Genetic diversity and population structure of Sicilian sheep breeds using microsatellite markers

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.

Genetic diversity assessment of the indigenous goat population of Benin using microsatellite markers

Improved knowledge of the diversity within and among local animal populations is increasingly necessary for their sustainable management. Accordingly, this study assessed the genetic diversity and structure of the indigenous goat population of Benin. Nine hundred and fifty-four goats were sampled across the three vegetation zones of Benin [i.e., Guineo-Congolese zone (GCZ), Guineo-Sudanian zone (GSZ), and Sudanian zone (SZ)] and genotyped with 12 multiplexed microsatellite markers. The genetic diversity and structure of the indigenous goat population of Benin were examined using the usual genetic indices (number of alleles Na, expected and observed heterozygosities He and Ho, Fixation index FST, coefficient of genetic differentiation GST), and three different methods of structure assessment [Bayesian admixture model in STRUCTURE, self-organizing map (SOM), and discriminant analysis of principal components (DAPC)]. The mean values of Na (11.25), He (0.69), Ho (0.66), FST (0.012), and GST (0.012) estimated in the indigenous Beninese goat population highlighted great genetic diversity. STRUCTURE and SOM results showed the existence of two distinct goat groups (Djallonké and Sahelian) with high crossbreeding effects. Furthermore, DAPC distinguished four clusters within the goat population descending from the two ancestry groups. Clusters 1 and 3 (most individuals from GCZ) respectively showed a mean Djallonké ancestry proportion of 73.79% and 71.18%, whereas cluster 4 (mainly of goats from SZ and some goats of GSZ) showed a mean Sahelian ancestry proportion of 78.65%. Cluster 2, which grouped almost all animals from the three zones, was also of Sahelian ancestry but with a high level of interbreeding, as shown by the mean membership proportion of only 62.73%. It is therefore urgent to develop community management programs and selection schemes for the main goat types to ensure the sustainability of goat production in Benin.

Genetic Variability and Population Structure of the Tunisian Sicilo-Sarde Dairy Sheep Breed Inferred from Microsatellites Analysis

This study analyzed the genetic variability, inbreeding and population structure of the Tunisian-North African dairy sheep breed, the Sicilo-Sarde (SS), created by crossing the Sarda and Comisana dairy breeds. The level of variability in the SS, considered as an endangered breed after a dramatic decrease, was assessed using 17 microsatellite markers by analyzing the two breed populations sampled from their respective cradles: SS of Beja (SSB, n = 27) and SS of Mateur (SSM, n = 25). High levels of genetic diversity in SS were revealed, with a total of 212 alleles, a high mean number of alleles (12.47 ± 4.17) and a high average polymorphism information content (PIC) (0.81 ± 0.10). The observed heterozygosity was considerable in SSB and SSM (0.795 and 0.785, respectively). The inbreeding level measured by the population inbreeding coefficient FIS is higher in the SSM population (0.121) than in the SSB population (0.090). The higher genetic diversity level detected in SSB reflected the effect of new Italian Sarda genes introduced by intra-uterine artificial insemination recently practiced in this population. The Wilcoxon test and the mode-shift distribution indicated that the SS breed is a non-bottlenecked population. The structural analysis reflected the historical miscegenation practiced during the breed creation and highlighted further ancient miscegenation, which could date back to the first waves of sheep introduction to the western Mediterranean region. Microsatellite markers were successfully applied in the assessment of the genetic variability of SS and should be used in monitoring this variability during the application of conservation strategies.

Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.

Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

Background

Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments.

Results

We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations.

Conclusions

Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01079-0.

Tick Infestation and Piroplasm Infection in Barbarine and Queue Fine de l'Ouest Autochthonous Sheep Breeds in Tunisia, North Africa

As ticks and tick-borne pathogens affect the productivity of livestock, searching for genetically resistant breeds to infestation by ticks may represent an alternative to the overuse of chemical drugs. The aim of this study was to assess if there is a difference in tick infestation among the main sheep breeds in Tunisia. The study was carried out between April 2018 and January 2020 in 17 small to middle-sized sheep flocks from 3 regions across Tunisia. Four hundred and thirty-nine ear-tagged ewes from Barbarine (n = 288, 65.6%) and Queue Fine de l'Ouest (QFO) (n = 151, 34.4%) breeds were examined and sampled each trimester. Ticks were identified to the species level, and piroplasms were detected using PCR that targets a common sequence ARNr18S to both Babesia and Theileria genera using catch-all primers. Totally, 707 adult ticks were collected from animals; 91.4% (646/707) of them were Rhipicephalus sanguineus s.l. Queue Fine de l'Ouest animals were markedly less infested by ticks, and no one of them was infected by piroplasms compared to the Barbarine breed. Indeed, during the first four seasons, 21 animals, all from the Barbarine breed, were detected positive for piroplasms. This is the first study in Tunisia about the low susceptibility of QFO ewes to infestation by ticks and to infection by piroplasms. The QFO sheep breed could be raised preferably at high-risk areas of tick occurrence and could be considered in concrete control strategies, including a breeding program.

Assessment of genetic diversity and population structure of Colombian Creole cattle using microsatellites

To establish the diversity, structure, and phylogenetic relationships among Colombian Creole cattle, six native breeds and one introduced breed were genotyped for 20 microsatellite loci. The average number of alleles per breed ranged from 7050 (Romosinuano) to 10,100 (Casanareño), and the expected heterozygosity ranged from 0.691 (San martinero) to 0.785 (Casanareño). The deviation from the Hardy-Weinberg equilibrium (HWE) was statistically significant (p < 0.05) in 59 out of 120 tests carried out in the six breeds for the 20 microsatellite loci analyzed. Colombian Creole bovine breeds have maintained a high level of genetic differentiation within the same populations (93%), and the rest is explained by differences between breeds (7%). The differentiation pattern and the genetic relationships between the Colombian Creole bovine breeds showed high consistency with the evolutionary history of each. Both the Bayesian grouping analysis and the neighbor-joining tree exhibited a reliable grouping pattern, which revealed two main groups: one comprised by the breeds Blanco Orejinegro, Hartón del Valle, Costeño Con Cuernos, Romosinuano, and San Martinero, and the other one by the Creole breed Casanareño and Zebu. These were probably caused by different historical, reproductive, and geographic isolation precedents, as well as by different levels of inbreeding. This study will help understand the genetic characteristics of Colombian Creole cattle and will benefit future conservation programs.

Genetic Connectedness Between Norwegian White Sheep and New Zealand Composite Sheep Populations With Similar Development History

The Norwegian White sheep (NWS) and New Zealand Terminal Sire Composite (NZC) sheep breeds have been developed based on crossing of multiple breeds, mainly of Northern European origin. A close genetic relationship between these populations could enable across-country genomic evaluations. The main objectives of this study were to assess the genetic connectedness between Norwegian and New Zealand sheep populations and estimate numerous genetic diversity metrics for these two populations. A total of 792 NWS and 16,912 NZC animals were genotyped using a high-density Illumina SNP chip panel (∼606K SNPs). The NZC animals were grouped based on their breed composition as: Finn, Lamb Supreme, Primera, Texel, “Other Dual Purpose”, and “Other Terminal Sire”. The average level of linkage disequilibrium ranged from 0.156 (for Primera) to 0.231 (for Finn). The lowest consistency of gametic phase was estimated between NWS and Finn (0.397), and between NWS and Texel (0.443), respectively. Similar consistency of gametic phase was estimated between NWS and the other NZC populations (∼ 0.52). For all composite sheep populations analyzed in this study, the majority of runs of homozygosity (ROH) segments identified had short length (<2,500 kb), indicating ancient (instead of recent) inbreeding. The variation in the number of ROH segments observed in the NWS was similar to the variation observed in Primera and Lamb Supreme. There was no clear discrimination between NWS and NZC based on the first few principal components. In addition, based on admixture analyses, there seems to be a significant overlap of the ancestral populations that contributed to the development of both NWS and NZC. There were no evident signatures of selection in these populations, which might be due to recent crossbreeding. In conclusion, the NWS composite breed was shown to be moderately related to NZC populations, especially Primera and Lamb Supreme. The findings reported here indicate a promising opportunity for collaborative genomic analyses involving NWS and NZC sheep populations.

Genetic diversity of wild wintering red-crowned crane (Grus japonensis) by microsatellite markers and mitochondrial Cyt B gene sequence in the Yancheng reserve

The red-crowned crane (Grus japonensis) is one of the most endangered cranes in the world, and its wild population is still declining. To characterize the genetic resources of East Asian migratory populations, we studied the genetic variation in wild red-crowned cranes at the Yancheng reserve. Based on a partial Cyt b gene sequence, 32 wild red-crowned crane samples were screened from 100 feathers with unknown sample information. Twelve haplotypes were detected using 32 wild red-crowned crane samples. Six pairs of published microsatellite primers were selected for genotyping. A total of 47 alleles were obtained, with an average of 7.8 alleles per locus. All microsatellite loci were highly polymorphic; the average polymorphic information content and expected heterozygosity were 0.721 ± 0.080 and 0.768 ± 0.071, respectively. These results show that the East Asian migratory population of wild red-crowned cranes exhibits high polymorphism. These data are useful for informing reintroduction efforts. The study results provide a basis for understanding the population genetic properties of an endangered crane.

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

The identification of individuals' breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. The results using independent analysis, such as admixture, F st, principal component analysis and random forest, confirmed the ability of these methods in selecting distinctive markers. The identified SNPs may constitute a starting point for the development of a SNP based identification test as a tool for breed assignment and traceability of animal products.

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed's genetic structure and its relationship with other breeds were investigated. Levels of pairwise linkage disequilibrium decreased with increasing distance between single nucleotide polymorphisms. An average correlation coefficient <0.25 was found for markers located up to 50 kb apart. Therefore, these results support the need to use denser single nucleotide polymorphism panels for high power association mapping and genomic selection efficiency in future breeding programs. The estimate of past effective population size ranged from 747 animals 250 generations ago to 28 animals five generations ago, whereas the contemporary effective population size was 25 animals. A total of 637 ROH were identified, most of which were short (67%) and ranged from 1 to 10 Mb. The genetic analyses revealed that the Barbaresca breed tended to display lower variability than other Sicilian breeds. Recent inbreeding was evident, according to the ROH analysis. All the investigated parameters showed a comparatively narrow genetic base and indicated an endangered status for Barbaresca. Multidimensional scaling, model-based clustering, measurement of population differentiation, neighbor networks and haplotype sharing distinguished Barbaresca from other breeds, showed a low level of admixture with the other breeds considered in this study, and indicated clear genetic differences compared with other breeds. Attention should be given to the conservation of Barbaresca due to its critical conservation status. In this context, genomic information may have a crucial role in management of small and endangered populations.

Population genetic structure and milk production traits in Girgentana goat breed

The aim of this work was to evaluate the genetic status of the Girgentana goat, an endangered breed from Sicily (Italy), using microsatellite markers. Furthermore, as the main purpose of the Girgentana breed is milk production, quantitative milk traits were investigated, including fatty acid profile. Molecular data from CSN1S1, CSN2, CSN1S2, and CSN3 casein genes were also used to infer haplotypes. A total of 264 individuals were collected. Samples of Maltese (n = 41) and Derivata di Siria (n = 33) goat breeds were also used to understand the genetic relationship among breeds. Test-day records for milk production were collected to determine daily milk yield, fat, protein, casein, lactose, and somatic cell count. Individual milk samples were also collected for fatty acid extraction. Wright’s statistics, gene flow, Nei genetic distance, factorial correspondence analysis, and Bayesian assignment test showed the existence of genetic variability and differentiation among breeds. The AMOVA results indicated that 89.96% of the total variance was partitioned within populations. The Girgentana breed appears to have a subdivided population, and has not experienced a recent bottleneck. A high variability in milk yield was observed. Mean morning milk yield was 1448 ± 404 g, with 4.30 ± 0.87% and 3.72 ± 0.44% of fat and protein percentages, respectively. The average somatic cell count found in Girgentana goat milk was higher than the threshold of 1 500 000 cells/mL advised in Europe for fresh milk. Gross milk and fatty acid composition were similar to that reported in the literature for other local goat breeds.

Evaluation of genetic variability within PrP genotyped sheep of endangered Italian Altamurana breed

In the last few decades, there has been increased awareness of preservation and exploitation of endangered breeds for the maintenance of biodiversity, as well as the concern for diseases in sheep breeding. This study was carried out in native endangered Altamurana dairy sheep breed from Southern Italy. The Altamurana breed was considered as two populations (Alt-Cav and Alt-Cra-Zoe), based on presumed cross-breed and remarkable differences in the PrP genotypes frequencies. The genetic diversity between the two Altamurana populations (Alt-Cav and Alt-Cra-Zoe) was evaluated in comparison to three Italian dairy breeds through fourteen microsatellite markers. Both measures of genetic distance and the population structure analysis highlighted that the Alt-Cav and Alt-Cra-Zoe sheep have a particular genetic background. The estimated fixation index (FST) and the genetic Nei's distances among the populations showed a higher level of genetic differentiation for Alt-Cav than Alt-Cra-Zoe. The Bayesian clustering analysis implemented in the STRUCTURE software showed clear and distinct clusters for the two Altamurana populations, confirming the hypothesis of Alt-Cav as a genetic group well differentiated from Alt-Cra-Zoe. Alt-Cav likely can be considered as belonging to the original strain of the Altamurana breed. This findings may be used to assist the programme for conservation and selection of scrapie resistance genotypes in endangered Altamurana sheep breed.

Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds

Background

The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array.

Results

Average r² between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r² estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r² was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, F_ST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, N_e) whereas the lowest value was found in Valle del Belice breed.

Conclusions

This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0108-5) contains supplementary material, which is available to authorized users.