was provided by some researchers in experiments where breed-related differences associated with imprinting were demonstrated. Therefore, we have now asked questions whether reactions to objects imitating chick's mother and a predator may differ between breeds and whether the history of selection of the breed may be associated with chicks' preference for specific objects. We have also tried to verify whether the fact that the chicks have not been in contact with such objects for many generations has an impact on their ability to discriminate between the objects.The study involved three breeds (Green-legged partridge - Zk, Leghorn - Lg, and Crested hen - Ch) differing in their selection history, laying performance, and purpose of breeding. Lg hens are particularly suitable for intensive farming, Zk is a primitive breed used in extensive farming, and Ch is a general-purpose breed intended for organic farming. The preference of 1- and 5-day-old chicks for an object imitating the mother (a stuffed hen) and a potential predator (a stuffed polecat) was examined. Chicks' activity and preference were assessed. The registered traits were subjected to one-way analysis taking into account Bernoulli distribution using the linear model of the GLIMMIX procedure of SAS software (Statistical Analysis System, 9.4, 2013). Orthogonal contrasts were used to verify comparisons of genetic group effects using the Holm-Bonferroni correction.A surprising finding was the preference of the Lg chicks for the stuffed polecat. The Zk and Ch chicks clearly preferred the hen. The differences in the preference for the object between the breeds were significant, whereas no differences were found between the chicks' activity. Each breed was dominated by active chicks making a specific choice. It seems that the intensive selection towards high laying performance may lead to social predisposition anomalies through a correlated reaction, and the Lg breed can be a research model for this type of disorders.

The Phenotype Variability, of the Racka Sheep in the Republic of Serbia

The intensification of sheep production, by permanent genetic selection and the development of breeding technology, has led to the creation of highly productive sheep breeds. In this way, many highly productive breeds were created which could demonstrate their high production potentials only under perfect conditions of nutrition, accommodation and care. Preservation of indigenous breeds is of great importance in order to protect and safeguard those breeds and, in this way, it is possible to restore some of the characteristics that are lost during intensive selection, which are mostly related to resistance. The Racka sheep (Serbian: Vitoroga žuja) is considered to be an autochthonous breed and a genetic resource in the Republic of Serbia. As a primitive breed with low productivity, it offers no economic profitability and, thus, there is no great interest in its breeding. According to the FAO data from 2008-2014, the number of these sheep ranges from 500 to 1000. The objective of this study was to determine the phenotypic variability and to assess the external measurements of the Racka sheep. One-hundred fifty Racka breed ewes were included in this study. The effects of three farms on the phenotypic characteristics and their body indexes were calculated. The significance of the research is reflected in the advancement of this breed and in the assessment of the possibilities of selection work in these herds.

The quality of traditionally smoked tenderloins obtained from meat of native pig breeds

The domestic (homeland, native) populations - breeds of pigs are grown in certain region and/or country as local, primitive breeds. In Poland following 3 pig breeds are considered as native: Pulawska, Zlotnicka White and Zlotnicka Spotted. The aim of this study was the assessment of the quality of meat and traditionally smoked tenderloins obtained from meat of native pigs breeds bred in a traditional way. Meat analysis showed that the highest fat content values were present in Zlotnicka Spotted (4.60 ? 0.33) and White (3.63 ? 0.41) while the lowest in Pulawska (2.78 ? 0.29). Smoked tenderloins shear force differed statistically. The hardness values were the highest for Zlotnicka White (65.66 ? 6.46) and the lowest for Zlotnicka Spotted (33.27 ? 4.12). Similar shear force values were recorded: the highest in Zlotnicka White (51.90 ? 7.11) and the lowest in Zlotnicka Spotted (30.43 ? 5.54). Regardless of the results obtained, meat products have good acceptance of sensory assessment test and low level of polycyclic aromatic hydrocarbons. We conclude that the meat of Pulawska, Zlotnicka White and Spotted breeds of pigs is a good quality raw material used for production of traditional and regional meat products gaining high sensory scores and good recognition among consumers. The traditionally smoked tenderloins produced from meats of above breeds, were characterized by very good quality parameters.

Genetic Variability in the Loci of FABP4, PPARγ and SCD Genes of Sheep Breeds Raised for Different Purposes

Abstract The present study was undertaken to analyse the genetic variation in coding sequences, splicing sites and regulatory sequences of FABP4, PPARγ and SCD genes in five breeds of sheep raised in Poland with different purposes: meat (Suffolk, Ile de France), dairy/prolific (Olkuska sheep, Kołuda) and primitive breeds (Polish Mountain Sheep). To identify genetic variability HRM-PCR, sequencing and PCR-RFLP method were used. Determining the genetic structure of the mentioned genes revealed six SNPs: FABP4 – c.73 + 13A&gt;T and c.348 + 85G&gt;A, PPARγ – c.391 – 66C&gt;T (c.481 – 66C&gt;T) and c.529 + 27G&gt;C (c.619 + 27G&gt;C), SCD – c.*945G&gt;A and c.*1116A&gt;G. For the c.*1116A&gt;G SNP, a potential association with specific sheep body type and breeding purpose was found. In turn, the substitution c.*945G&gt;A located in the regulatory region of the 3'-UTR of the Ovis aries SCD gene was identified for the first time. Based on the relationship demonstrated between sheep body constitution and productive type (dairy, meat) and the polymorphism of the SCD gene, further research is needed. The correlation between c.*1116A&gt;G polymorphism and growth rate, slaughter and carcass value as well as meat quality of lambs needs to be studied in more detail. Such studies may lead to more effective selection processes in sheep breeding in the future.

Whole genome studies of origin, selection and adaptation of the Russian cattle breeds

Our review presents several recent studies on the genetic history and signatures of selection in genomes of the native Russian cattle breeds. Most of these works are not easily accessible for the Russian-speaking audience. We describe the origins of appearance of the Russian cattle breeds from the genetics perspective. We point to the links between most of the Russian breeds with the taurine breeds of the European origin and for some Russian breeds with the breeds of the Asian origin. We describe major phylogenetic clusters of the Russian breeds and point to those that still maintain their unique genetics, meaning that their preservation is a priority. In addition, we review the results of the search for signatures of selection in genomes of the Russian cattle breeds. Some unique signatures of selection present in the genomes of so-called “turano-mongolian” cattle (i. e. the Yakut cattle) are described which allowed the Yakut cattle to adapt to harsh environments found above the Polar Circle. Signatures of selection which could help other cattle breeds of the Russian origin to adapt to various climatic condition of the Russian Federation are reviewed. The Russian cattle genomes also contain known signatures of selection related to cattle domestication about 8–10 thousand years ago. The most profound ones include genes related to changes of the coat colour. This phenotype in many cases could be related to the distinction of the first domesticated populations and lead to the formation of so-called land races (primitive breeds). Whole-genome association studies of Russian cattle breeds pointed to a novel gene which could be related to the “white-faced” phenotype and to a gene which is related to body temperature support under the acute cold stress. The data presented in our review could be used for identification of genetic markers to focus on in future efforts on designing new highly productive cattle breeds adapted to climates of the Russian Federation and other countries with similar climates.

Genetic variability and history of a native Finnish horse breed

BackgroundThe 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.ResultsWe 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 (FST = 0.007–0.018), whereas based on mitochondrial DNA data, it was strongest between the trotters and the pony-sized and riding horses (ΦST = 0.054–0.068).ConclusionsThe 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.

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

BackgroundIberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.ResultsWe sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow.ConclusionsOur results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.

The Disappearing Lamellae: Implications of New Findings in the Family Equidae Suggest the Loss of Nuchal Ligament Lamellae on C6 and C7 Occurred After Domestication

Conflicting data predominantly describes the equine nuchal ligament lamellae (NLL) attachments as C2–C6 or C2–C7; however, preliminary evidence suggests C2–C5. This study aimed to identify morphological variations in the attachments of the NLL in four species of the family equidae and determine if the variations were species or breed linked. Cadaveric examination evaluated 98 equids; Equusasinus (n = 2), Equus ferus caballus (n = 93), Equus przewalskii (n = 2), and Equus quagga boehmi (n = 1). Twenty breeds of E. f. caballus were included according to breed type—modern horse (n = 81), ancient type (n = 10), primitive (n = 4). Of the 98 equids, observations were divided into three categories according to the NLL attachments: C2–C5, C2–C6, and C2–C7; in category C2–C7, E. f. caballus (n = 3/93), modern horse 0 of 81, ancient 1 of 8, primitive 2 of 4; in category C2–C6, modern horse 2 of 81; in category C2–C5, modern horse 79 of 81, ancient type 7 of 8, primitive 2 of 4. Equus asinus, E. przewalskii, and E. q. boehmi all expressed category C2–C7. In total, 88 of 98 expressed category C2–C5; 2 of 98 category C2–C6; and 8 of 98 category C2–C7. These findings suggest that category C2–C5 provides sufficient evidence to suggest a normal occurrence. The high incidence of an absent NLL on C6 and C7 may be considered a contributing factor in caudal cervical osteoarthritis. Furthermore, category C2–C7 still exists in an ancient and primitive breed closely related to the tarpan, implying the NLL may have been attached from C2 to C7 in prehistoric horse before domestication. This hypothesis is supported by the findings of E. asinus, E. przewalskii, and E. q. boehmi, displaying attachments from C2 to C7.

Genetic diversity analysis of the Mexican Lidia bovine breed population and its relation with the Spanish population by using a subset of SNPs under low gametic disequilibrium

Retaining features of the auroch (Bos taurus primigenius), the Lidia bovine is a primitive breed originated ~250 yr ago in the Iberian Peninsula, where is still distributed, along with France and several American countries. Selected upon a behavior, which enhances their aggressiveness; these bovines were raised to participate in popular festivities that nowadays reinforce the identity of regional cultures. Different festivities demanded diverse behavior patterns, prompting a fragmentation of the breed into small lineages. In Mexico, where these bovines reached high popularity, mainly two families of breeders imported Lidia bovines from Spain in the early XX century specializing their production either reproducing the new arrivals among them or realizing systematic crosses with local populations. Genetic diversity and structure of the Mexican and Spanish Lidia populations has been assessed with microsatellite data, but nowadays SNP molecular markers allows higher resolution level. Genetic diversity of the Mexican and Spanish Lidia populations and their relationship were assessed by using 573 SNPs with a low gametic disequilibrium (r2&lt;0.01) from the 50K BeadChip on 468 individuals from both populations. In both populations, similar gene diversity values were observed. Significant FIS values in both populations means strong subdivision, higher FST genetic distances were observed in the Spanish than in the Mexican population. Genetic structure analysis showed similarity of three Spanish lineages with González family and some Llaguno breeders, but most Llaguno family clustered separated: genetic differentiation along with high gene diversity suggest an introgression of creole cattle in the constitution of the Mexican population.