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Petretto E, Dettori ML, Luigi-Sierra MG, Noce A, Pazzola M, Vacca GM, Molina A, Martínez A, Goyache F, Carolan S, Amills M. Investigating the footprint of post-domestication dispersal on the diversity of modern European, African and Asian goats. Genet Sel Evol 2024; 56:55. [PMID: 39068382 PMCID: PMC11282621 DOI: 10.1186/s12711-024-00923-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 07/05/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Goats were domesticated in the Fertile Crescent about 10,000 years before present (YBP) and subsequently spread across Eurasia and Africa. This dispersal is expected to generate a gradient of declining genetic diversity with increasing distance from the areas of early livestock management. Previous studies have reported the existence of such genetic cline in European goat populations, but they were based on a limited number of microsatellite markers. Here, we have analyzed data generated by the AdaptMap project and other studies. More specifically, we have used the geographic coordinates and estimates of the observed (Ho) and expected (He) heterozygosities of 1077 European, 1187 African and 617 Asian goats belonging to 38, 43 and 22 different breeds, respectively, to find out whether genetic diversity and distance to Ganj Dareh, a Neolithic settlement in western Iran for which evidence of an early management of domestic goats has been obtained, are significantly correlated. RESULTS Principal component and ADMIXTURE analyses revealed an incomplete regional differentiation of European breeds, but two genetic clusters representing Northern Europe and the British-Irish Isles were remarkably differentiated from the remaining European populations. In African breeds, we observed five main clusters: (1) North Africa, (2) West Africa, (3) East Africa, (4) South Africa, and (5) Madagascar. Regarding Asian breeds, three well differentiated West Asian, South Asian and East Asian groups were observed. For European and Asian goats, no strong evidence of significant correlations between Ho and He and distance to Ganj Dareh was found. In contrast, in African breeds we detected a significant gradient of diversity, which decreased with distance to Ganj Dareh. CONCLUSIONS The detection of a genetic cline associated with distance to the Ganj Dareh in African but not in European or Asian goat breeds might reflect differences in the post-domestication dispersal process and subsequent migratory movements associated with the management of caprine populations from these three continents.
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Affiliation(s)
- Elena Petretto
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | - María Gracia Luigi-Sierra
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antonia Noce
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | | | - Antonio Molina
- Department of Genetics, University of Cordoba, 14071, Córdoba, Spain
| | - Amparo Martínez
- Department of Genetics, University of Cordoba, 14071, Córdoba, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | | | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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Kusza S, Badaoui B, Wanjala G. Insights into the genomic homogeneity of Moroccan indigenous sheep breeds though the lens of runs of homozygosity. Sci Rep 2024; 14:16515. [PMID: 39019985 PMCID: PMC11255268 DOI: 10.1038/s41598-024-67558-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024] Open
Abstract
Numerous studies have indicated that Morocco's indigenous sheep breeds are genetically homogenous, posing a risk to their survival in the challenging harsh climate conditions where they predominantly inhabit. To understand the genetic behind genetic homogeneity through the lens of runs of homozygosity (ROH), we analyzed the whole genome sequences of five indigenous sheep breeds (Beni Guil, Ouled Djellal, D'man, Sardi, Timahdite and Admixed).The results from principal component, admixture, Fst, and neighbour joining tree analyses consistently showed a homogenous genetic structure. This structure was characterized by an average length of 1.83 Mb for runs of homozygosity (ROH) segments, with a limited number of long ROH segments (24-48 Mb and > 48 Mb). The most common ROH segments were those ranging from 1-6 Mb. The most significant regions of homozygosity (ROH Islands) were mostly observed in two chromosomes, namely Chr1 and Chr5. Specifically, ROH Islands were exclusively discovered in the Ouled Djellal breed on Chr1, whereas Chr5 exhibited ROH Islands in all breeds. The analysis of ROH Island and iHS technique was employed to detect signatures of selection on Chr1 and Chr5. The results indicate that Chr5 had a high level of homogeneity, with the same genes being discovered across all breeds. In contrast, Chr1 displays some genetic variances between breeds. Genes identified on Chr5 included SLC39A1, IL23A, CAST, IL5, IL13, and IL4 which are responsible for immune response while genes identified on Chr1 include SOD1, SLAMF9, RTP4, CLDN1, and PRKAA2. ROH segment profile and effective population sizes patterns suggests that the genetic uniformity of studied breeds is the outcome of events that transpired between 250 and 300 generations ago. This research not only contributes to the understanding of ROH distribution across breeds but helps design and implement native sheep breeding and conservation strategies in Morocco. Future research, incorporating a broader sample size and utilizing the pangenome for reference, is recommended to further elucidate these breeds' genomic landscapes and adaptive mechanisms.
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Affiliation(s)
- Szilvia Kusza
- Faculty of Agricultural and Food Sciences and Environmental Management, Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary.
| | - Bouabid Badaoui
- Faculty of Sciences, Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Mohammed V University in Rabat, Rabat, Morocco
- African Sustainable Agriculture Research Institute (ASARI),, Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - George Wanjala
- Faculty of Agricultural and Food Sciences and Environmental Management, Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
- Doctoral School of Animal Science, University of Debrecen, Böszörményi út 138., 4032, Debrecen, Hungary
- Institute of Animal Sciences and Wildlife Management, University of Szeged, Andrássy út 15., 6800, Hódmezővásárhely, Hungary
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Blondeau Da Silva S, Mwacharo JM, Li M, Ahbara A, Muchadeyi FC, Dzomba EF, Lenstra JA, Da Silva A. IBD sharing patterns as intra-breed admixture indicators in small ruminants. Heredity (Edinb) 2024; 132:30-42. [PMID: 37919398 PMCID: PMC10799084 DOI: 10.1038/s41437-023-00658-x] [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] [Received: 10/09/2022] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023] Open
Abstract
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.
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Affiliation(s)
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotlands Rural College (SRUC) and Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, EH25 9RG, Midlothian, UK
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Menghua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Abulgasim Ahbara
- Animal and Veterinary Sciences, Scotlands Rural College (SRUC) and Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, EH25 9RG, Midlothian, UK
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
| | | | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anne Da Silva
- Faculté des Sciences et Techniques de Limoges, E2LIM, 87000, Limoges, France.
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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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Panigrahi M, Kumar H, Saravanan KA, Rajawat D, Sonejita Nayak S, Ghildiyal K, Kaisa K, Parida S, Bhushan B, Dutt T. Trajectory of livestock genomics in South Asia: A comprehensive review. Gene 2022; 843:146808. [PMID: 35973570 DOI: 10.1016/j.gene.2022.146808] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kaiho Kaisa
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Belhout C, Elgroud R, Butaye P. Methicillin-Resistant Staphylococcus aureus (MRSA) and Other Methicillin-Resistant Staphylococci and Mammaliicoccus (MRNaS) Associated with Animals and Food Products in Arab Countries: A Review. Vet Sci 2022; 9:vetsci9070317. [PMID: 35878334 PMCID: PMC9320237 DOI: 10.3390/vetsci9070317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/11/2022] [Accepted: 06/21/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Staphylococci are present in the microbiota of both humans and animal species, being recognized as the most important opportunistic pathogens. Antimicrobial resistance (AMR) has become a global public health issue presenting a significant risk because it severely limits treatment options. Methicillin resistance in staphylococci (MRS) poses a specific problem as it may cause serious human and animal infections, eventually resulting in death. The increasing observation of MRS in different animal species has raised the concern of their impact on animal health and the potential of zoonotic transmission. The availability of comprehensive data on the ecology and distribution of MRS in animals and food products worldwide is necessary to understand their relevance in the “One Health” domain. However, there is a gap in information in terms of MRS and the Arab countries. Therefore, our study aimed to provide an overview of the situation of MRS in these countries by reviewing the available data on livestock and animal products and making recommendations for the future. Abstract The prevalence of methicillin resistance in staphylococci has been increasing globally and is currently one of the major public health concerns. In particular, treating infections caused by staphylococci with acquired antimicrobial resistance is problematic, as their treatment is more difficult. The resistance is found both in human and animal staphylococcal strains. Methicillin-resistant staphylococci (MRS) have also been increasingly reported in wildlife. In Arab countries, MRS has been detected in food producing animals and food products; however, the risk this poses is somewhat unclear, and still a significant lack of information on the trend and distribution of these pathogens in these countries, which have a specific ecosystem (desert) and traditions (Muslim culture). In this manuscript, we aim to provide an overview of the prevalence and the major MRS clonal lineages circulating in these specific countries and compare to them other situations with different ecosystems and cultures.
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Affiliation(s)
- Chahrazed Belhout
- HASAQ Laboratory, High National Veterinary School, Issad Abbes Avenue, Oued Smar, El Harrach, Algiers 16270, Algeria
- Correspondence:
| | - Rachid Elgroud
- Institute of Veterinary Sciences, University Frères Mentouri Constantine 1, Constantine 25017, Algeria;
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium;
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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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Serranito B, Taurisson-Mouret D, Harkat S, Laoun A, Ouchene-Khelifi NA, Pompanon F, Benjelloun B, Cecchi G, Thevenon S, Lenstra JA, Da Silva A. Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats. Front Genet 2021; 12:715732. [PMID: 34413881 PMCID: PMC8369930 DOI: 10.3389/fgene.2021.715732] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Livestock is heavily affected by trypanosomosis in Africa. Through strong selective pressure, several African indigenous breeds of cattle and small ruminants have acquired varying degrees of tolerance against this disease. In this study, we combined LFMM and PCAdapt for analyzing two datasets of goats from West-Central Africa and East Africa, respectively, both comprising breeds with different assumed levels of trypanotolerance. The objectives were (i) to identify molecular signatures of selection related to trypanotolerance; and (ii) to guide an optimal sampling for subsequent studies. From 33 identified signatures, 18 had been detected previously in the literature as being mainly associated with climatic adaptations. The most plausible signatures of trypanotolerance indicate the genes DIS3L2, COPS7B, PD5A, UBE2K, and UBR1. The last gene is of particular interest since previous literature has already identified E3-ubiquitin ligases as playing a decisive role in the immune response. For following-up on these findings, the West-Central African area appears particularly relevant because of (i) a clear parasitic load gradient related to a humidity gradient, and (ii) still restricted admixture levels between goat breeds. This study illustrates the importance of protecting local breeds, which have retained unique allelic combinations conferring their remarkable adaptations.
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Affiliation(s)
- Bruno Serranito
- Museum National d’Histoire Naturelle, CRESCO, Dinard, France
- University of Limoges, PEREINE, E2LIM, Limoges, France
| | | | - Sahraoui Harkat
- Science Veterinary Institute, University of Blida, Blida, Algeria
| | | | | | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Badr Benjelloun
- National Institute of Agronomic Research, Regional Centre of Agronomic Research, Beni-Mellal, Morocco
| | - Giuliano Cecchi
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Sophie Thevenon
- CIRAD, UMR INTERTRYP, Montpellier, France
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France
| | | | - Anne Da Silva
- University of Limoges, PEREINE, E2LIM, Limoges, France
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9
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Ishibashi Y, Takahashi K. Role of individual dispersal in genetic resilience in fluctuating populations of the gray-sided vole Myodes rufocanus. Ecol Evol 2021; 11:3407-3421. [PMID: 33841793 PMCID: PMC8019057 DOI: 10.1002/ece3.7300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022] Open
Abstract
Population densities of the gray-sided vole Myodes rufocanus fluctuate greatly within and across years in Japan. Here, to investigate the role of individual dispersal in maintaining population genetic diversity, we examined how genetic diversity varied during fluctuations in density by analyzing eight microsatellite loci in voles sampled three times per year for 5 years, using two fixed trapping grids (approximately 0.5 ha each). At each trapping session, all captured voles at each trapping grid were removed. The STRUCTURE program was used to analyze serially collected samples to examine how population crashes were related to temporal variability, based on local-scale genetic compositions in each population. In total, 461 and 527 voles were captured at each trapping grid during this study. The number of voles captured during each trapping session (i.e., vole density) varied considerably at both grids. Although patterns in fluctuations were not synchronized between grids, the peak densities were similar. At both grids, the mean allele number recorded at each trapping session was strongly, positively, and nonlinearly correlated with density. STRUCTURE analyses revealed that the proportions of cluster compositions among individuals at each grid differed markedly before and after the crash phase, implying the long-distance dispersal of voles from remote areas at periods of low density. The present results suggest that, in gray-sided vole populations, genetic diversity varies with density largely at the local scale; in contrast, genetic variation in a metapopulation is well-preserved at the regional scale due to the density-dependent dispersal behaviors of individuals. By influencing the dispersal patterns of individuals, fluctuations in density affect metapopulation structure spatially and temporally, while the levels of genetic diversity are preserved in a metapopulation.
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Affiliation(s)
- Yasuyuki Ishibashi
- Hokkaido Research CenterForestry and Forest Products Research InstituteSapporoJapan
| | - Kenichi Takahashi
- Hokkaido Institute of Public HealthSapporoJapan
- Present address:
Hokkaido Pest Control AssociationSapporoJapan
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Ouchene-Khelifi NA, Ouchene N. Relationships between age, body measurements, and testicular measurements in Arabia bucks in Algeria. Trop Anim Health Prod 2021; 53:91. [PMID: 33415493 DOI: 10.1007/s11250-020-02500-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/03/2020] [Indexed: 11/30/2022]
Abstract
Body size and testicular measurements were found to be important parameters for the evaluation of the breeding quality. A study was therefore carried out on Arabia bucks (n = 180) to record normal testicular characteristics and to evaluate the effect of age on body (BCS, BW, WH, CG, AC, CS, and BL) and testicular (SC, TW, EW, TL, TD, and TL) measurements. Animals were classified into three age classes (less than or equal to 12 months, from 12 to 24 months, and over 24 months). The BW, BCS, testicular, and body measurements of the 3rd age group were significantly higher than those of age groups 1 and 2 (p < 0.01). Male age had a significant effect (p < 0.01) on BW, BCS, and body measurements. Indeed, the parameters of the 3rd age group were significantly higher than those of the 1st and 2nd age groups (p < 0.01). The same was true for testicular measurements (SC, TL, TW, EW, and EL) except for testicular diameter (TD) where the results of the first two age groups had no significant difference. The highest correlation coefficients were recorded between BW and all body (r = 0.7-0.9) and testicular traits (r = 0.72-0.85), BCS and body measurements (r = 0.73-0.89), and scrotal circumference and testicular measurements (r = 0.77-0.85). In conclusion, it was found that the use of BCS is readily measurable in live animals and is expected to be the best indicator of testicular and epididymal measurements. These results, particularly the predictive models developed, could be useful in the selection of males for reproduction.
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Affiliation(s)
- N A Ouchene-Khelifi
- Veterinary Sciences Institute, Saad Dahleb University Blida 1, Road of Soumaa, B.P. 270, 09000, Blida, Algeria.
| | - N Ouchene
- Veterinary Sciences Institute, Saad Dahleb University Blida 1, Road of Soumaa, B.P. 270, 09000, Blida, Algeria
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Genetic homogenization of indigenous sheep breeds in Northwest Africa. Sci Rep 2019; 9:7920. [PMID: 31138837 PMCID: PMC6538629 DOI: 10.1038/s41598-019-44137-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/07/2019] [Indexed: 11/17/2022] Open
Abstract
Northwest-African sheep represent an ideal case-study for assessing the potential impact of genetic homogenization as a threat to the future of traditional breeds that are adapted to local conditions. We studied ten Algerian and Moroccan breeds of sheep, including three transboundary breeds, distributed over a large part of the Maghreb region, which represents a geographically and historically coherent unit. Our analysis of the dataset that involved carrying out Genome-wide SNP genotyping, revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE and IBD segments analyses), in such a way that some breeds from different origins appeared genetically undistinguished: by grouping the eight most admixed populations, we obtained a mean global FST value of 0.0024. The sPCA analysis revealed that the major part of Morocco and the Northern part of Algeria were affected by the phenomenon, including most of the breeds considered. Unsupervised cross-breeding with the popular Ouled-Djellal breed was identified as a proximate cause of this homogenization. The issue of transboundary breeds was investigated, and the Hamra breed in particular was examined via ROH fragments analysis. Genetic diversity was considered in the light of historical archives and anthropological works. All of these elements taken together suggest that homogenization as a factor affecting the Maghrebin sheep stock, has been particularly significant over the last few decades, although this process probably started much earlier. In particular, we have identified the policies set by the French administration during the colonial period of the region’s history as a causal factor that probably contributed significantly to this process. The genetic homogenization that we have observed calls into question the integrity of the farm animal genomic resources represented by these local breeds, whose conservation is of critical importance to the future of the livestock sector.
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