Mitochondrial Sequence Reveals High Levels of Gene Flow Between Breeds of Domestic Sheep from Asia and Europe

The evolution of contemporary livestock species: Insights from mitochondrial genome

The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.

Phenotype transition from wild mouflon to domestic sheep

The domestication of animals started around 12,000 years ago in the Near East region. This "endless process" is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today's domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.

Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia

Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429-3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429-3556 BP) found in the Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429-3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.

Assessment of genetic diversity of the fat-tailed Dumba sheep of India by mitochondrial and microsatellite markers

India has a centuries-old tradition of sheep production and breeding that accomplish economic, agricultural, and religious roles. In addition to the 44 registered sheep breeds, there is a fat-tailed sheep population referred to as Dumba. This study evaluated genetic variation in Dumba sheep and its differentiation from other Indian sheep breeds using mitochondrial DNA and genomic microsatellite loci. Haplotype and nucleotide diversity based on mitochondrial DNA analysis revealed substantially high maternal genetic diversity in Dumba sheep. Major ovine haplogroups A and B observed in sheep populations across the globe registered their presence in the Dumba sheep. The molecular genetic analysis using microsatellite markers also showed high measures of allele (10.125 ± 0.762) and gene diversity (0.749 ± 0.029). Results correspond to the non-bottleneck population that is near mutation-drift equilibrium despite some deficiency in the number of heterozygotes (FIS = 0.043 ± 0.059). Phylogenetic clustering confirmed Dumba to be a distinct population. Results of this study endow authorities with critical information imperative for sustainable utilization and conservation of Indian fat-tailed sheep, which is considered to be an untapped genetic resource contributing to the food security, livelihood, and economic sustainability of rural households in marginal areas of the country.

Genetic diversity and relationship among Indonesian local sheep breeds on Java Island based on mitochondrial cytochrome b gene sequences

BACKGROUND

The cytochrome b (Cyt b) gene is one of the most studied mitochondrial DNA (mtDNA) genes to determine sheep's genetic profile. This study aimed to determine the genetic diversity and relationships of several Indonesian local sheep populations on Java Island, Indonesia, based on the mtDNA Cyt b gene sequences. Blood samples were collected from forty-one individual sheep in seven populations of Indonesia local sheep breeds on Java Island (Priangan = 6, Garut = 6, Batur = 7, Wonosobo = 5, Javanese Thin-Tailed/JTT = 7, Javanese Fat-Tailed/JFT = 5, and Sapudi = 5). DNA extraction was performed on blood samples, and the mtDNA Cyt b gene was amplified using specific primers (Alek-CBF: 5'-CAACCCCACCACTTACAA-3' and Alek-CBR: 5'-CCTTGAGTCTTAGGGAGGTT-3'). The polymerase chain reaction (PCR) products were then sequenced, and data were analyzed using the MEGA version 7.0, DNA SP version 6.0, and NTSYS-pc version 2.11 software.

RESULTS

A total of 1140 bp complete mtDNA Cyt b gene sequences in this study obtained 1134 monomorphic sites (I), six polymorphic sites (V), one segregation site (S), and five parsimony informative sites (P) with a nucleotide diversity (Pi), the average number of nucleotide differences (K), and sequence conservation (SC) were 0.00119, 1.35610, and 0.9947, respectively. There were six haplotypes consisting of two unique haplotypes and four shared haplotypes with a haplotype diversity (Hd) of 0.5415. The genetic distance within and between populations ranged from 0.0000 to 0.0016 and 0.0000 to 0.0020, respectively. Wonosobo, JFT, and Sapudi sheep have the closest relationship, and then these three breeds were close to JTT sheep, followed by Batur, Priangan, and Garut sheep. Two haplogroups have been found based on the Ovine haplogroup clustering. All Wonosobo, JTT, JFT, Sapudi sheep, and most Batur sheep were clustered into haplogroup B. In contrast, Garut sheep were mostly clustered into haplogroup A, while Priangan sheep were clustered into both haplogroups with the same percentage.

CONCLUSION

Seven Indonesian local sheep breeds on Java Island have a close relationship clustered into two haplogroups, namely haplogroups A and B. Most Indonesian local sheep breeds on Java Island in this study were clustered into haplogroup B, except for Garut and Priangan sheep.

Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes

Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.

Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros

We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).

Maternal Relationships among Ancient and Modern Southern African Sheep: Newly Discovered Mitochondrial Haplogroups

Simple Summary

The genetic diversity of southern African sheep remains under-studied. We present here the complete mitochondrial genomes of archaeological southern African sheep, as well as the genomes from three indigenous southern African breeds—Damara, Namaqua Afrikaner, and Ronderib Afrikaner. We show that southern African sheep exhibit limited genetic diversity which is consistent with our understanding of their migration south from northernmost Africa. Intriguingly, many of the modern sheep show close relationships with the archaeological sheep, implying an ancestor-descendant relationship. Similarly, the sheep that do not exhibit a close relationship with the archaeological sheep nonetheless cluster closely with each other and do not show a close relationship with European and Asian sheep. This suggests that they too are descendants of indigenous sheep and not the product of historic introductions of exotic breeds.

Abstract

We investigated the genetic diversity and historic relationships among southern African sheep as well as the relationships between them and sheep outside the continent by sourcing both archaeological and modern sheep samples. Archaeological sheep samples derived from the site Die Kelders 1, near Cape Town, date to approximately 1500 years ago. The modern samples were taken as ear snips from Damara, Namaqua Afrikaner, and Ronderib Afrikaner sheep on a farm in Prieska in the Northern Cape. Illumina sequencing libraries were constructed for both ancient and modern specimens. Ancient specimens were enriched for the mitochondrial genome using an in-solution hybridization protocol and modern specimens were subjected to shotgun sequencing. Sequences were mapped to the Ovis aries reference genome, assigned to haplogroups and subhaplogroups, and used to calculate a phylogenetic tree using previously published, geographically dispersed mitochondrial genome sheep sequences. Genetic diversity statistics show that southern African sheep have lower diversity than sheep in other regions. Phylogenetic analysis reveals that many modern southern African sheep are likely descended from prehistoric indigenous sheep populations and not from sheep imported from Europe during the historic period.

Origin, demographics, inbreeding, phylogenetics, and phenogenetics of Karamaniko breed, a major common ancestor of the autochthonous Greek sheep

Greece has a long history in autochthonous sheep, the genetic ancestry of which has been associated with four subtypes known to inhabit Greece at the end of the nineteenth century. Among them, the Karamaniko breed is still surviving, however endangered. This study was designed in order to (a) determine the phylogenetic status, (b) to evaluate the levels of inbreeding, and (c) to assess the genetic basis of coat color of Karamaniko breed. For these purposes, the mitochondrial cyt b gene was sequenced, the AFLP methodology was applied, and the MC1R was genotyped, respectively, in 72 female sheep from the Karamaniko breed. Four different novel cyt b haplotypes were defined and three MC1R genotypes were scored, whereas inbreeding levels estimated using AFLPs by the means of relatedness coefficient (r) were 0.287, with gene diversity at the levels of 0.105. Phylogenetic analysis indicated an eastern Asian tropical and subtropical origin of the Karamaniko breed, close with breeds originating from central Turkey, or a clustering within western European or Mediterranean sheep, mirroring a recent genetic divergence, with a non-random spread towards the formation of lowland breeds. The MC1R genotypes were all associated with the white coat color, in which selective breeding has probably been based on traditional morphological characters. Finally, levels of inbreeding do not constitute an indication for a particular mating plan to prevent unpleasant phenomena such as inbreeding depression, probably because of the special attention paid by the farmers towards the avoidance of relative recurrent mating.

Evaluation of Maternal Genetic Background of Two Hungarian Autochthonous Sheep Breeds Coming from Different Geographical Directions

The aim of our research was the evaluation of the maternal genetic background of two Hungarian autochthonous sheep breeds of different geographical origin. A major argument for the preservation of endangered animal breeds is their documented past and historical importance. These also include the registration of pedigree data. This is the first study to evaluate and compare Tsigai and Cikta sheep in Hungary. Our investigation is based on two complete sequences of mitochondrial DNA (cytochrome b gene and control region). Our research was performed on these two sheep breeds with markedly different breed histories and breed characteristics to determine a possible common maternal genetic background, as ultimately the origin of both breeds can be traced back to Asia Minor. Between 2015 and 2017, a total of 203 biological samples were taken using a newly introduced founder sampling method. We found that the prevailing haplogroup B accounted for over 80% of both breeds, strengthening the common ancestral root. However, the pairwise genetic differentiation estimates (KST) calculated using the sequence-based statistics for cytochrome b gene and control region were 0.034 and 0.021, respectively (both at level p < 0.05); thus, revealing genetic differentiation in both sequences between the Tsigai and Cikta. We note that the known different history of the breeds is clearly justified by the currently studied deviations in their maternal genetic background.

An ancient positively selected BMPRIB missense variant increases litter size of Mongolian sheep populations following latitudinal gradient

New gene mutation origination is a driving force for the evolution of organisms. The effect of FecB mutation in BMPRIB gene on the litter size of sheep has been well known for a long time, each copy of the mutant allele increases litter size by 0.4-0.5. However, the origin and adaptive evolution mechanism of FecB mutation are still unclear. Here we carried on the thorough analysis on evolutionary features of BMPRIB gene and found that 150 species as a whole is under purifying selection while sheep lineage shows evidence of positive selection. The results of allele age estimation revealed that the FecB mutation in Mongolian sheep of China originated in Mongolian Plateau at about 5000 years ago. Due the two shape drops in temperature subsequently, Mongolian sheep migrated from north to south following the northern nomadic people. Accordingly, the FecB mutant allele frequency increased, with the lowest in sheep locating at Mongolian plateau (0.01) and the highest in sheep locating at Yangtze River valley (0.96). In conclusion, the FecB mutation in Mongolian sheep of China originated in Mongolian Plateau at about 5000 years ago, and the differentiated litter size of Mongolian sheep might be the result of adaptation to various environments during the migration following latitudinal gradient. This study may well exemplify selection on an ancient variation triggered by drastic ecological shifts, and is also helpful to analyze the adaptive evolution mechanism of economic traits of domestic animals and identify major genes and molecular markers.

Detection of candidate genes affecting milk production traits in sheep using whole-genome sequencing analysis

BACKGROUND

Artificial and natural selection for important economic traits and genetic adaptation of the populations to specific environments have led to the changes on the sheep genome. Recent advances in genome sequencing methods have made it possible to use comparative genomics tools to identify genes under selection for traits of economic interest in domestic animals.

OBJECTIVES

In this study, we compared the genomes of Assaf and Awassi sheep breeds with those of the Cambridge, Romanov and British du cher sheep breeds to explore positive selection signatures for milk traits using nucleotide diversity (Pi) and FST statistical methods.

METHODS

Genome sequences from fourteen sheep with a mean sequence depth of 9.32X per sample were analysed, and a total of 23 million single nucleotide polymorphisms (SNPs) were called and applied for this study. Genomic clustering of breeds was identified using ADMIXTURE software. The FST and Pi values for each SNP were computed between population A (Assaf and Awassi) and population B (Cambridge, British du cher, and Romanov).

RESULTS

The results of the PCA grouped two classes for these five dairy sheep breeds. The selection signatures analysis displayed 735 and 515 genes from FST and nucleotide diversity (Pi) statistical methods, respectively. Among all these, 12 genes were shared between the two approaches. The most conspicuous genes were related to milk traits, including ST3GAL1 (the synthesis of oligosacáridos), CSN1S1 (milk protein), CSN2 (milk protein), OSBPL8 (fatty acid traits), SLC35A3 (milk fat and protein percentage), VPS13B (total milk production, fat yield, and protein yield), DPY19L1 (peak yield), CCDC152 (lactation persistency and somatic cell count), NT5DC1 (lactation persistency), P4HTM (test day protein), CYTH4 (FAT Production) and METRNL (somatic cell), U1 (milk traits), U6 (milk traits) and 5S_RRNA (milk traits).

CONCLUSIONS

The findings provide new insight into the genetic basis of sheep milk properties and can play a role in designing sheep breeding programs incorporating genomic information.

Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches

Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.

Genome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds

The assignment of an individual to the true population of origin is one of the most important applications of genomic data for practical use in animal breeding. The aim of this study was to develop a statistical method and then, to identify the minimum number of informative SNP markers from high-throughput genotyping data that would be able to trace the true breed of unknown samples in indigenous sheep breeds. The total numbers of 217 animals were genotyped using Illumina OvineSNP50K BeadChip in Zel, Lori-Bakhtiari, Afshari, Moqani, Qezel and a wild-type Iranian sheep breed. After SNP quality check, the principal component analysis (PCA) was used to determine how the animals allocated to the groups using all genotyped markers. The results revealed that the first principal component (PC1) separated out the two domestic and wild sheep breeds, and all domestic breeds were separated from each other for PC2. The genetic distance between different breeds was calculated using FST and Reynold methods and the results showed that the breeds were well differentiated. A statistical method was developed using the stepwise discriminant analysis (SDA) and the linear discriminant analysis (LDA) to reduce the number of SNPs for discriminating 6 different Iranian sheep populations and K-fold cross-validation technique was employed to evaluate the potential of a selected subset of SNPs in assignment success rate. The procedure selected reduced pools of markers into 201 SNPs that were able to exactly discriminate all sheep populations with 100% accuracy. Moreover, a discriminate analysis of principal components (DAPC) developed using 201 linearly independent SNPs revealed that these markers were able to assign all individuals into true breed. Finally, these 201 identified SNPs were successfully used in an independent out-group breed consisting of 96 samples of Baluchi sheep breed and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. In general, the results of this study indicated that the combined use of the SDA and LDA techniques represents an efficient strategy for selecting a reduced pool of highly discriminant markers.

Comparison of mtDNA control region among descendant breeds of the extinct Zaupel sheep revealed haplogroup C and D in Central Europe

The consideration of the descendance is indispensable in the preservation of endangered animal breeds. The authors compared mitochondrial DNA (mtDNA) control region sequence in three descendant breeds of the extinct Zaupel sheep, firstly. Their investigation was carried out in order to prove the common origin of Waldschaf (Austria), Bovec sheep (Slovenia) and Cikta (Hungary). A total of 118 biological samples were taken from non-related representatives of the three breeds between 2015 and 2017. A newly designed primer pair was also used to amplify the segment (1180 bp) to be tested. The total number of haplotypes in the whole study population was 49. The majority of which fell into haplogroup B. The significant negative value of the Fu's Fs statistic (Fs statistic = -3.296, p = 0.013) based on haplotype frequencies demonstrated a moderate foreign gene flow. As a novel observation haplogroups C and D appeared in Cikta and Bovec sheep, respectively. The Tajima D-test value in the entire study population was -0.914 (p > 0.10), meaning that the separation of the three descendant breeds did not cause genetic drift, these are collectively in genetic equilibrium. The genetic information confirmed the common origin of the breeds known from the breed history.

The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences

Background and Aim:

Java Island is one of the islands in Indonesia which has local sheep breeds with specific characteristics and native development geography in certain regions. This study aimed to determine the genetic profiles and maternal origin of six local sheep breeds on Java Island.

Materials and Methods:

This study was conducted by identifying the profiles of complete mitochondrial DNA (mtDNA) displacement loop (D-loop) region sequences on a total of 22 individual in six local sheep breeds on Java Island, including Javanese thin-tailed (JTT), Javanese Fat-Tailed (JFT), Batur (BTR), Wonosobo (WSB), Garut (GRT), and Priangan (PRG) sheep. The D-loop region was amplified using specific primers, and the polymerase chain reaction (PCR) was performed. The PCR products were purified and sequenced.

Results:

The mtDNA D-loop analysis identified 21 haplotypes in the analyzed 22 animals with 123 polymorphic sites (V) consisting of 60 singleton variable sites (S) and 63 parsimony informative sites (P). Within all breeds tested, the haplotype diversity, the average number of pairwise differences (K), and nucleotide diversity (Pi) were 0.99567, 25.36364, and 0.02153, respectively. The genetic distance (D) within groups and between groups was 0.001-0.006 and 0.004-0.036, respectively. The phylogeny resulted in the presence of two haplogroups (Hap), which are 5 Hap A and 16 Hap B. All JTT, JFT, BTR, and WSB breeds were in the same cluster in Hap B, whereas GRT and PRG breeds were in clusters in both Hap A and Hap B.

Conclusion:

The high genetic diversity in six local sheep breeds on Java Island suggests that they originated from different genetic sources. JTT sheep have closer genetic relationships to JFT, BTR, and WSB sheep, and they are close to European sheep, whereas GRT sheep have closer genetic relationships to PRG sheep. Both are closer to Asian sheep than to European sheep.

Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India

Sheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (F_ST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.

Genetic diversity analysis among Indian goat breeds based on mitochondrial DNA

India ranks second in goat population with 34 genetically recognized and registered breeds. Information on their diversity and origin and ancestry is little known. Hence, the mtDNA based genetic diversity analysis of Indian goats; targeting mitochondrial HVR1 region from 21 Indian breeds belonging to different geographical regions was undertaken. A total of 124 haplotypes were identified and haplotype diversity estimate ranged from 0.67 to 1.0 with an average value of 0.99. The average nucleotide diversity was minimum (0.02) in Kanniadu and maximum in Surti breeds. Analysis of molecular variance revealed 5.16% variation among the breeds and 94.84% within breeds indicating weak phylogeographic structure. Neighbor-joining tree analysis revealed that the maximum number of individuals of Indian goats fall under A and few in B and C lineages. Principal component analyses of the Indian goat breeds revealed that Kanniadu goats clustered distantly from rest of the breeds of the country. Mantel test revealed a significant correlation between FST and geographical distance (r=0.29) among the goat breeds. The mismatch distribution analysis of the Indian goat breeds revealed bimodal distribution patterns. The analysis revealed that Kanniadu is highly distinct from the rest of the breeds.

Microsatellite and mitochondrial DNA based genetic diversity analysis of a lesser known Chitarangi sheep of north-western India

Microsatellite and mitochondrial DNA based genetic characterization of Chitarangi sheep population inhabiting Fazilka and Muktsar districts of Punjab and Sriganganagar district and adjoining areas of Rajasthan was carried out, and genetic diversity measures were analysed. High estimates of allele diversity (9.875±0.641) and gene diversity (0.712±0.027) were observed across the population. A significant positive FIS (0.096±0.031) value suggested a deficiency in the number of heterozygotes in Chitarangi sheep. The population revealed presence of substantial genetic diversity and the typical L-type distribution of allelic frequencies indicated the absence of any recent bottlenecks in Chitarangi sheep and no mode shift was detected in this population. Majority of haplotypes identified through mitochondrial DNA based analysis of Chitarangi sheep grouped with major haplogroup A that is predominantly of Asian origin. The genetic characterization of Chitarangi sheep will help in devising suitable strategies for its genetic improvement, management and recognition at National level.

Maternal origins, population structure and demographic history of ten Chinese indigenous goat breeds from Yunnan

Yunnan as a frontier zone that connects China with South and Southeast Asia, has 11 well-recognized goat breeds. However, the knowledge about maternal origins, population structure and demographic history of Chinese indigenous goats from Yunnan is limited. In this study, we analysed a 481-bp fragment of first hypervariable segment (HVSI) of the mitochondrial DNA (mtDNA) control region sequences of 749 individuals from 10 Yunnan indigenous goat breeds, of which 556 sequences were newly determined. There were 110 polymorphic sites that defined 158 haplotypes among all sequences. The haplotype and nucleotide diversity of these breeds ranged from 0.782 ± 0.079 to 0.982 ± 0.015 and from 0.028 ± 0.003 to 0.043 ± 0.005, respectively. Phylogenetic analysis identified two lineages A and B, of which the lineage A had higher frequency (68.1%) and distributed in all Yunnan breeds. We combined previously reported sequences with our sequences belonging to the lineage B and detected two subclades B1 and B2, in which the B1 subclade shared individuals from Eastern Asia, Southeast Asia and Southern Asia. Given higher level of diversity and more unique haplotypes, the B2 subclade probably originated from Southwestern China. The haplotype network, analysis of molecular variance (AMOVA) and a Mantel test revealed no significant phylogeographic structuring among Yunnan goat breeds. This can be explained by high gene flow and genetic admixture among these breeds from different geographic regions in Yunnan. Additionally, both the lineages A and B reflected different demographic histories. This study will provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.

Phylogeography and Phylogenetic Evolution in Tibetan Sheep Based on MT-CYB Sequences

Simple Summary

The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries) is not well understood, and little is known about this species’ genetic diversity. The aim of the present research was to explore phylogeography and phylogenetic evolution of Tibetan sheep populations, on the basis of mitochondrial DNA (mtDNA) gene MT-CYB (1140 base pairs). The results of this study will add information to the Tibetan sheep populations and help enlighten upcoming programs related to conservation of Tibetan sheep living in the Qinghai–Tibetan Plateau.

Abstract

To date, molecular genetics and population studies in Tibetan sheep (Ovis aries) have been limited, and little is known about the phylogenetic evolution and phylogeography of Tibetan sheep populations. The aim of the present research was to explore phylogeography and phylogenetic evolution of Tibetan sheep populations, on the basis of mitochondrial DNA (mtDNA) gene MT-CYB (1140 base pairs). Our dataset consisted of 641 MT-CYB sequences from the same amount of animals belonging to 15 populations of Tibetan sheep living in the Qinghai–Tibetan Plateau, China. Haplotype and nucleotide diversities were 0.748 ± 0.010 and 0.003 ± 0.001, respectively. The analysis of phylogeography revealed the presence of two formerly described haplogroups in 15 populations of Tibetan sheep, however only one haplogroup was present in Awang sheep. Moreover, 641 Tibetan sheep were distributed into a minimum of two clusters by clustering analysis. The 15 Tibetan sheep populations and 19 reference populations of 878 individuals were separated into six main groups based on their substitutions per site, from which we constructed a phylogenetic tree. Minor differences in branching order of various taxa between trees acquired from either gene were observed. This study provides insights on the origins and phylogenetic evolution of populations residing in the Qinghai–Tibetan Plateau, which will aid information of future conservation programs aimed at conserving this valuable genetic resource.

Mitochondrial DNA variation and phylogeography of native Mongolian goats

OBJECTIVE

Mongolia is one of a few countries that supports over 25 million goats, but genetic diversity, demographic history, and the origin of goat populations in Mongolia have not been well studied. This study was conducted to assess the genetic diversity, phylogenetic status and population structure of Mongolian native goats, as well as to discuss their origin together with other foreign breeds from different countries using hypervariable region 1 (HV1) in mtDNA.

METHODS

In this study, we examined the genetic diversity and phylogenetic status of Mongolian native goat populations using a 452 base-pair long fragment of HVI of mitochondrial DNA from 174 individuals representing 12 populations. In addition, 329 previously published reference sequences from different regions were included in our phylogenetic analyses.

RESULTS

Investigated native Mongolian goats displayed relatively high genetic diversities. After sequencing, we found a total of 109 polymorphic sites that defined 137 haplotypes among investigated populations. Of these, haplotype and nucleotide diversities of Mongolian goats were calculated as 0.997±0.001 and 0.0283±0.002, respectively. These haplotypes clearly clustered into four haplogroups (A, B, C, and D), with the predominance of haplogroup A (90.8%). Estimates of pairwise differences (Fst) and the analysis of molecular variance values among goat populations in Mongolia showed low genetic differentiation and weak geographical structure. In addition, Kazakh, Chinese (from Huanghuai and Leizhou), and Arabian (Turkish and Baladi breeds) goats had smaller genetic differentiation compared to Mongolian goats.

CONCLUSION

In summary, we report novel information regarding genetic diversity, population structure, and origin of Mongolian goats. The findings obtained from this study reveal that abundant haplogroups (A to D) occur in goat populations in Mongolia, with high levels of haplotype and nucleotide diversity.

Genetic diversity and matrilineal genetic origin of fat-rumped sheep in Ethiopia

Ethiopia is home to a diverse gene pool of indigenous sheep populations. Therefore, a better understanding of genetic variation holds the key to future utilization through conservation. Three of these breeds, Afar, Blackhead Somali, and Hararghe Highland, are found in eastern Ethiopia where they contribute significantly to the livelihood of most pastoralist, agro-pastoralist, and smallholder farmers. These indigenous sheep are recognized on the basis of morphotype and their genetic distinction remains unknown. Here, to assess genetic variation, and matrilineal genetic origin and relationship of fat-rumed sheep found in eastern Ethiopia, 300 individuals from the three breeds were genotyped for 22 microsatellite markers and sequenced for the mitochondrial DNA displacement loop (mtDNA d-loop) region. The overall HO and HE were 0.57 and 0.75, respectively. Differentiation statistics revealed that a high proportion (97%) of the total genetic variation was explained by differences between individuals within populations. Genotype assignment independent of the population of origin showed K = 2 to be the optimum number of genetic backgrounds present in the dataset. This result was further confirmed by mtDNA D-loop sequences comparison in which the matrilineal genetic origin of eastern Ethiopia sheep is from two haplotype groups (types A and B) among the five haplotypes globally observed. Taken together, our findings suggest that the sheep populations from three breeds originated from two ancestral genetic backgrounds that may have diverged prior to their introduction to Ethiopia. However, to obtain a complete picture of the evolutionary dynamics of Ethiopian indigenous sheep, more samples and populations from within and outside of the country will need to be analyzed.

Mitochondrial DNA sequence analysis of the Mexican Creole sheep (Ovis aries) reveals a narrow Iberian maternal origin

The Creole sheep in America is supposed to have originated specifically from the Iberian Peninsula and introduced by the Spaniards during the colonization. However, it is not clear their genetic relationship with Iberian breeds. The genetic origin and diversity of the Mexican Creole sheep (MCS) were investigated by mitochondrial DNA control region nucleotide sequences. DNA sequence from 33 MCS samples from three regions of México revealed 21 different haplotypes. Phylogenetic analysis including European and Iberian sheep haplotypes showed that the MCS population belongs to a differentiated and defined genetic lineage. This finding suggests that the MCS populations may be the result of a founder effect originating from a discrete Iberian population. MCS haplotypes were related to haplotypes found in the Churro Trunk and the Entrefino Trunk groups of Iberian breeds, supporting historical reports. In the Mexican genetic branch, there were also haplotypes reported from Lacaune and Awassi sheep breeds. Although it is uncertain whether a particular breed was involved as a founder of the MCS, these populations have a common phylogenetic origin.

Two ovine mitochondrial DNAs harboring a fifth 75/76 bp repeat motif without altered gene expression in Northern Spain

The Basque Country is home to the Latxa sheep breed, which is divided in several varieties such as Latxa Black Face (LBKF) and Latxa Blonde Face (LBLF). Mitochondrial DNA control region analysis of 174 male sheep (97 LBKF and 77 LBLF) was performed with the objective of characterizing the maternal lineages of these two varieties that are the basis to produce the cheese with Idiazabal quality label. The percentage of unique haplotypes was 77.32% in LBKF and 67.53% in LBLF. Most of the individuals were classified into B haplogroup (98.85%), while A haplogroup was much less frequent. Two Latxa individuals (one LBKF and one LBLF), both belonging to B haplogroup, displayed an additional 75/76 bp tandem repeat motif. Only 33 other sequences with this repeat motif were found among 11 061 sheep sequences included in the GenBank database. Gene expression was analyzed in peripheral blood leukocytes since the additional 75/76 bp repeat motif falls within ETAS1, a domain with a possible function in regulation of replication and transcription. The mRNA expression from four mitochondrial genes (COI, cyt b, ND1, and ND2) was analyzed in the two individuals of this study with a fifth repeat motif and in four without it. Although lower transcription was observed when the additional 75/76 bp repeat motif was present, no statistically significant differences were observed. Therefore, the variation in the number of the 75/76 repeat motif does not seem to modify the gene expression rate in mitochondrial genes.

Mitochondrial control region diversity in Polish sheep breeds

Abstract. The aim of the study was to determine the genetic variability of the Polish sheep breeds Świniarka, Wrzosówka, Pomorska, and Wielkopolska based on mitochondrial control region polymorphism. A comprehensive phylogenetic analysis and information about the genetic origin of the breeds were also obtained. The genetic variability of the breeds studied has been assessed based on the number of haplotypes, haplotype diversity, nucleotide diversity, the average number of nucleotide differences, the number of mutations, and phylogenetically informative sites. Sequence divergence between identified haplogroup A (HA) and haplogroup B (HB) was also calculated. Moreover, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura's two-parameter genetic distance calculation. Finally, the history of the population was investigated by mismatch distribution and Fu's F statistics. The 559 bp long mitochondrial DNA (mtDNA) control region (CR) sequences of 143 sheep were analysed. The 65 haplotypes were defined by 45 parsimony informative sites. Among the four Polish breeds, Wrzosówka had the highest while Świniarka the lowest values of haplotype (Hd) and sequence diversity (π) (Hd =  0.9735 and π =  0.0040 for Wrzosówka; Hd =  0.8975 and π =  0.0030 for Świniarka). Five haplotypes were shared between breeds, whereas the remaining 60 were unique. The NJ phylogenetic tree has revealed that 61 haplotypes of all analysed breeds clustered into clade B while the remaining 4 haplotypes representing all but the Świniarka breed pooled together with clade A. None of the other reported mitochondrial haplogroups were identified. The haplotypes representing HB formed a star-like network with the single central haplotype, which in association with extensive haplotype sharing reveals a weak structure of Polish breeds and the existence of gene flow between the breeds studied.

Meta-analysis evidence of maternal lineages in Chinese Tibetan sheep using mtDNA D-loop panel

The Tibetan sheep is an indigenous breed living in the entire Tibetan Plateau, and its origin and phylogenic relationships are still uncertain and controversial. In this study, we analyzed partial mtDNA D-loop sequences of 156 Chinese Tibetan sheep individuals from 12 distributed geographic ecotype populations. Phylogenetic analysis indicated that three maternal lineages (haplogroups A, B and C) were found in this breed and that Ovis vignei and Ovis ammon have possibly contributed to the original Tibetan sheep. The absence of haplogroups D and E in Tibetan sheep suggests that this breed did not originate in the Middle East, China.

Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post-medieval period and comparison with other regions in Eurasia

Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations.

Genetic characterization of Egyptian and Italian sheep breeds using mitochondrial DNA

A 721-bp fragment from 15,541 to 16,261 bp (NC_001941.1) of the mtDNA control region from different Egyptian and Italian sheep breeds was amplified. The PCR products were purified and sequenced. From the amplified fragment of 721-bp, a region of 423 bp after excluding a central region rich in tandem repeats was analyzed. Within all tested breeds, the haplotype diversity and average number of pairwise differences were 0.97571 and 7.01484, respectively. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Laticauda and Italian Muflon followed by distance between Sarda and Italian Muflon while the highest distance was observed between Barki and Sarda followed by distance between Barki and Laticauda. Phylogenetic analysis showed the presence of three haplogroups - HapA, HapB and HapC - in the examined samples with the absence of other two haplogroups HapD and HapE. All Italian samples cluster with B haplogroup and also in the Egyptian breeds the most dominant haplogroup was B (62 out of 67 analyzed samples). In Egyptian Barki breed one individual clusters with A haplogroup and another individual with C haplogroup. In Ossimi breed two individuals cluster with C haplogroup and in Rahmani there is one sample belonging to A haplogroup. The matrix of pairwise differences among breeds was used to perform a Principal Component Analysis (PCA). This analysis showed that the Italian breeds are clearly separated from the Egyptian breeds; moreover the Egyptian Barki breed is separated from Ossimi and Rahmani.

Y chromosomal haplotype characteristics of domestic sheep (Ovis aries) in China

Investigations on the variation present at the male-specific Y chromosome region provide strong information to understand the origin and evolution of domestic sheep. One SNP OY1 (g.88A>G) in the upstream region of SRY gene, and the microsatellite SRYM18 locus within ovine Y chromosome were analyzed in one hundred and forty five samples collected from eleven breeds in China. SNP OY1 was analyzed using PCR-SSCP method and sequencing. Two different PCR-SSCP patterns represented two specific sequences with sequence analysis revealing SNP-OY1 (g.88A>G) were observed, while SNP A-OY1 showed the most common frequency (82.8%). Sequencing of the SRYM18 region revealed one novel size fragment (A2) with different repetitive units. Seven haplotypes (H4, H5, H6, H7, H8, H9 and H12) and two novel haplotypes (Ha and Hb) were established using combined genotype analysis. H6 showed the highest frequency (43.4%) across all breeds, and H8 showed the second frequency (24.1%). Ha was only found in one breed (Tan), while Hb was present in three breeds (Gansu alpine, White Suffolk and Duolang). Our findings reveal one novel allele in SRYM18 region and two novel male haplotypes of domestic sheep in China.

K. T, Ramasamy S, Ellahi MB, Mohammed F, Teneva A, Shamsuddin M, Podesta MG, Diallo A. Candidate gene approach for parasite resistance in sheep--variation in immune pathway genes and association with fecal egg count

Sheep chromosome 3 (Oar3) has the largest number of QTLs reported to be significantly associated with resistance to gastro-intestinal nematodes. This study aimed to identify single nucleotide polymorphisms (SNPs) within candidate genes located in sheep chromosome 3 as well as genes involved in major immune pathways. A total of 41 SNPs were identified across 38 candidate genes in a panel of unrelated sheep and genotyped in 713 animals belonging to 22 breeds across Asia, Europe and South America. The variations and evolution of immune pathway genes were assessed in sheep populations across these macro-environmental regions that significantly differ in the diversity and load of pathogens. The mean minor allele frequency (MAF) did not vary between Asian and European sheep reflecting the absence of ascertainment bias. Phylogenetic analysis revealed two major clusters with most of South Asian, South East Asian and South West Asian breeds clustering together while European and South American sheep breeds clustered together distinctly. Analysis of molecular variance revealed strong phylogeographic structure at loci located in immune pathway genes, unlike microsatellite and genome wide SNP markers. To understand the influence of natural selection processes, SNP loci located in chromosome 3 were utilized to reconstruct haplotypes, the diversity of which showed significant deviations from selective neutrality. Reduced Median network of reconstructed haplotypes showed balancing selection in force at these loci. Preliminary association of SNP genotypes with phenotypes recorded 42 days post challenge revealed significant differences (P<0.05) in fecal egg count, body weight change and packed cell volume at two, four and six SNP loci respectively. In conclusion, the present study reports strong phylogeographic structure and balancing selection operating at SNP loci located within immune pathway genes. Further, SNP loci identified in the study were found to have potential for future large scale association studies in naturally exposed sheep populations.

Mitochondrial DNA diversity of modern, ancient and wild sheep(Ovis gmelinii anatolica) from Turkey: new insights on the evolutionary history of sheep

In the present study, to contribute to the understanding of the evolutionary history of sheep, the mitochondrial (mt) DNA polymorphisms occurring in modern Turkish native domestic (n = 628), modern wild (Ovis gmelinii anatolica) (n = 30) and ancient domestic sheep from Oylum Höyük in Kilis (n = 33) were examined comparatively with the accumulated data in the literature. The lengths (75 bp/76 bp) of the second and subsequent repeat units of the mtDNA control region (CR) sequences differentiated the five haplogroups (HPGs) observed in the domestic sheep into two genetic clusters as was already implied by other mtDNA markers: the first cluster being composed of HPGs A, B, D and the second cluster harboring HPGs C, E.

To manifest genetic relatedness between wild Ovis gmelinii and domestic sheep haplogroups, their partial cytochrome B sequences were examined together on a median-joining network. The two parallel but wider aforementioned clusters were observed also on the network of Ovis gmelenii individuals, within which domestic haplogroups were embedded. The Ovis gmelinii wilds of the present day appeared to be distributed on two partially overlapping geographic areas parallel to the genetic clusters that they belong to (the first cluster being in the western part of the overall distribution). Thus, the analyses suggested that the domestic sheep may be the products of two maternally distinct ancestral Ovis gmelinii populations.

Furthermore, Ovis gmelinii anatolica individuals exhibited a haplotype of HPG A (n = 22) and another haplotype (n = 8) from the second cluster which was not observed among the modern domestic sheep. HPG E, with the newly observed members (n = 11), showed signs of expansion. Studies of ancient and modern mtDNA suggest that HPG C frequency increased in the Southeast Anatolia from 6% to 22% some time after the beginning of the Hellenistic period, 500 years Before Common Era (BCE).

Extensive variation and sub-structuring in lineage A mtDNA in Indian sheep: genetic evidence for domestication of sheep in India

Previous studies on mitochondrial DNA analysis of sheep from different regions of the world have revealed the presence of two major- A and B, and three minor- C, D and E maternal lineages. Lineage A is more frequent in Asia and lineage B is more abundant in regions other than Asia. We have analyzed mitochondrial DNA sequences of 330 sheep from 12 different breeds of India. Neighbor-joining analysis revealed lineage A, B and C in Indian sheep. Surprisingly, multidimensional scaling plot based on F_ST values of control region of mtDNA sequences showed significant breed differentiation in contrast to poor geographical structuring reported earlier in this species. The breed differentiation in Indian sheep was essentially due to variable contribution of two major lineages to different breeds, and sub- structuring of lineage A, possibly the latter resulting from genetic drift. Nucleotide diversity of this lineage was higher in Indian sheep (0.014 ± 0.007) as compared to that of sheep from other regions of the world (0.009 ± 0.005 to 0.01 ± 0.005). Reduced median network analysis of control region and cytochrome b gene sequences of Indian sheep when analyzed along with available published sequences of sheep from other regions of the world showed that several haplotypes of lineage A were exclusive to Indian sheep. Given the high nucleotide diversity in Indian sheep and the poor sharing of lineage A haplotypes between Indian and non-Indian sheep, we propose that lineage A sheep has also been domesticated in the east of Near East, possibly in Indian sub-continent. Finally, our data provide support that lineage B and additional lineage A haplotypes of sheep might have been introduced to Indian sub-continent from Near East, probably by ancient sea trade route.

Phylogenetic relationships of three Italian merino-derived sheep breeds evaluated through a complete mitogenome analysis

In Italy, the crisis of the wool industry triggered the necessity to reconvert the two traditional Merino-derived breeds, Gentile di Puglia and Sopravissana, to meat production, by creating the Merinizzata Italiana. The aim of the present study was to assess the genetic diversity of these three Italian Merino-derived (IMd) breeds by examining the molecular information encoded in the maternally-inherited mitochondrial DNA (mtDNA). A parallel molecular investigation was performed on the putative paternal and maternal breeds, the Merino from Spain and the Appenninica from Italy, respectively, as well as on three unrelated dairy breeds (Sarda and Comisana from Italy, and Lacaune from France). Firstly, the mtDNA control region of 291 samples was analyzed. When comparing the overall genetic distances among the eight stocks, the three IMd breeds clustered together close to the Appenninica, thus confirming its parental role. Among the 90 IMd samples, 82 different haplotypes were observed, almost all belonging to haplogroup B, and only one to A. For 23 mtDNAs, including nine IMd, the analysis was then brought to the level of entire mitogenomes. Three distinct sub-haplogroups within B were found to encompass the IMd samples, with one clade (B1a2a1) apparently restricted to those sheep. Thus, despite experiencing a drastic reduction in number (mainly due to changes in breeding practices driven by the economy), the IMd breeds still represent a reservoir of distinctive mitochondrial variants, which could potentially contribute to the development of conservation and management programs of Italian sheep breeds.

Investigation of the genetic diversity among native Turkish sheep breeds using mtDNA polymorphisms

A total of 135 unrelated sheep from nine Turkish native sheep breeds (Daglıc, Kivircik, Imroz, Chios, Morkaraman, Ivesi, Hemsin, Karayaka and Akkaraman) were investigated to determinate the maternal genetic diversity using a sequence of a 531-bp segment of the mtDNA control region. Analysis of the mtDNA control region sequence revealed 63 haplotypes and 53 polymorphic sites. Haplotype diversity, nucleotide diversity and the average number of nucleotide differences were estimated to be 0.9496 ± 0.011, 0.01407 ± 0.00060 and 7.456, respectively. The sequence analysis also revealed high level of genetic diversity among the native Turkish breeds. These breeds were grouped into three major maternal haplogroups: A, B and C, with one animal belonging from the Akkaraman breed to the rare haplogroup E. Irregular shape of mismatch distribution of haplogroup C could be an indicator that haplogroup C may represent different haplogroups. Contrarily to previous studies carried out on Turkish native breeds, majority of animals grouped in haplogroup A in the present study. This result and the irregular shape of mismatch curve of haplogroup C indicate that genetic structure of Turkish native sheep breeds could be more complicated than it is thought.

Mitochondrial analysis sheds light on the origin of hair sheep

A total of 180 mtDNA sequences from hair Caribbean (93), West African (73) and Canarian-wooled (14) sheep were analysed to shed light on the origin of hair sheep. A comparison of 360 Iberian sheep sequences retrieved from GenBank was performed to assess a possible European origin of the Caribbean hair sheep. These 180 sequences gave 48 different haplotypes (16 in Caribbean sheep). All Caribbean and Canarian-wooled sequences and 91.8% of the West African samples belonged to haplogroup B. The sheep analysed showed wide haplotypic identity. Caribbean sheep shared roughly two-thirds of their samples with Canarian-wooled and West African samples, respectively. Principal component analysis showed that the Caribbean and the Canarian-wooled sheep clustered together. Additional analyses showed that hair and Iberian sheep had wide genetic identity. It was not possible to ascertain a single Canarian, African or European origin of the Caribbean hair sheep using mtDNA markers only. European, African and Caribbean hair sheep maternal genetic backgrounds likely result from related domestication events.

Tracking the emergence of a new breed using 49,034 SNP in sheep

Domestic animals are unique in that they have been organised into managed populations called breeds. The strength of genetic divergence between breeds may vary dependent on the age of the breed, the scenario under which it emerged and the strength of reproductive isolation it has from other breeds. In this study, we investigated the Gulf Coast Native breed of sheep to determine if it contains lines of animals that are sufficiently divergent to be considered separate breeds. Allele sharing and principal component analysis (PCA) using nearly 50,000 SNP loci revealed a clear genetic division that corresponded with membership of either the Florida or Louisiana Native lines. Subsequent analysis aimed to determine if the strength of the divergence exceeded that found between recognised breed pairs. Genotypes from 14 breeds sampled from Europe and Asia were used to obtain estimates of pair-wise population divergence measured as F(ST). The divergence separating the Florida and Louisiana Native (F(ST) = 6.2%) was approximately 50% higher than the average divergence separating breeds developed within the same region of Europe (F(ST) = 4.2%). This strongly indicated that the two Gulf Coast Native lines are sufficiently different to be considered separate breeds. PCA using small SNP sets successfully distinguished between the Florida and Louisiana Native animals, suggesting that allele frequency differences have accumulated across the genome. This is consistent with a population history involving geographic separation and genetic drift. Suggestive evidence was detected for divergence at the poll locus on sheep chromosome 10; however drift at neutral markers has been the largest contributor to the genetic separation observed. These results document the emergence of populations that can be considered separate breeds, with practical consequences for bio-conservation priorities, animal registration and the establishment of separate breed societies.

Mitochondrial DNA and Y-chromosome diversity in East Adriatic sheep

Variation in mitochondrial DNA (mtDNA) and Y-chromosome haplotypes was analysed in nine domestic sheep breeds (159 rams) and 21 mouflon (Ovis musimon) sampled in the East Adriatic. Mitochondrial DNA analyses revealed a high frequency of type B haplotypes, predominantly in European breeds, and a very low frequency of type A haplotypes, which are more frequent in some Asian breeds. Mitochondrial haplotype Hmt-3 was the most frequent (26.4%), and 37.1%, 20.8% and 7.6% of rams had haplotypes one, two and three mutations remote from Hmt-3 respectively. In contrast, Y-chromosome analyses revealed extraordinary paternal allelic richness: HY-6, 89.3%; HY-8, 5.0%; HY-18, 3.1%; HY-7, 1.3%; and HY-5, 1.3%. In fact, the number of haplotypes observed is comparable to the number found in Turkish breeds and greater than the number found in European breeds so far. Haplotype HY-18 (A-oY1/135-SRYM18), identified here for the first time, provides a link between the haplotype HY-12 (A-oY1/139-SRYM18) found in a few rams in Turkey and haplotype HY-9 (A-oY1/131-SRYM18) found in one ram in Ethiopia. All mouflons had type B mtDNA haplotypes, including the private haplotype (Hmt-55), and all were paternally monomorphic for haplotype HY-6. Our data support a quite homogeneous maternal origin of East Adriatic sheep, which is a characteristic of European breeds. At the same time, the high number of haplotypes found was surprising and intriguing, and it begs for further analysis. Simultaneous analysis of mtDNA and Y-chromosome information allowed us to detect a large discrepancy between maternal and paternal lineages in some populations. This is most likely the result of breeder efforts to 'upgrade' local populations using rams with different paternal origins.

Genetic diversity and networks of exchange: a combined approach to assess intra-breed diversity

BACKGROUND

Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow due to exchanges between herds. To quantify this relation, molecular data and analyses of the exchanges were combined for three endangered Belgian breeds.

METHODS

For each breed, between 91 and 225 sheep were genotyped with 19 microsatellites. Genetic differentiations between breeds and among herds within a breed were evaluated and the genetic structure of the breeds was described using Bayesian clustering (Structure). Exchanges of animals between 20, 46 and 95 herds according to breed were identified via semi-directed interviews and were analyzed using the concepts of the network theory to calculate average degrees and shortest path lengths between herds. Correlation between the Reynolds' genetic distances and the shortest path lengths between each pair of herds was assessed by a Mantel test approach.

RESULTS

Genetic differentiation between breeds was high (0.16). Overall Fst values among herds were high in each breed (0.17, 0.11 and 0.10). Use of the Bayesian approach made it possible to identify genetic groups of herds within a breed. Significant correlations between the shortest path lengths and the Reynolds' genetic distances were found in each breed (0.87, 0.33 and 0.41), which demonstrate the influence of exchanges between herds on the genetic diversity. Correlation differences between breeds could be explained by differences in the average degree of the animal exchange networks, which is a measure of the number of exchanges per herd. The two breeds with the highest average degree showed the lowest correlation. Information from the exchange networks was used to assign individuals to the genetic groups when molecular information was incomplete or missing to identify donors for a cryobank.

CONCLUSIONS

A fine-scale picture of the population genetic structure at the herd level was obtained for the three breeds. Network analysis made it possible to highlight the influence of exchanges on genetic structure and to complete or replace molecular information in establishing a conservation program.

Phylogenetic position of a copper age sheep (Ovis aries) mitochondrial DNA

BACKGROUND

Sheep (Ovis aries) were domesticated in the Fertile Crescent region about 9,000-8,000 years ago. Currently, few mitochondrial (mt) DNA studies are available on archaeological sheep. In particular, no data on archaeological European sheep are available.

METHODOLOGY/PRINCIPAL FINDINGS

Here we describe the first portion of mtDNA sequence of a Copper Age European sheep. DNA was extracted from hair shafts which were part of the clothes of the so-called Tyrolean Iceman or Ötzi (5,350-5,100 years before present). Mitochondrial DNA (a total of 2,429 base pairs, encompassing a portion of the control region, tRNA(Phe), a portion of the 12S rRNA gene, and the whole cytochrome B gene) was sequenced using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products. We have compared the sequence with the corresponding sequence of 334 extant lineages.

CONCLUSIONS/SIGNIFICANCE

A phylogenetic network based on a new cladistic notation for the mitochondrial diversity of domestic sheep shows that the Ötzi's sheep falls within haplogroup B, thus demonstrating that sheep belonging to this haplogroup were already present in the Alps more than 5,000 years ago. On the other hand, the lineage of the Ötzi's sheep is defined by two transitions (16147, and 16440) which, assembled together, define a motif that has not yet been identified in modern sheep populations.

Enucleated ovine oocyte supports human somatic cells reprogramming back to the embryonic stage

Increased possibility of universality of ooplasmic reprogramming factors resulted in a parallel increased interest to use interspecies somatic cell nuclear transfer (iSCNT) to address basic questions of developmental biology and to improve the feasibility of cell therapy. In this study, the interactions between human somatic cells and ovine oocytes were investigated. Nuclear remodeling events were first observed 3 h post-iSCNT as nuclear swelling, chromosome condensation, and spindle formation. A time-dependent decrease in maturation promoting activity of inactivated reconstructs coincided with increased aberrations in chromosome and spindle organization of the newly developed embryos. The sequence and duration of nuclear remodeling events were irrespective of donor cell type used. Although the majority of the reconstituted embryos arrested before embryonic genome activation (8-16-cell) stage, less than 5% of them could progress beyond transcription-requiring developmental stage and formed blastocyst-like structures with distinct inner cell mass and trophectoderm at days 7 and 8 post-SCNT. Importantly, real-time assessment of three developmentally important genes (Oct4, Sox2, and Nanog) indicated their upregulation in iSCNT blastocysts. Blastocyst-derived outgrowths had alkaline phosphatase activity that was lost upon passage. Collectively, this study introduced ovine oocyte as a credible cytoplast for remodeling and reprogramming of human somatic cells back to the embryonic stage and provided a platform for further studies to unravel possible differences exist between reprogramming ability of oocytes of different mammalian species.