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47 results for “sheep breeds”
Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds
<p>The current study was conducted from 2009 to 2019 in three hot and dry agroecological zones in Egypt: Western Desert coastal zone, New Valley desert oasis, and hot-dry Upper Egypt. Within these zones, three local sheep breeds were studied: Barki (83 ewes), Wahati (55 ewes) and Saidi (68 ewes). During the study period, the animals exercised under natural heat stress (simulating summer grazing on poor pasture). Meteorological and physiological parameters were measured and recorded. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on the animals' response to the five main physiological parameters (scale from 0 to 5). DNA samples were extracted for genomic analysis. The genetic diversity measurements showed a significant influence of breed and location on the populations. The influence of breed is more significant than that of location. The inbreeding analysis shows that the desert breeds (Wahati and Barki) have lower values than the urban breed (Saidi). The high rate of sub-clustering indicates the process of sub-population through inbreeding pressure. Wahati and Barki are very distinct breeds with strong identification, while Saidi breed has crosses with other breeds. The most significant SNPs associated with heat tolerance were found in MYO5A, PRKG1, GSTCD, and RTN1 genes (P < 0.0001). MYO5A had an effect of 0.74 on the trait heat tolerance in the studied population. It produces a protein that is widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1 18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. GWAS analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C , PEBP4, and GPAT2 genes.</p>
Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes
Background <p>Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree.</p> Results <p>The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they've been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree.</p> Conclusions <p>We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep.</p>
High-density genomic characterization of native Croatian sheep breeds
<p class="MsoNormal"><span>A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (F<sub>ROH > 2 Mb</sub>) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.</span></p>
Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom
<p><strong>Background: </strong>Sheep breeds native to the United Kingdom are noted for high breed variability and exhibit a striking diversity of different traits in phenotypes and genetic diversity. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including 6 on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture.</p> <p><strong>Results: </strong>In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds.</p> <p><strong>Conclusion: </strong>Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small populations sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.</p>
Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes
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High-density genomic characterization of native Croatian sheep breeds
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Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom
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Data from: Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds
A dataset consisting of 787 animals with high density SNP chip genotypes (346,774 SNP) and 939 animals with medium density SNP chip genotypes (33,828 SNP) from a total of 8 indigenous Swiss sheep breeds was analyzed to characterize population structures, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between FPED and FROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean FROH estimates from medium density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion we identified differences in the genetic make-up of Swiss sheep breeds and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.
Data from: Population structure and history of the Welsh sheep breeds determined by whole genome genotyping
Background: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project. Results: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise FST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825. Conclusions: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.
Data from: Mapping the four-horned locus and testing the polled locus in three Chinese sheep breeds
Four-horned sheep are an ideal animal model for illuminating the genetic basis of horn development. The objective of this study was to locate the genetic region responsible for the four-horned phenotype and to verify a previously reported polled locus in three Chinese breeds. A genome-wide association study (GWAS) was performed using 34 two-horned and 32 four-horned sheep from three Chinese indigenous breeds: Altay, Mongolian and Sishui Fur sheep. The top two significant single nucleotide polymorphisms (SNPs) associated with the four-horned phenotype were both located in a region spanning positions 132.6 to 132.7 Mb on sheep chromosome 2. Similar locations for the four-horned trait were previously identified in Jacob, Navajo-Churro, Damara and Sishui Fur sheep, suggesting a common genetic component underlying the four-horned phenotype. The two identified SNPs were both downstream of the metaxin 2 (MTX2) gene and the HOXD gene cluster. For the top SNP—OAR2:g.132619300G>A—the strong associations of the AA and AG genotypes with the four-horned phenotype and the GG genotype with the two-horned phenotype indicated the dominant inheritance of the four-horned trait. No significant SNPs for the polled phenotype were identified in the GWAS analysis, and a PCR analysis for the detection of the 1.8-kb insertion associated with polled sheep in other breeds failed to verify the association with polledness in the three Chinese breeds. This study supports the hypothesis that two different loci are responsible for horn existence and number. This study contributes to the understanding of the molecular regulation of horn development and enriches the knowledge of qualitative traits in domestic animals.
Data from: Genetic homogenization of indigenous sheep breeds in Northwest Africa
Northwest-African sheep represent an ideal case-study for assessing the potential impact of genetic homogenization as a threat to the future of traditional breeds that are adapted to local conditions. We studied ten Algerian and Moroccan breeds of sheep, including three transboundary breeds, distributed over a large part of the Maghreb region, which represents a geographically and historically coherent unit. Our analysis of the dataset that involved carrying out Genome-wide SNP genotyping, revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE and IBD segments analyses), in such a way that some breeds from different origins appeared genetically undistinguished: by grouping the eight most admixed populations, we obtained a mean global FST value of 0.0024. The sPCA analysis revealed that the major part of Morocco and the Northern part of Algeria were affected by the phenomenon, including most of the breeds considered. Unsupervised cross-breeding with the popular Ouled-Djellal breed was identified as a proximate cause of this homogenization. The issue of transboundary breeds was investigated, and the Hamra breed in particular was examined via ROH fragments analysis. Genetic diversity was considered in the light of historical archives and anthropological works. All of these elements taken together suggest that homogenization as a factor affecting the Maghrebin sheep stock, has been particularly significant over the last few decades, although this process probably started much earlier. In particular, we have identified the policies set by the French administration during the colonial period of the region's history as a causal factor that probably contributed significantly to this process. The genetic homogenization that we have observed calls into question the integrity of the farm animal genomic resources represented by these local breeds, whose conservation is of critical importance to the future of the livestock sector.
Population structure and genetic diversity of sheep breeds in the Kyrgyzstan
<p><span>Sheep are a main livestock </span><span>species of Kyrgyzstan, a Central Asian country with predominating mountain terrain. </span>The current gene pool of local sheep resources has been forming under diverse climate conditions from the era of the trading caravans of the Great Silk Road, through the Soviet period of <span>large-scale livestock improvements</span>, which was followed by the deep crisis at the end of the 20th century, up to now. However, not much is known about the genetic background and variability of the local sheep populations. Therefore, our aims were to provide a characterization of the population structure and genetic relations within the Kyrgyz sheep breeds and to study their genetic connections with the global sheep breeds using SNP analysis. Samples of the Alai (n=31), Gissar (n=30), Kyrgyz coarse wool (n=13), Aykol (n=31), and Tien-Shan (n=24) breeds were genotyped with the OvineSNP50 BeadChip or the <span>Ovine Infinium HD BeadChip </span>(Illumina Inc., USA). The measure of inbreeding based on runs of homozygosity showed a minimum value in the Aykol breed (F<sub>ROH</sub> = 0.034), while the maximum was found in the Alai breed (F<sub>ROH</sub> = 0.071). Short ROH segments (ROH≤4Mb) were predominant in all breeds. Long ROH segments (ROH>16Mb) were absent in the Gissar breed. The Gissar and Aykol breeds had the highest values of the effective population sizes estimated for five generations ago (<i>Ne<sub>5</sub>=</i>660 and 563), whereas the Alai and Kyrgyz coarse wool displayed lower values (<i>Ne<sub>5</sub> </i>=176 and 128, respectively). The synthetic origin of the Aykol breed was clearly evidenced by all analyses applied. Based on the network and admixture analyses of the Kyrgyz and global sheep breeds, the Tien-Shan and the Russian semi-fine wool breeds demonstrated a common ancestry that most likely is due to a contribution of the Lincoln breed. The Gissar, Aykol and Kyrgyz coarse wool breeds showed a genetic background predominating in sheep populations from Iran and China whereas the Alai demonstrated the different ancestry type. The revealed admixture patterns probably resulted from the exchange and trade during the era of the Great Silk Road, which partly overlapped with historical and archeological findings.</p>
Data from: Genetic homogenization of indigenous sheep breeds in Northwest Africa
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Data from: Merino and Merino-derived sheep breeds: a genome-wide intercontinental study
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Population structure and genetic diversity of sheep breeds in the Kyrgyzstan
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Data from: Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds
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Data from: Mapping the four-horned locus and testing the polled locus in three Chinese sheep breeds
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Data from: Population structure and history of the Welsh sheep breeds determined by whole genome genotyping
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Dataset used for: Breeding migrations by bighorn sheep males: searching for mates increases vulnerability to hunting
<p>In some species where male mating success largely depends on intrasexual competition, males can adopt migratory orresident strategies to seek breeding opportunities. The resulting mixture of resident and migrant tactics within a population can have important ecological, genetic and evolutionary consequences at the metapopulation level. Bighorn sheep <em>Ovis canadensis</em> males establish a linear dominance hierarchy that influences their mating tactics. Some males perform breeding migrations during the pre-rut and rut to seek mating opportunities, but little is known about these seasonal movements. We analysed presence/absence data for 62 marked bighorn males during six mating seasons (20-32 males/year) in the Sheep River Provincial Park, Alberta, Canada, where hunting was not allowed. On average, about half of males left their natal population to rut elsewhere. The proportion of males leaving (yearly range 15% - 69%) increased as the number of resident mature males increased and the populational sex ratio decreased, with fewer females during the pre-rut. Among those leaving the park, 24% did so in October, while the trophy sheep hunting season was open. Detailed monitoring of breeding migrations in protected populations could inform management strategies to limit evolutionary impacts of hunting.</p>
Dataset used for: Breeding migrations by bighorn sheep males: searching for mates increases vulnerability to hunting
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