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Rambaldi Migliore N, Bigi D, Milanesi M, Zambonelli P, Negrini R, Morabito S, Verini-Supplizi A, Liotta L, Chegdani F, Agha S, Salim B, Beja-Pereira A, Torroni A, Ajmone‐Marsan P, Achilli A, Colli L. Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys. PLoS One 2024; 19:e0307511. [PMID: 39197009 PMCID: PMC11356394 DOI: 10.1371/journal.pone.0307511] [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: 01/15/2024] [Accepted: 07/05/2024] [Indexed: 08/30/2024] Open
Abstract
Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata, Pavia, Italy
| | - Daniele Bigi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Alma Mater Studiorum Università di Bologna, Viale Giuseppe Fanin, Bologna, Italy
| | - Marco Milanesi
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
| | - Paolo Zambonelli
- Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Alma Mater Studiorum Università di Bologna, Viale Giuseppe Fanin, Bologna, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
| | - Simone Morabito
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
| | | | - Luigi Liotta
- Department of Veterinary Sciences, University of Messina, V.le Palatucci, Messina, Italy
| | - Fatima Chegdani
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
| | - Saif Agha
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, Khartoum-North, Sudan
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- DGAOT, Faculty of Sciences, Universidade do Porto, Rua Campo Alegre, Porto, Portugal
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata, Pavia, Italy
| | - Paolo Ajmone‐Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
- CREI Romeo and Enrica Invernizzi Research Center on Sustainable Dairy Production, Università Cattolica del S. Cuore, Piacenza (PC), Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata, Pavia, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
- BioDNA Centro di Ricerca Sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza (PC), 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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Cinar MU, Oliveira RD, Hadfield TS, Lichtenwalner A, Brzozowski RJ, Settlemire CT, Schoenian SG, Parker C, Neibergs HL, Cockett NE, White SN. Genome-wide association with footrot in hair and wool sheep. Front Genet 2024; 14:1297444. [PMID: 38288162 PMCID: PMC10822918 DOI: 10.3389/fgene.2023.1297444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/31/2023] [Indexed: 01/31/2024] Open
Abstract
Ovine footrot is an infectious disease with important contributions from Dichelobacter nodosus and Fusobacterium necrophorum. Footrot is characterized by separation of the hoof from underlying tissue, and this causes severe lameness that negatively impacts animal wellbeing, growth, and profitability. Large economic losses result from lost production as well as treatment costs, and improved genetic tools to address footrot are a valuable long-term goal. Prior genetic studies had examined European wool sheep, but hair sheep breeds such as Katahdin and Blackbelly have been reported to have increased resistance to footrot, as well as to intestinal parasites. Thus, footrot condition scores were collected from 251 U.S. sheep including Katahdin, Blackbelly, and European-influenced crossbred sheep with direct and imputed genotypes at OvineHD array (>500,000 single nucleotide polymorphism) density. Genome-wide association was performed with a mixed model accounting for farm and principal components derived from animal genotypes, as well as a random term for the genomic relationship matrix. We identified three genome-wide significant associations, including SNPs in or near GBP6 and TCHH. We also identified 33 additional associated SNPs with genome-wide suggestive evidence, including a cluster of 6 SNPs in a peak near the genome-wide significance threshold located near the glutamine transporter gene SLC38A1. These findings suggest genetic susceptibility to footrot may be influenced by genes involved in divergent biological processes such as immune responses, nutrient availability, and hoof growth and integrity. This is the first genome-wide study to investigate susceptibility to footrot by including hair sheep and also the first study of any kind to identify multiple genome-wide significant associations with ovine footrot. These results provide a foundation for developing genetic tests for marker-assisted selection to improve resistance to ovine footrot once additional steps like fine mapping and validation are complete.
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Affiliation(s)
- Mehmet Ulas Cinar
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri, Turkiye
| | - Ryan D. Oliveira
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Tracy S. Hadfield
- Department of Animal, Agricultural Experiment Station, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Anne Lichtenwalner
- School of Food and Agriculture, University of Maine, Orono, ME, United States
- Cooperative Extension, University of Maine, Orono, ME, United States
| | | | | | - Susan G. Schoenian
- Western Maryland Research and Education Center, University of Maryland, College Park, MD, United States
| | - Charles Parker
- Department of Animal Sciences, Professor Emeritus, The Ohio State University, Columbus, OH, United States
| | - Holly L. Neibergs
- Department of Animal Science, Washington State University, Pullman, WA, United States
| | - Noelle E. Cockett
- Department of Animal, Agricultural Experiment Station, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Stephen N. White
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
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Woolley SA, Salavati M, Clark EL. Recent advances in the genomic resources for sheep. Mamm Genome 2023; 34:545-558. [PMID: 37752302 PMCID: PMC10627984 DOI: 10.1007/s00335-023-10018-z] [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: 04/11/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.
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Affiliation(s)
- Shernae A Woolley
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Mazdak Salavati
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Scotland's Rural College, Parkgate, Barony Campus, Dumfries, DG1 3NE, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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Tadesse D, Patra AK, Puchala R, Hussein A, Goetsch AL. Differentiation of Hair Sheep Breeds Based on the Physiological and Blood Biochemical Changes in Response to Different Stressors Using Multivariate Analysis Techniques. Animals (Basel) 2023; 13:2643. [PMID: 37627434 PMCID: PMC10451155 DOI: 10.3390/ani13162643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Physiological and blood measurement changes due to high heat load, restricted feed intake, and limited drinking water availability in 135 animals of three hair sheep breeds (Dorper, Katahdin, and St. Croix) were subjected to multivariate analysis techniques. The objective of this analysis was to evaluate the ability of these variables to separate individual hair sheep into groups based on adaptation characteristics in response to three physiological stressors and identify variables with greater discriminatory power. There were 16, 8, and 13 physiological and blood variables obtained from high heat load, restricted feed consumption, and water intake studies, respectively, for multivariate analysis. Physiological variables such as respiration rate, rectal and skin temperature, and panting score were measured only in the heat stress study. The results of the cluster and canonical discriminant analyses showed the presence of wide divergence (p < 0.05) between St. Croix and other breeds in their responses to high heat loads and restricted-feed- and -water-intake conditions. Dorper and Katahdin were grouped (p > 0.05) together based on the changes in physiological variables, which were separated (p < 0.05) from those of St. Croix as a resilient group. The stepwise discriminant analysis indicated that skin temperature, panting score, rectal temperature, respiration rate, and blood urea nitrogen and oxygen concentrations were the significant (p < 0.05) discriminating variables in clustering individual sheep into groups based on their responses to the high-heat-stress condition. Under the limited feed intake condition, the significant (p < 0.05) traits responsible for the separation of St. Croix from Dorper and Katahdin were blood triglyceride and cholesterol concentrations, whereas blood hemoglobin, osmolality, protein, and albumin were most important discriminating variables under the limited water intake condition. In conclusion, the results of the present study suggest that the stress responses of Dorper and Katahdin are similar and different from that of St. Croix. This finding can be useful information for future decisions in developing climate-resilient sheep through selective breeding.
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Affiliation(s)
- Dereje Tadesse
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA; (D.T.); (R.P.); (A.H.); (A.L.G.)
- Department of Animal Sciences, Debre Berhan University, Debre Berhan P.O. Box 445, Ethiopia
| | - Amlan Kumar Patra
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA; (D.T.); (R.P.); (A.H.); (A.L.G.)
| | - Ryszard Puchala
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA; (D.T.); (R.P.); (A.H.); (A.L.G.)
| | - Ali Hussein
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA; (D.T.); (R.P.); (A.H.); (A.L.G.)
| | - Arthur Louis Goetsch
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA; (D.T.); (R.P.); (A.H.); (A.L.G.)
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Chessari G, Criscione A, Tolone M, Bordonaro S, Rizzuto I, Riggio S, Macaluso V, Moscarelli A, Portolano B, Sardina MT, Mastrangelo S. High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context. Front Vet Sci 2023; 10:1127354. [PMID: 37205231 PMCID: PMC10185747 DOI: 10.3389/fvets.2023.1127354] [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: 12/19/2022] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Bordonaro
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Ilaria Rizzuto
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Vito Macaluso
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 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
- *Correspondence: Salvatore Mastrangelo,
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Senczuk G, Di Civita M, Rillo L, Macciocchi A, Occidente M, Saralli G, D’Onofrio V, Galli T, Persichilli C, Di Giovannantonio C, Pilla F, Matassino D. The ancestral origin of the critically endangered Quadricorna sheep as revealed by genome-wide analysis. PLoS One 2022; 17:e0275989. [PMID: 36288337 PMCID: PMC9605034 DOI: 10.1371/journal.pone.0275989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Livestock European diffusion followed different human migration waves from the Fertile Crescent. In sheep, at least two diffusion waves have shaped the current breeds' biodiversity generating a complex genetic pattern composed by either primitive or fine-wool selected breeds. Among primitive breeds, aside from sharing common ancestral genomic components, they also show several traits such as the policeraty, large horns in the ram, short tail, and a moulting fleece, considered as ancestral. Although most of the primitive breeds characterized by these traits are confined on the very edge of Northern Europe, several residual populations are also scattered in the Mediterranean region. In fact, although in Italy a large number of local breeds are already extinct, others are listed as critically endangered, and among these there is the Quadricorna breed which is a four-horned sheep characterized by several ancestral traits. In this context we genotyped 47 individuals belonging to the Quadricorna sheep breed, a relict and endangered breed, from Central and Southern Italy. In doing so we used the Illumina OvineSNP50K array in order to explore its genetic diversity and to compare it with other 33 primitive traits-related, Mediterranean and Middle-East breeds, with the specific aim to reconstruct its origin. After retaining 35,680 SNPs following data filtering, the overall genomic architecture has been explored by using genetic diversity indices, Principal Component Analysis (PCA) and admixture analysis, while the genetic relationships and migration events have been inferred using a neighbor-joining tree based on Reynolds' distances and by the maximum likelihood tree as implemented in treemix. Multiple convergent evidence from all our population genetics analyses, indicated that the two Quadricorna populations differ from all the other Italian breeds, while they resulted to be very close to the Middle Eastern and primitive European breeds. In addition, the genetic diversity indices highlighted values comparable with those of most of the other analyzed breeds, despite the two populations exhibit slightly different genetic indices suggesting different levels of genomic inbreeding and drift (FIS and FROH). The admixture analysis does not suggest any signal of recent gene exchange with other Italian local breeds, highlighting a rather ancestral purity of the two populations, while on the other hand the treemix analysis seems to suggest an ancient admixture with other primitive European breeds. Finally, all these evidences seem to trace back the residual Quadricorna sheep to an early Neolithic spread, probably following a Mediterranean route and that urgent conservation actions are needed in order to keep the breed and all related cultural products alive.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
- * E-mail:
| | - Marika Di Civita
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Luigina Rillo
- Consortium for Experimentation, Dissemination and Application of Innovative Biotechniques, (ConSDABI), Benevento, Italy
| | - Alessandra Macciocchi
- Agenzia Regionale per lo Sviluppo e l’Innovazione dell’Agricoltura del Lazio (ARSIAL), Roma, Italy
| | - Mariaconsiglia Occidente
- Consortium for Experimentation, Dissemination and Application of Innovative Biotechniques, (ConSDABI), Benevento, Italy
| | - Giorgio Saralli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri (IZSLT), Roma, Italy
| | - Valentina D’Onofrio
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri (IZSLT), Roma, Italy
| | - Tiziana Galli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri (IZSLT), Roma, Italy
| | - Christian Persichilli
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | | | - Fabio Pilla
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Donato Matassino
- Consortium for Experimentation, Dissemination and Application of Innovative Biotechniques, (ConSDABI), Benevento, Italy
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8
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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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9
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New Insight into the Genome-Wide Diversity and Admixture of Six Colombian Sheep Populations. Genes (Basel) 2022; 13:genes13081415. [PMID: 36011325 PMCID: PMC9407362 DOI: 10.3390/genes13081415] [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: 06/30/2022] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Creole sheep represent a strategic genetic resource for populations living in marginal areas under financial restrictions on the American continent. Six Colombian sheep breeds (two wool (BCL-Boyacá and NCL-Nariño, 12 and 14 samples) and four hair (OPCE-Ethiopian, 54 samples; OPCS-Sudan, 74 samples; OPCP-Pelibeuy, 59 samples; OPCW-Wayúu, 24 samples) were genotyped using the Illumina Ovine SNP50 BeadChip. Data was also included from international 44 breeds from International Sheep Genomics Consortium (ISGC) and from data published in previous a previous work on the Caribbean and African breeds. Although geographically separated, wool (NCL, BCL) and hair types (OPCE, OPCS, OPCW) presented little genetic differentiation (FST 0.05) at a global level but several groups of animals separated suggesting local clustering due to geographical isolation. The OPCP underwent a recent crossing with Mexican Pelibuey, explaining its differentiation. Findings in this work such as the proximity to West African Djallonké (WAD) and Barbados Black Belly (BBB), suggest different introductions of African type animals from the Caribbean region on a pre-existing genetic basis formed by animals deriving from the first importations coming from Europe in colonial times. As expected, Colombian wool breeds showed, in particular in Admixture software results, a greater genomic component in common with European breeds and in particular with Iberian ones (Churra). This study provides a basis for future research into the genetic diversity within and between the Colombian sheep breeds analysed, and scientific data for policy decisions on Farm Animal Genetic Resources (FAnGR).
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10
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Analysis of the Genetic Diversity and Population Structure of Four Senegalese Sheep Breeds Using Medium-Density Single-Nucleotide Polymorphisms. Animals (Basel) 2022; 12:ani12121512. [PMID: 35739849 PMCID: PMC9219475 DOI: 10.3390/ani12121512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/23/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary This paper reported genetic parameters of four Senegalese sheep breeds, in relation to inbreeding, diversity and genetic proximity. The results provide informations on genetic conservation and adaptability of the breeds in the Senegalese context. Abstract In Senegal, sheep breeds have adapted to their environment and play a key socio-economic role. This study aimed to explore the genetic diversity and structure of four Senegalese sheep breeds (Peul-peul, Djallonke, Touabire, and Ladoum) and their relationships with global sheep breeds. To that end, forty-seven sheep were genotyped using the OvineSNP50 BeadChip, and these genotypic data were analysed with those of 73 sheep breeds representative of worldwide ovine diversity (2729 animals). The average observed heterozygosity (Ho) ranged from 0.293 in Djallonke sheep to 0.339 in Touabire sheep. The estimated Fis values were low, ranging from 0.019 for Ladoum to 0.034 for Peul-peul sheep. The estimated Fst values were low (0.003–0.044) among the trypanosusceptible breeds (Peul-peul, Touabire, and Ladoum) but high between the previous breeds and the trypanotolerant Djallonke breed (0.075–0.116), indicating better genetic conservation of the Djallonke sheep. A principal component analysis revealed clustering of the Senegalese sheep breeds according to their geographic distribution. However, owing to genetic improvement practices, the introgression of Touabire sheep blood seems to have reshaped the genetic landscape of the trypanosusceptible sheep breeds in Senegal. The Senegalese sheep breeds showed lower genetic diversity than their presumed ancestral sheep breeds of the Middle East. They also presented some relatedness with Caribbean sheep breeds, which reveals their contribution to the global genetic diversity and to the development of Caribbean sheep breeds.
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11
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Machová K, Málková A, Vostrý L. Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes. Genes (Basel) 2022; 13:genes13040613. [PMID: 35456419 PMCID: PMC9025449 DOI: 10.3390/genes13040613] [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: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/26/2022] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.
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Affiliation(s)
- Karolína Machová
- Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
- Correspondence:
| | - Anežka Málková
- Department of Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | - Luboš Vostrý
- Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
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12
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Drouilhet L, Moreno C, Plisson-Petit F, Marcon D, Fabre S, Hazard D. Variability in Global DNA Methylation Rate Across Tissues and Over Time in Sheep. Front Genet 2022; 13:791283. [PMID: 35360841 PMCID: PMC8961874 DOI: 10.3389/fgene.2022.791283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
Recent studies highlighted the influence of epigenetic marks in the variability of many complex traits, both in plants and animals. These studied focused only on specific sites of the genome having differentially methylated profiles among individuals and/or tissues. In contrast, we recently used the methylation rate of the entire genome as a unique measure considered as a novel quantitative phenotype in sheep. This phenotype named global DNA methylation rate (GDMR), measured by luminometric assay, integrates the methylation level of each CpG dinucleotide within the 6 million of CCGG sites along the ovine genome. GDMR measured in blood previously showed moderate heritability of 0.20 and provided evidence for a genetic determinism. The main objective of the present study was to better characterize the GDMR phenotype in various tissues and investigate its variability in several breeds of sheep reared in the same environment. GDMR was measured on blood samples collected monthly from 59 growing male and female lambs (24 Romane, 23 Blackbelly and 12 Charollais), between birth and 4 months of age. Blood GDMR was on average around 80% and was influenced by the sampling date (p < 0.001), the breed (p = 0.002) and the sex (p = 0.002). In addition, GDMR was determined in 12 somatic (frontal lobe, pituitary gland, heart, lung, sub cutaneous and perirenal adipose tissue, skeletal muscle, liver, spleen, adrenal gland, medulla and cortical kidney) and 6 reproductive tissues (ovary, oviduct, uterus, testis, epididymis and seminal vesicle). GDMR was on average 70% in somatic tissues but marked variation was observed depending on the tissue. The GDMR measured in blood was higher than that measured in other somatic tissues, and is not a good proxy of less accessible tissues. Female reproductive tissues had a 10% higher GDMR than male reproductive tissues. We demonstrated a significant influence of the breed on blood GDMR, certainly reflecting the influence of different genetic backgrounds. The effect of the breed on GDMR may be related to their specific abilities to adapt to and live in different conditions.
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Affiliation(s)
- Laurence Drouilhet
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
- *Correspondence: Laurence Drouilhet,
| | - Carole Moreno
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | | | - Stéphane Fabre
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Dominique Hazard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
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13
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Lv FH, Cao YH, Liu GJ, Luo LY, Lu R, Liu MJ, Li WR, Zhou P, Wang XH, Shen M, Gao L, Yang JQ, Yang H, Yang YL, Liu CB, Wan PC, Zhang YS, Pi WH, Ren YL, Shen ZQ, Wang F, Wang YT, Li JQ, Salehian-Dehkordi H, Hehua E, Liu YG, Chen JF, Wang JK, Deng XM, Esmailizadeh A, Dehghani-Qanatqestani M, Charati H, Nosrati M, Štěpánek O, Rushdi HE, Olsaker I, Curik I, Gorkhali NA, Paiva SR, Caetano AR, Ciani E, Amills M, Weimann C, Erhardt G, Amane A, Mwacharo JM, Han JL, Hanotte O, Periasamy K, Johansson AM, Hallsson JH, Kantanen J, Coltman DW, Bruford MW, Lenstra JA, Li MH. Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci. Mol Biol Evol 2021; 39:6459180. [PMID: 34893856 PMCID: PMC8826587 DOI: 10.1093/molbev/msab353] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3′-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.
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Affiliation(s)
- Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ran Lu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yong-Lin Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jian-Fei Chen
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Kui Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xue-Mei Deng
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Hadi Charati
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Neena A Gorkhali
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, DF, Brazil
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, DF, Brazil
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24 Moro, Bari, Italy
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Animal Sciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Agraw Amane
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
- CTLGH and SRUC, The Roslin Institute Building, Easter Bush Campus, Edinburgh, Scotland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jón H Hallsson
- Faculty of Natural Resources and Environmental Sciences, Agricultural University of Iceland, Borgarnes, Iceland
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, Wales, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Wales, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Corresponding author: E-mail:
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14
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Paim TP, Paiva SR, de Toledo NM, Yamaghishi MB, Carneiro PLS, Facó O, de Araújo AM, Azevedo HC, Caetano AR, Braga RM, McManus C. Origin and population structure of Brazilian hair sheep breeds. Anim Genet 2021; 52:492-504. [PMID: 34087001 DOI: 10.1111/age.13093] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 12/01/2022]
Abstract
Brazilian hair sheep constitute a genetic diversity hotspot. These animals are found in the harsh environments of the Brazilian Northwest (semi-arid) region. Genotypes (50K SNP chip) from seven Brazilian sheep breeds (five hair and two coarse wool types) and 87 worldwide breeds were used to test for population structure, admixture and genetic diversity. Moreover, phylogenetic trees evaluating migration events between genetic groups were built. Brazilian Somali, a fat-tailed breed, had a close relationship with East African breeds and clustered distinctly from other Brazilian breeds. Brazilian Blackbelly and Barbados Blackbelly had a close relationship. The Morada Nova breed did not show close relationships with European or African breeds, revealing a single migration event from an Algerian hair breed. Brazilian Fat-tail and Morada Nova share a common ancestor, but the former showed introgressions from Brazilian Somali and Afrikaner breeds, explaining the fat-tail phenotype. The Santa Inês breed received a substantial contribution from Brazilian Bergamasca and showed an admixed origin with recent introgressions from other breeds, mainly from Suffolk. Furthermore, Brazilian Somali and Brazilian Fat-tail are the most endangered sheep genetic resources in Brazil and should be the focus for ex situ conservation programs. In conclusion, Brazilian hair sheep show an African origin and are characterized by diverse genetic composition, reinforcing the need for conservation of these genetic resources, and at the same time, this highly diverse group has variability that can be used in breeding programs.
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Affiliation(s)
- T P Paim
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, Distrito Federal, 70910-900, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia Goiano, Iporá, Goiás, 76200-000, Brazil
| | - S R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, 70770-917, Brazil
| | - N M de Toledo
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, Distrito Federal, 70910-900, Brazil
| | - M B Yamaghishi
- Embrapa Informática Agropecuária, Campinas, São Paulo, 13083-886, Brazil
| | - P L S Carneiro
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Bahia, 45205-490, Brazil
| | - O Facó
- Embrapa Caprinos e Ovinos, Sobral, Ceará, 62010-970, Brazil
| | - A M de Araújo
- Embrapa Meio-Norte, Teresina, Piaui, 64008-780, Brazil
| | - H C Azevedo
- Embrapa Tabuleiros Costeiros, Aracaju, Sergipe, 49025-040, Brazil
| | - A R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, 70770-917, Brazil
| | - R M Braga
- Embrapa Roraima, Boa Vista, Roraima, 69301-970, Brazil
| | - C McManus
- Instituto de Biologia, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
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15
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Revelo HA, López-Alvarez D, Landi V, Rizzo L, Alvarez LA. Mitochondrial DNA Variations in Colombian Creole Sheep Confirm an Iberian Origin and Shed Light on the Dynamics of Introduction Events of African Genotypes. Animals (Basel) 2020; 10:E1594. [PMID: 32911657 PMCID: PMC7552328 DOI: 10.3390/ani10091594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 11/16/2022] Open
Abstract
The genetic origins and diversity of Creole sheep from five regions of Colombia were investigated based on mitochondrial DNA (mtDNA) variations across 89 sequences from five breeds: one wool Creole sheep (CL) and four hair Creole sheep, including Ethiopian (OPCE), Sudan (OPCS), Pelibuey (OPCP) and Wayúu (OPCW). A global comparison was done using 62 haplotypes from Iberian, African, Indian, Caribbean, Mexican, Caucasian and European sheep based on sequences retrieved from GenBank. This study aimed to identify the maternal origin of Colombian Creole sheep and their genetic relationships at a global level. The results showed 31 different haplotypes from Colombian Creole sheep, which can be assigned to maternal lineage B, the most common lineage found in European sheep breeds and the only one found in several Iberian breed (e.g., Churra, Spanish Merino) that most likely participated in the Creole formation. Additional analyses showed that wool and hair sheep retained a broad genetic identity despite being geographically separated. The global-level phylogenetic analysis revealed that Colombian Creole sheep belong to a distinct and defined genetic lineage that is likely the result of a founder effect with ecotypes of Iberian descent and the subsequent introduction of foreign breeds. This is consistent with historical reports on the presence of sheep in South America and, particularly, Colombia.
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Affiliation(s)
- Herman Alberto Revelo
- Department of Animal Science Animal, Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Palmira 763533, Colombia; (H.A.R.); (L.A.A.)
| | - Diana López-Alvarez
- Department of Animal Science Animal, Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Palmira 763533, Colombia; (H.A.R.); (L.A.A.)
- Department of Biological Science, Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Palmira 763533, Colombia
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, 70010 Valenzano, BA, Italy;
| | - Lauden Rizzo
- Faculty of Livestock Science, Universidad Técnica Estatal de Quevedo, Quevedo 091050, Los Ríos, Ecuador;
| | - Luz Angela Alvarez
- Department of Animal Science Animal, Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Palmira 763533, Colombia; (H.A.R.); (L.A.A.)
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16
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Genetic diversity evolution of a sheep breed reintroduced after extinction: Tracing back Christopher Columbus' first imported sheep. Res Vet Sci 2020; 132:207-216. [PMID: 32604044 DOI: 10.1016/j.rvsc.2020.06.007] [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: 01/17/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 11/22/2022]
Abstract
New World's hair sheep breeds may genetically stem from West African introgression into established ecotypes of Spanish descent presumably extinct in the XIX Century. However, present Canary non-wooled breeds have presumably regressively resulted from the absorption of primitive individuals through Venezuelan descendants. We studied genetic diversity, structure, and evolution of the Canary hair sheep since its reintroduction in the 1950s. Demographic and genetic variability were evaluated using ENDOG (v4.8). Effective population size based on individual inbreeding rate was around one third higher than when based on individual coancestry rate. Nei's distances and equivalent subpopulations number indicated a highly-structured population. Although genetic diversity loss since the founder generations could be considered small, narrower pedigree bottlenecks could result from intraflock breeding policies and excessive contribution of few ancestors. Long generation intervals could be considered when reducing inbreeding. Wright's fixation statistics indicated slight interflock inbreeding. Pedigree completeness suggested genetic parameters were reliable, hence controlling inbreeding negative effects, could indeed, be crucial preserving these animal resources, consolidating the population in the archipelago after reintroduction.
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Campos E, Cuéllar J, Salvador O, García-Trejo EA, Pereira F. The genetic diversity and phylogeography of Mexican domestic sheep. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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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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The global diversity of Haemonchus contortus is shaped by human intervention and climate. Nat Commun 2019; 10:4811. [PMID: 31641125 PMCID: PMC6805936 DOI: 10.1038/s41467-019-12695-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Haemonchus contortus is a haematophagous parasitic nematode of veterinary interest. We have performed a survey of its genome-wide diversity using single-worm whole genome sequencing of 223 individuals sampled from 19 isolates spanning five continents. We find an African origin for the species, together with evidence for parasites spreading during the transatlantic slave trade and colonisation of Australia. Strong selective sweeps surrounding the β-tubulin locus, a target of benzimidazole anthelmintic drug, are identified in independent populations. These sweeps are further supported by signals of diversifying selection enriched in genes involved in response to drugs and other anthelmintic-associated biological functions. We also identify some candidate genes that may play a role in ivermectin resistance. Finally, genetic signatures of climate-driven adaptation are described, revealing a gene acting as an epigenetic regulator and components of the dauer pathway. These results begin to define genetic adaptation to climate in a parasitic nematode. Based on single worm whole genome sequencing, the authors here characterise the global evolution of the gastrointestinal parasite Haemonchus contortus and identify genes that play a role in drug resistance as well as climate-driven adaptations involving an epigenetic regulator.
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Ben Jemaa S, Kdidi S, Gdura AM, Dayhum AS, Eldaghayes IM, Boussaha M, Rebours E, Yahyaoui MH. Inferring the population structure of the Maghreb sheep breeds using a medium-density SNP chip. Anim Genet 2019; 50:526-533. [PMID: 31385357 DOI: 10.1111/age.12831] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2019] [Indexed: 01/26/2023]
Abstract
North Africa has a great diversity of indigenous sheep breeds whose origin is linked to its environmental characteristics and to certain historical events that took place in the region. To date, few genome-wide studies have been conducted to investigate the population structure of North African indigenous sheep. The objective of the present study was to provide a detailed assessment of the genetic structure and admixture patterns of six Maghreb sheep populations using the Illumina 50K Ovine BeadChip and comparisons with 22 global populations of sheep and mouflon. Regardless of the method of analysis used, patterns of multiple hybridization events were observed within all North African populations, leading to a heterogeneous genetic architecture that varies according to the breed. The Barbarine population showed the lowest genetic heterogeneity and major southwest Asian ancestry, providing additional support to the Asian origin of the North African fat-tailed sheep. All other breeds presented substantial Merino introgression ranging from 15% for D'man to 31% for Black Thibar. We highlighted several signals of ancestral introgression between North African and southern European sheep. In addition, we identified two opposite gradients of ancestry, southwest Asian and central European, occurring between North Africa and central Europe. Our results provide further evidence of the weak global population structure of sheep resulting from high levels of gene flow among breeds occurring worldwide. At the regional level, signs of recent admixture among North African populations, resulting in a change of the original genomic architecture of minority breeds, were also detected.
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Affiliation(s)
- S Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - S Kdidi
- Livestock and Wildlife Laboratory, Arid Lands Institute, Route Djorf Km 22, 4119, Medenine, Tunisia
| | - A M Gdura
- Animal Improvement Project, Ministry of Agriculture, Tripoli, Libya
| | - A S Dayhum
- Faculty of Veterinary Medicine, University of Tripoli, 13662, Tripoli, Libya
| | - I M Eldaghayes
- Faculty of Veterinary Medicine, University of Tripoli, 13662, Tripoli, Libya
| | - M Boussaha
- GABI, INRA, AgroParisTech, Paris Saclay University, 78350, Jouy-en-Josas, France
| | - E Rebours
- GABI, INRA, AgroParisTech, Paris Saclay University, 78350, Jouy-en-Josas, France
| | - M H Yahyaoui
- Livestock and Wildlife Laboratory, Arid Lands Institute, Route Djorf Km 22, 4119, Medenine, Tunisia
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21
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Colli L, Milanesi M, Talenti A, Bertolini F, Chen M, Crisà A, Daly KG, Del Corvo M, Guldbrandtsen B, Lenstra JA, Rosen BD, Vajana E, Catillo G, Joost S, Nicolazzi EL, Rochat E, Rothschild MF, Servin B, Sonstegard TS, Steri R, Van Tassell CP, Ajmone-Marsan P, Crepaldi P, Stella A. Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes. Genet Sel Evol 2018; 50:58. [PMID: 30449284 PMCID: PMC6240949 DOI: 10.1186/s12711-018-0422-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/15/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. RESULTS A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. CONCLUSIONS After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.
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Affiliation(s)
- Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy. .,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy.
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,School of Veterinary Medicine, Department of Support, Production and Animal Health, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, USA.,National Institute of Aquatic Resources, Technical University of Denmark, DTU, Lyngby, Denmark
| | - Minhui Chen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark.,Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alessandra Crisà
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Kevin Gerard Daly
- Population Genetics Lab, Smurfit Institute of Genetics, Trinity College of Dublin, Dublin, Ireland
| | - Marcello Del Corvo
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Elia Vajana
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | | | - Roberto Steri
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Paolo Ajmone-Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano, Lodi, Italy.,Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy
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Edea Z, Dessie T, Dadi H, Do KT, Kim KS. Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers. Front Genet 2017; 8:218. [PMID: 29312441 PMCID: PMC5744078 DOI: 10.3389/fgene.2017.00218] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/05/2017] [Indexed: 11/13/2022] Open
Abstract
Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin-i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered together, suggesting that these breeds were introduced to the African continent via the Horn and migrated further south.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju, South Korea
| | - Tadelle Dessie
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Hailu Dadi
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Kyoung-Tag Do
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, South Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju, South Korea
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