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Giovannini S, Chessari G, Riggio S, Marletta D, Sardina MT, Mastrangelo S, Sarti FM. Insight into the current genomic diversity, conservation status and population structure of Tunisian Barbarine sheep breed. Front Genet 2024; 15:1379086. [PMID: 38881792 PMCID: PMC11176520 DOI: 10.3389/fgene.2024.1379086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/07/2024] [Indexed: 06/18/2024] Open
Abstract
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.
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Affiliation(s)
- Samira Giovannini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Francesca Maria Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
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Baazaoui I, Bedhiaf-Romdhani S, Mastrangelo S, Lenstra JA, Da Silva A, Benjelloun B, Ciani E. Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data. Front Vet Sci 2024; 11:1339321. [PMID: 38487707 PMCID: PMC10938946 DOI: 10.3389/fvets.2024.1339321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024] Open
Abstract
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.
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Affiliation(s)
- Imen Baazaoui
- Laboratory of Animal and Fodder Production, National Institute of Agronomic Research of Tunisia, Ariana, Tunisia
| | - Sonia Bedhiaf-Romdhani
- Laboratory of Animal and Fodder Production, National Institute of Agronomic Research of Tunisia, Ariana, Tunisia
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anne Da Silva
- Faculté des Sciences et Techniques de Limoges, E2LIM, Limoges, France
| | - Badr Benjelloun
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, Beni Mellal, Morocco
| | - Elena Ciani
- Dipartamento Bioscienze, Biotecnologie, Biofarmaceutica, University of Bari Aldo Moro, Bari, Italy
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He X, Wang W, Du X, Chu M. Association between single-nucleotide polymorphism in PIK3CD gene and litter size in Small Tail Han sheep. Anim Biotechnol 2023; 34:3337-3342. [PMID: 36332162 DOI: 10.1080/10495398.2022.2140059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The p110δ isoform of the PI3K catalytic subunit (encoded by the PIK3CD gene) is a key component of the PI3K pathway for follicle growth in mammalian ovarian granulosa cells. Nevertheless, little is known about the association of its polymorphisms with ovine litter size. In this study, the distribution of different genotypes of two SNPs in the PIK3CD gene was calculated in more than forty sheep breeds, and the associations between SNPs and litter size in Small Tail Han (STH) sheep were also analyzed. Besides, the mRNA expression of the PIK3CD gene was also detected in some reproduction-related tissues. The results showed that the "A" allele frequency was higher in rs412889931 (g.41926327G > A) in a typical polytocous sheep breed (p < 0.01). The association's analysis showed rs412889931 was correlated with ovine fecundity as assessed by three parity litter sizes (p < 0.05). Finally, we found the expression of PIK3CD in the ovary had significant differences in different fecundity sheep breeds, indicating that SNP may regulate the litter size by influencing the PIK3CD gene expression. The present results demonstrated that rs412889931 could be used in the marker-assisted selection of the litter size in sheep breeding.
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Affiliation(s)
- Xiaoyun He
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolong Du
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Machová K, Marina H, Arranz JJ, Pelayo R, Rychtářová J, Milerski M, Vostrý L, Suárez-Vega A. Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms. Animal 2023; 17:100690. [PMID: 36566708 DOI: 10.1016/j.animal.2022.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
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 FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne 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 (FHOM) 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.
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Affiliation(s)
- Karolína Machová
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic.
| | - Héctor Marina
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Juan Jose Arranz
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Rocío Pelayo
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Jana Rychtářová
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Michal Milerski
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Luboš Vostrý
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic
| | - Aroa Suárez-Vega
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
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Ben Sassi-Zaidy Y, Mohamed-Brahmi A, Chaouch M, Maretto F, Cendron F, Charfi-Cheikhrouha F, Ben Abderrazak S, Djemali M, Cassandro M. Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds. Genes (Basel) 2022; 13:genes13081421. [PMID: 36011332 PMCID: PMC9408117 DOI: 10.3390/genes13081421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 01/18/2023] Open
Abstract
In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.
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Affiliation(s)
- Yousra Ben Sassi-Zaidy
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis (INAT), University of Carthage, Tunis-Mahragène Tunis 2078, Tunisia
- Correspondence: (Y.B.S.-Z.); (F.C.); Tel.: +39-049-8272871 (F.C.); Fax: +39-049-8272633 (F.C.)
| | - Aziza Mohamed-Brahmi
- Laboratory of Agricultural Production Systems Sustainability in the North Western Region of Tunisia, Department of Animal Production, Ecole Supérieure d’Agriculture du Kef Boulifa, University of Jendouba, Le Kef 7119, Tunisia
| | - Melek Chaouch
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR11IPT06), Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Fabio Maretto
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
| | - Filippo Cendron
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
- Correspondence: (Y.B.S.-Z.); (F.C.); Tel.: +39-049-8272871 (F.C.); Fax: +39-049-8272633 (F.C.)
| | - Faouzia Charfi-Cheikhrouha
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Souha Ben Abderrazak
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR11IPT06), Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Mnaour Djemali
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis (INAT), University of Carthage, Tunis-Mahragène Tunis 2078, Tunisia
| | - Martino Cassandro
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
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Genomic Population Structure of the Main Historical Genetic Lines of Spanish Merino Sheep. Animals (Basel) 2022; 12:ani12101327. [PMID: 35625173 PMCID: PMC9138057 DOI: 10.3390/ani12101327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Historical documentation shows that the Spanish Merino sheep was selected over many centuries due to the quality of wool, following which it was used to originate all other Merino breeds around the world, mainly by crossbreeding with local breeds. Today, the historical genetic lines that originated the Spanish Merino are still preserved in several closed herds in which they have been bred for nearly 200 years, maintaining their original genetic purity. Our study demonstrates, using a genomic approach, the exceptional genetic richness and variability of these lines, which are clearly differentiated from modern Merino breeds, and must therefore be protected to safeguard the large genetic pool they represent. Abstract According to historiographical documentation, the Romans first began to select Merino sheep in the Iberian Peninsula during the first century, with the aim of obtaining a breed appreciated for the quality of its wool. This process continued locally during the Middle Ages, when Spanish sheep were protected, and their export to foreign countries was banned. It was during the 16th century when individual Merino sheep were allowed to spread around the world to be used to improve the wool quality of local breeds. However, the wool crisis of the 1960s shifted the selection criteria of the Merino breed towards meat production at the expenses of wool. Consequently, individuals that display the genetic and phenotypic characteristics of those sheep originally bred in the kingdom of Spain in the Middle Ages are extremely difficult to find in commercial herds. In this study, we characterized the genetic basis of 403 individuals from the main historical Spanish Merino genetic lines (Granda, Hidalgo, Lopez-Montenegro, Maeso, Donoso and Egea), which were bred in isolation over the last 200 years, using a genomic approach based on genotyping data from the Axiom™ Ovine 50K SNP Genotyping Array. Our analysis included measuring population structure, genomic differentiation indexes, runs of homozygosity (ROH) patterns, and an analysis of molecular variance (AMOVA). The results showed large genetic differences between the historical lines, even though they belong to the same breed. In addition, ROH analysis showed differences due to increased inbreeding among the ancient generations compared with the modern Merino lines, confirming the breed’s ancestral and closed origin. However, our results also showed a high variability and richness within the Spanish historical Merino lines from a genetic viewpoint. This fact, together with their great ability to produce high-quality wool, suggests that ancestral Merino lines from Spain should be considered a valuable genetic population to be maintained as a resource for the improvement of wool-producing sheep breeds all around the world.
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Ben Sassi-Zaidy Y, Mohamed-Brahmi A, Nouairia G, Charfi-Cheikhrouha F, Djemali M, Cassandro M. Genetic Variability and Population Structure of the Tunisian Sicilo-Sarde Dairy Sheep Breed Inferred from Microsatellites Analysis. Genes (Basel) 2022; 13:genes13020304. [PMID: 35205349 PMCID: PMC8872596 DOI: 10.3390/genes13020304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 12/10/2022] Open
Abstract
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 breed creation and highlighted further ancient miscegenation, which could date back to the introduction of the first sheep wave introduction to the western Mediterranean. 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.
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Affiliation(s)
- Yousra Ben Sassi-Zaidy
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, El Manar II Tunis 2092, Tunisia;
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy;
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis, University of Carthage, Tunis-Mahrajène Tunis 1082, Tunisia;
- Correspondence: (Y.B.S.-Z.); (M.C.); Tel.: +39-049-8272871 (M.C.); Fax: +39-049-8272633 (M.C.)
| | - Aziza Mohamed-Brahmi
- Laboratory of Agricultural Production Systems Sustainability in the North Western Region of Tunisia, Department of Animal Production, Ecole Supérieure d’Agriculture du Kef Boulifa, University of Jendouba, Le Kef 7119, Tunisia;
| | - Ghada Nouairia
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy;
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Faouzia Charfi-Cheikhrouha
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, El Manar II Tunis 2092, Tunisia;
| | - M’Naouer Djemali
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis, University of Carthage, Tunis-Mahrajène Tunis 1082, Tunisia;
| | - Martino Cassandro
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy;
- Correspondence: (Y.B.S.-Z.); (M.C.); Tel.: +39-049-8272871 (M.C.); Fax: +39-049-8272633 (M.C.)
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Kandoussi A, Badaoui B, Boujenane I, Piro M, Petit D. How have sheep breeds differentiated from each other in Morocco? Genetic structure and geographical distribution patterns. Genet Sel Evol 2021; 53:83. [PMID: 34736399 PMCID: PMC8567669 DOI: 10.1186/s12711-021-00679-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
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 FST 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.
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Affiliation(s)
- Asmae Kandoussi
- Department of Animal Production and Biotechnology, Institut Agronomique et Vétérinaire Hassan II, Rabat-Instituts, PO Box 6202, 10101, Rabat, Morocco.,Glycosylation et Différenciation Cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges Cedex, France
| | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology and Genome, Mohammed V University, 4 Avenue Ibn Battouta, B.P. 1014 RP, Rabat, Morocco
| | - Ismaïl Boujenane
- Department of Animal Production and Biotechnology, Institut Agronomique et Vétérinaire Hassan II, Rabat-Instituts, PO Box 6202, 10101, Rabat, Morocco
| | - Mohammed Piro
- Department of Medicine, Surgery and Reproduction, Institut Agronomique et Vétérinaire Hassan II, Rabat-Instituts, PO Box 6202, 10101, Rabat, Morocco
| | - Daniel Petit
- Glycosylation et Différenciation Cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges Cedex, France.
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Leroy G, Boettcher P, Besbes B, Peña CR, Jaffrezic F, Baumung R. Food securers or invasive aliens? Trends and consequences of non-native livestock introgression in developing countries. GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT 2020; 26:100420. [PMID: 32844086 PMCID: PMC7439832 DOI: 10.1016/j.gfs.2020.100420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 11/02/2022]
Abstract
Importation of livestock genetic resources from industrialized countries for introgression of specific traits and other forms of crossbreeding is often indicative of a shift in production systems toward greater intensification and specialization. In developing countries, imported genetic resources are regarded as both a solution to improve the performance of local livestock and as one of the main threats to local populations. Using international databases, censuses and technical reports, we investigate ongoing trends and consequences of these two phenomena in 40 countries from Africa, Asia and Latin America. In these countries, the share of locally adapted breeds within species has decreased by an average of 0.76% per year over the last 20 years. The corresponding increase has been distributed between pure exotic breeds and crossbred animals, with differences across regions. In several countries, increased utilization of exotic cattle breeds and crossbreeding has been accompanied by a trend in increased milk yield per cow. The shift from local genetic resources to crossbred and exotic animals must be considered in the context of challenges such as food security, erosion of agrobiodiversity, interactions with other agricultural production, reduction of poverty and provision of ecosystem services, as well as resilience to and mitigation of climate change.
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Affiliation(s)
- Gregoire Leroy
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Paul Boettcher
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Badi Besbes
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Carlos Raúl Peña
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Florence Jaffrezic
- INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Roswitha Baumung
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
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Ciani E, Mastrangelo S, Da Silva A, Marroni F, Ferenčaković M, Ajmone-Marsan P, Baird H, Barbato M, Colli L, Delvento C, Dovenski T, Gorjanc G, Hall SJG, Hoda A, Li MH, Marković B, McEwan J, Moradi MH, Ruiz-Larrañaga O, Ružić-Muslić D, Šalamon D, Simčič M, Stepanek O, Curik I, Cubric-Curik V, Lenstra JA. On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools. Genet Sel Evol 2020; 52:25. [PMID: 32408891 PMCID: PMC7227234 DOI: 10.1186/s12711-020-00545-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/30/2020] [Indexed: 11/26/2022] Open
Abstract
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}
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\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.
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Affiliation(s)
- Elena Ciani
- Dipartamento Bioscienze, Biotecnologie, Biofarmaceutica, Universita. degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Universita Studi di Palermo, Palermo, Italy
| | - Anne Da Silva
- Université de Limoges, INRAE, Pereine EA7500, USC1061 Gamaa, 87000, Limoges, France
| | - Fabio Marroni
- Dipartamento Scienze Agroalimentari, Ambientali e Animali, Universita Udine, Udine, Italy
| | | | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Universita Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Mario Barbato
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Universita Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Universita Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Chiara Delvento
- Dipartamento Bioscienze, Biotecnologie, Biofarmaceutica, Universita. degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Toni Dovenski
- Department of Reproduction and Biomedicine, Faculty of Veterinary Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Gregor Gorjanc
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, Scotland, UK
| | | | - Anila Hoda
- Department of Animal Production, Faculty of Agriculture and Environment, Agricultural University ofTirana, Tirana, Albania
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | | | - John McEwan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Universita Cattolica del S. Cuore di Piacenza, Piacenza, Italy
| | - Mohammad H Moradi
- Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - Otsanda Ruiz-Larrañaga
- Department of Genetics, Physical Anthropology and Animal Physiology, University of Basque Country, Leioa, Spain
| | | | - Dragica Šalamon
- Department of Animal Science, University of Zagreb, Zagreb, Croatia
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | - Ino Curik
- Department of Animal Science, University of Zagreb, Zagreb, Croatia
| | | | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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