Genetic homogenization of indigenous sheep breeds in Northwest Africa

Insight into the current genomic diversity, conservation status and population structure of Tunisian Barbarine sheep breed

Local livestock breeds play a crucial role in global biodiversity, connecting natural and human-influenced environments and contributing significantly to ecosystem services. While commercial breeds dominate industrial systems, local livestock breeds in developing countries, like Barbarine sheep in Tunisia, are vital for food security and community maintenance. The Tunisian Barbarine sheep, known for its adaptability and distinctive fat-tailed morphology, faces challenges due to historical crossbreeding. In this study, the Illumina Ovine SNP50K BeadChip array was used to perform a genome-wide characterization of Tunisian Barbarine sheep to investigate its genetic diversity, the genome structure, and the relationship within the context of Mediterranean breeds. The results show moderate genetic diversity and low inbreeding. Runs of Homozygosity analysis find genomic regions linked to important traits, including fat tail characteristics. Genomic relationship analysis shows proximity to Algerian thin-tailed breeds, suggesting crossbreeding impacts. Admixture analysis reveals unique genetic patterns, emphasizing the Tunisian Barbarine's identity within the Mediterranean context and its closeness to African breeds. Current results represent a starting point for the creation of monitoring and conservation plans. In summary, despite genetic dilution due to crossbreeding, the identification of genomic regions offers crucial insights for conservation. The study confirms the importance of preserving unique genetic characteristics of local breeds, particularly in the face of ongoing crossbreeding practices and environmental challenges. These findings contribute valuable insights for the sustainable management of this unique genetic reservoir, supporting local economies and preserving sheep species biodiversity.

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

Introduction

The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.

Methods

In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.

Results and discussion

We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.

IBD sharing patterns as intra-breed admixture indicators in small ruminants

In this study, we investigated how IBD patterns shared between individuals of the same breed could be informative of its admixture level, with the underlying assumption that the most admixed breeds, i.e. the least genetically isolated, should have a much more fragmented genome. We considered 111 goat breeds (i.e. 2501 individuals) and 156 sheep breeds (i.e. 3304 individuals) from Europe, Africa and Asia, for which beadchip SNP genotypes had been performed. We inferred the breed's level of admixture from: (i) the proportion of the genome shared by breed's members (i.e. "genetic integrity level" assessed from ADMIXTURE software analyses), and (ii) the "AV index" (calculated from Reynolds' genetic distances), used as a proxy for the "genetic distinctiveness". In both goat and sheep datasets, the statistical analyses (comparison of means, Spearman correlations, LM and GAM models) revealed that the most genetically isolated breeds, also showed IBD profiles made up of more shared IBD segments, which were also longer. These results pave the way for further research that could lead to the development of admixture indicators, based on the characterization of intra-breed shared IBD segments, particularly effective as they would be independent of the knowledge of the whole genetic landscape in which the breeds evolve. Finally, by highlighting the fragmentation experienced by the genomes subjected to crossbreeding carried out over the last few generations, the study reminds us of the need to preserve local breeds and the integrity of their adaptive architectures that have been shaped over the centuries.

Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms

Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of F_ST were higher in Wallachian sheep (F_ST = 0.14) than in Sumava sheep (F_ST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the N_e estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (F_HOM) among individuals, from -0.04 to 0.16 in Sumava and from -0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise F_ST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and F_ST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

Genetic Characterization and Alternative Preservation Ways of Locally Adapted Sheep Breeds: Cases of Private and Public Sheep Sectors in Tunisia and Italy

Simple Summary

The genetic characterization of native sheep breeds from the Tunisian-Italian Mediterranean corridor, the earliest westward introduction route of sheep breeding from the domestication center, was carried out using microsatellite markers in order to compare the genetic diversity level between both Mediterranean sides’ local sheep breeds, and to investigate their level of risk for conservation purposes. Sampling concerned both private and public/institutional farms of all the native Tunisian breeds in the case of the southern Mediterranean side, and one center Italian and the Venetian native breeds from the northern side. The results revealed that the genetic diversity level of the Tunisian native breeds was higher than that of the Italian ones, with a lower inbreeding level. The comparison between private and public farms in terms of genetic diversity, consanguinity, and conservation decisions highlighted the superiority of the public/institutional breeding management strategies over private ones in both Tunisian and Italian cases. The present study illustrated the efficiency of genomic characterization in making genetic diversity evaluations and preservation decisions of native and well-adapted sheep breeds in both developing and developed countries’ rearing conditions.

Abstract

Non-commercialized sheep breeds known as local or native breeds are well adapted to their environmental constraints and constitute precious genetic resources that need prioritization for genetic diversity characterization and preservation. The aim of the present study was to assess the genetic diversity level and the related preservation decisions of very old and traditional native Mediterranean sheep breeds from Tunisia and Italy using 17 microsatellite markers. In total, 975 sheep were sampled from five Tunisian, one Center Italian, and four Venetian native breeds. Both private and publicly available farms were considered for each breed for breeding strategies’ comparison purposes. The microsatellite set used was highly informative (PIC = 0.80 ± 0.08), with a total of 383 alleles. Moderate genetic differentiation was revealed between the native sheep of the two Mediterranean sides (global overall loci F_ST = 0.081). The genetic diversity level was higher in the case of the Tunisian native breeds compared to the Italian ones, as evidenced by higher mean allelic richness, higher expected and observed heterozygosities, and lower inbreeding levels. Priority for conservation suggestions was carried out for each private or public breed population based on the contribution of each population to the diversity of the whole data. The four Venetian breeds, already undergoing conservation, the Tunisian dairy breed, and the very ancient Maghrebian breed, would be favored for conservation. In conclusion, our results highlighted the importance of the analyzed Mediterranean native sheep breeds as valuable inherited genetic reservoirs and supported previous conservation decisions made for the threatened breeds.

Genetic Differentiation among Livestock Breeds—Values for Fst

Simple Summary

The degree of relationship among livestock breeds can be quantified by the F_st statistic, which measures the extent of genetic differentiation between them. An F_st value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, F_st values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that F_st > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of F_st data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds.

Abstract

(1) Background: The F_st statistic is widely used to characterize between-breed relationships. F_st = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding F_st values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed F_st were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of F_st data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed F_st of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated F_st data may have value for interdisciplinary research.

Genomic Uniqueness of Local Sheep Breeds From Morocco

Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

How have sheep breeds differentiated from each other in Morocco? Genetic structure and geographical distribution patterns

Background

Based on the relatively homogeneous origin of the sheep breeds in Morocco that originate mainly from Iberia, it is highly relevant to address the question of how these very diverse sheep populations differentiated from each other. The Mountains of the High Atlas and Middle Atlas are expected to constitute North–South and West–East geographical barriers, respectively, which could have shaped the history of the differentiation of sheep breeds. The aim of this study was to test this hypothesis by considering the genetic structure and the spatial distribution of five major breeds (Sardi, Timahdite, Beni Guil, Boujaad and D’man) and one minor breed (Blanche de Montagne), by analysing the mtDNA control region, using 30 individuals per breed.

Results

Phylogenetic and network analyses did not indicate any clear separation among the studied breeds and discriminant component principal analysis showed some overlap between them, which indicates a common genetic background. The calculated pairwise F_ST values and Nei’s genetic distances revealed that most breeds showed a moderate genetic differentiation. The lowest and highest degrees of differentiation were retrieved in the Beni Guil and Boujaad breeds, respectively. Analysis of molecular variance (AMOVA) indicated that more than 95% of the genetic diversity occurs within individuals, while between- and within-population variabilities represent only 1.332% and 2.881%, respectively. Isolation-by-distance, spatial Principal Component Analysis (sPCA), and spatial AMOVA analyses evidenced clear examples of geographical structuration among the breeds, both between and within breeds. However, several enigmatic relationships remain, which suggest the occurrence of complex events leading to breed differentiation.

Conclusions

The approaches used here resulted in a convergent view on the hypothetic events that could have led to the progressive differentiation between the Moroccan breeds. The major split seems to be linked to the West–East barrier of the Middle Atlas, whereas the influence of the High Atlas is less obvious and incompletely resolved. The study of additional breeds that have settled near the High Atlas should clarify the relationships between the breeds of the West part of the country, in spite of their small population size.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00679-2.

Genome-wide insights on gastrointestinal nematode resistance in autochthonous Tunisian sheep

Gastrointestinal nematode (GIN) infections have negative impacts on animal health, welfare and production. Information from molecular studies can highlight the underlying genetic mechanisms that enhance host resistance to GIN. However, such information often lacks for traditionally managed indigenous livestock. Here, we analysed 600 K single nucleotide polymorphism genotypes of GIN infected and non-infected traditionally managed autochthonous Tunisian sheep grazing communal natural pastures. Population structure analysis did not find genetic differentiation that is consistent with infection status. However, by contrasting the infected versus non-infected cohorts using ROH, LR-GWAS, F_ST and XP-EHH, we identified 35 candidate regions that overlapped between at least two methods. Nineteen regions harboured QTLs for parasite resistance, immune capacity and disease susceptibility and, ten regions harboured QTLs for production (growth) and meat and carcass (fatness and anatomy) traits. The analysis also revealed candidate regions spanning genes enhancing innate immune defence (SLC22A4, SLC22A5, IL-4, IL-13), intestinal wound healing/repair (IL-4, VIL1, CXCR1, CXCR2) and GIN expulsion (IL-4, IL-13). Our results suggest that traditionally managed indigenous sheep have evolved multiple strategies that evoke and enhance GIN resistance and developmental stability. They confirm the importance of obtaining information from indigenous sheep to investigate genomic regions of functional significance in understanding the architecture of GIN resistance.

Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area

Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (IBS) distance matrix highlighted a recent introgression of QFO into the BAR and a genetic differentiation of NDT samples, possibly explained by past introgression of European gene pools. Genome-wide scan for ROH across breeds and within the BAR sample set identified an outstanding signal on chromosome 13 (46.58-49.61 Mbp). These results were confirmed using F_ST index, differentiating fat vs. thin-tailed individuals. Candidate genes under selection pressure (CDS2, PROKR1, and BMP2) were associated to lipid storage and probably preferentially selected in fat-tailed BAR animals. Our findings suggest paying more attention to preserve the genetic integrity and adaptive alleles of local sheep breeds.

Clustering patterns mirror the geographical distribution and genetic history of Lemnos and Lesvos sheep populations

Elucidating the genetic variation and structure of Lemnos and Lesvos sheep is critical for maintaining local genetic diversity, ecosystem integrity and resilience of local food production of the two North Aegean islands. In the present study, we explored genetic diversity and differentiation as well as population structure of the Lemnos and Lesvos sheep. Furthermore, we sought to identify a small panel of markers with the highest discriminatory power to assign animals across islands. A total number of n = 424 (n = 307, Lemnos and n = 117, Lesvos) ewes, sampled from n = 24 herds dispersed at different geographic regions on the two islands, were genotyped with the 50K SNP array. Mean observed heterozygosity was higher (but not statistically significantly different) in Lesvos than in Lemnos population (0.384 vs. 0.377) while inbreeding levels were higher in Lemnos than Lesvos herds (0.065 vs. 0.031). Results of principal components along with that of admixture analysis and estimated genetic distances revealed genetic clusters corresponding to Lesvos and Lemnos origin and the existence of infrastructure within islands that were associated with geographical isolation and genetic history of the studied populations. In particular, genetic analyses highlighted three geographically isolated herds in Lemnos that are located at mountainous areas of the island and are characterized as representatives of the local sheep by historic data and reports. Admixture analysis also showed a shared genetic background between Lemnos and Lesvos sheep attributable to past gene flow. Little overall genetic differentiation was detected between the two island sheep populations, while 150 discriminatory SNPs could accurately assign animals to their origin. Present results are comparable with those reported in the worldwide sheep breeds, suggesting geography related genetic patterns across and within islands and the existence of the local Lemnos sheep.

The origin of sheep settlement in Western Mediterranean

The arrival of Neolithic culture in North Africa, especially domestic animals has been essentially documented from archaeological records. As the data relative to sheep are scarce, we studied the genetic relationship between Moroccan sheep breeds and Mediterranean ones using the sequencing of 628 bp of the mitochondrial DNA control region in 193 Moroccan individuals, belonging to six breeds, and 652 sequences from other breeds in Europe and Middle East. Through Network analysis and an original phylogenetically derived method, the connection proportions of each Moroccan breed to foreign ones were estimated, highlighting the strong links between Moroccan and Iberian breeds. The first founders of Moroccan sheep population were issued at 79% from Iberia and 21% from a territory between Middle East and Africa. Their calculated expansion times were respectively 7,100 and 8,600 years B.P. This suggests that Neolithization was introduced by a double influence, from Iberia and from another route, maybe Oriental or Sub-Saharan. The consequence of the environmental changes encountered by founders from Iberia was tested using different neutrality tests. There are significant selection signatures at the level of Moroccan and European breeds settled in elevated altitudes, and an erosion of nucleotide diversity in Moroccan breeds living in arid areas.

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

Background

In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation.

Results

We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$f_{4}$$\end{document}f4 profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds.

Conclusions

Our results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population.

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance

Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, F_ST), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise F_ST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number.