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Mishra AK, Ahlawat S, Sharma R, Arora R, Singh S, Jain A. Assessment of genetic diversity of the fat-tailed Dumba sheep of India by mitochondrial and microsatellite markers. Anim Biotechnol 2023; 34:3545-3554. [PMID: 36794377 DOI: 10.1080/10495398.2023.2176316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
India has a centuries-old tradition of sheep production and breeding that accomplish economic, agricultural, and religious roles. In addition to the 44 registered sheep breeds, there is a fat-tailed sheep population referred to as Dumba. This study evaluated genetic variation in Dumba sheep and its differentiation from other Indian sheep breeds using mitochondrial DNA and genomic microsatellite loci. Haplotype and nucleotide diversity based on mitochondrial DNA analysis revealed substantially high maternal genetic diversity in Dumba sheep. Major ovine haplogroups A and B observed in sheep populations across the globe registered their presence in the Dumba sheep. The molecular genetic analysis using microsatellite markers also showed high measures of allele (10.125 ± 0.762) and gene diversity (0.749 ± 0.029). Results correspond to the non-bottleneck population that is near mutation-drift equilibrium despite some deficiency in the number of heterozygotes (FIS = 0.043 ± 0.059). Phylogenetic clustering confirmed Dumba to be a distinct population. Results of this study endow authorities with critical information imperative for sustainable utilization and conservation of Indian fat-tailed sheep, which is considered to be an untapped genetic resource contributing to the food security, livelihood, and economic sustainability of rural households in marginal areas of the country.
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Affiliation(s)
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Sanjeev Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Anand Jain
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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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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Her C, Rezaei HR, Hughes S, Naderi S, Duffraisse M, Mashkour M, Naghash HR, Bălășescu A, Luikart G, Jordan S, Özüt D, Kence A, Bruford MW, Tresset A, Vigne JD, Taberlet P, Hänni C, Pompanon F. Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros. Anim Genet 2022; 53:452-459. [PMID: 35288946 DOI: 10.1111/age.13191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 01/12/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).
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Affiliation(s)
- Charlotte Her
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - Hamid-Reza Rezaei
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France.,Environmental Sciences Department, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, ENSL, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Saeid Naderi
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France.,Department of Environment, Natural Resources Faculty, University of Guilan, Guilan, Iran
| | - Marilyne Duffraisse
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, ENSL, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Marjan Mashkour
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Hamid-Reza Naghash
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - Adrian Bălășescu
- Department of Bioarchaeology, 'Vasile Pârvan' Institute of Archaeology, Romanian Academy, Bucharest, Romania
| | - Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, Montana, USA
| | - Steve Jordan
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Deniz Özüt
- Biology Department, Middle East Technical University, Ankara, Turkey
| | - Aykut Kence
- Biology Department, Middle East Technical University, Ankara, Turkey
| | | | - Anne Tresset
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Jean-Denis Vigne
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Pierre Taberlet
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway
| | - Catherine Hänni
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - François Pompanon
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
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Gáspárdy A, Zenke P, Kovács E, Annus K, Posta J, Sáfár L, Maróti-Agóts Á. Evaluation of Maternal Genetic Background of Two Hungarian Autochthonous Sheep Breeds Coming from Different Geographical Directions. Animals (Basel) 2022; 12:ani12030218. [PMID: 35158542 PMCID: PMC8833378 DOI: 10.3390/ani12030218] [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: 12/09/2021] [Revised: 01/05/2022] [Accepted: 01/14/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of our research was the evaluation of the maternal genetic background of two Hungarian autochthonous sheep breeds of different geographical origin. A major argument for the preservation of endangered animal breeds is their documented past and historical importance. These also include the registration of pedigree data. This is the first study to evaluate and compare Tsigai and Cikta sheep in Hungary. Our investigation is based on two complete sequences of mitochondrial DNA (cytochrome b gene and control region). Our research was performed on these two sheep breeds with markedly different breed histories and breed characteristics to determine a possible common maternal genetic background, as ultimately the origin of both breeds can be traced back to Asia Minor. Between 2015 and 2017, a total of 203 biological samples were taken using a newly introduced founder sampling method. We found that the prevailing haplogroup B accounted for over 80% of both breeds, strengthening the common ancestral root. However, the pairwise genetic differentiation estimates (KST) calculated using the sequence-based statistics for cytochrome b gene and control region were 0.034 and 0.021, respectively (both at level p < 0.05); thus, revealing genetic differentiation in both sequences between the Tsigai and Cikta. We note that the known different history of the breeds is clearly justified by the currently studied deviations in their maternal genetic background.
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Affiliation(s)
- András Gáspárdy
- Department for Animal Breeding and Genetics, University of Veterinary Medicine, István u. 2, H-1078 Budapest, Hungary; (E.K.); (Á.M.-A.)
- Correspondence: (A.G.); (P.Z.)
| | - Petra Zenke
- Rex Pet Clinic, Lakkozó u. 13, H-1048 Budapest, Hungary;
- Correspondence: (A.G.); (P.Z.)
| | - Endre Kovács
- Department for Animal Breeding and Genetics, University of Veterinary Medicine, István u. 2, H-1078 Budapest, Hungary; (E.K.); (Á.M.-A.)
| | - Kata Annus
- Rex Pet Clinic, Lakkozó u. 13, H-1048 Budapest, Hungary;
| | - János Posta
- Department of Animal Husbandry, University of Debrecen, Böszörményi u. 138, H-4032 Debrecen, Hungary;
| | - László Sáfár
- Hungarian Sheep- and Goat Breeders’ Association, Lőportár u. 16, H-1134 Budapest, Hungary;
| | - Ákos Maróti-Agóts
- Department for Animal Breeding and Genetics, University of Veterinary Medicine, István u. 2, H-1078 Budapest, Hungary; (E.K.); (Á.M.-A.)
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Evidence for independent domestication of sheep mtDNA lineage A in India and introduction of lineage B through Arabian sea route. Sci Rep 2021; 11:19733. [PMID: 34611177 PMCID: PMC8492717 DOI: 10.1038/s41598-021-97761-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
India ranks the second in the world in terms of its sheep population with approximately 74.26 million represented by 44 well-described breeds in addition to several non-descript populations. Genetic diversity and phylogeography of Indian sheep breeds remain poorly understood, particularly for south Indian breeds. To have a comprehensive view of the domestication history of Indian sheep, we sequenced the mitochondrial DNA (mtDNA) control region (D-loop) and cytochrome b gene (CYTB) of 16 Indian domestic sheep breeds, most of them (13) from the south India. We analysed these sequences along with published data of domestic and wild sheep from different countries, including India. The haplotype diversity was relatively high in Indian sheep, which were classified into the three known mtDNA lineages, namely A, B and C. Lineage A was predominant among Indian sheep whereas lineages B and C were observed at low frequencies but C was restricted to the breeds of north and east India. The median joining network showed five major expanding haplogroups of lineage A (A1–A5). Out of which, A2, A4 and A5 were more frequent in Indian sheep in contrast to breeds from other parts of the world. Among the 27 Indian sheep breeds analysed, Mandya and Sonadi breeds were significantly different from other Indian breeds in the MDS analyses. This was explained by a very high contribution of lineage B into these two breeds. The Approximate Bayesian Computation (ABC) provided evidence for the domestication of lineage A sheep in the Indian subcontinent. Contrary to the current knowledge, we also found strong support for the introduction of lineage B into Indian subcontinent through sea route rather than from the Mongolian Plateau. The neighbour-joining tree of domestic and wild sheep revealed the close genetic relationship of Indian domestic sheep with Pakistani wild sheep O. vignei blanfordi. Based on our analyses and archaeological evidences, we suggest the Indian subcontinent as one of the domestication centres of the lineage A sheep, while lineage B sheep might have arrived into India from elsewhere via Arabian sea route. To the best of our knowledge, this is the first comprehensive study on Indian sheep where we have analysed more than 740 animals belonging to 27 sheep breeds raised in various regions of India. Our study provides insight into the understanding of the origin and migratory history of Indian sheep.
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Kandoussi A, Boujenane I, Piro M, Petit D. mtDNA genetic characterization of an isolated sheep breed in South of Moroccan Atlas. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Sharma R, Ahlawat S, Sharma H, Sharma P, Panchal P, Arora R, Tantia MS. Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India. Sci Rep 2020; 10:20422. [PMID: 33235268 PMCID: PMC7687881 DOI: 10.1038/s41598-020-77480-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
Sheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.
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Affiliation(s)
- Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Himani Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Priyanka Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Poonam Panchal
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Fadhil IA, Al-Shuhaib MBS. Phylogenetic differentiation between Awassi and Hamdani sheep using the mitochondrial 12S rRNA. Anim Biotechnol 2020; 33:801-809. [PMID: 33108945 DOI: 10.1080/10495398.2020.1837146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This study was conducted to assess the role of the mitochondrial 12S rRNA variations in the phylogenetic discrimination between two Iraqi breeds of sheep that differ in geographical distribution. A total of 122 animals (68 Awassi and 54 Hamdani) were included in the study. Direct sequencing of amplicons followed by the construction of a median-joining network and several trees were performed to identify the possible phylogenetic differences between both involved breeds. Genetic diversity, relative frequencies, and analysis of molecular variance (AMOVA) were performed to assess the genetic correlation between both populations. The median-joining network and minimized tree values showed that all observed haplotypes were separated into two groups according to their breed. Comprehensive phylogenetic data revealed only one Asian ancestor for all observed haplotypes. As indicated by AMOVA, the observed diversity was mostly due to between-population variation (1.24836%), while within-population variation (0.91221%) accounted for much less. The currently investigated rRNA amplicons exhibited different mitochondrial manifestations between Awassi and Hamdani breeds. Due to the ability of these 12S rRNA amplicons to mimic the geographical diversity for the currently investigated breeds, it is highly recommended to be used as potent mitochondrial genetic markers among broader ovine sequences.
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Affiliation(s)
- Israa A Fadhil
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, Iraq
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MISHRA AK, JAIN ANAND, SINGH S, AHLAWAT S, SHARMA R. Microsatellite and mitochondrial DNA based genetic diversity analysis of a lesser known Chitarangi sheep of north-western India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i3.102521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Microsatellite and mitochondrial DNA based genetic characterization of Chitarangi sheep population inhabiting Fazilka and Muktsar districts of Punjab and Sriganganagar district and adjoining areas of Rajasthan was carried out, and genetic diversity measures were analysed. High estimates of allele diversity (9.875±0.641) and gene diversity (0.712±0.027) were observed across the population. A significant positive FIS (0.096±0.031) value suggested a deficiency in the number of heterozygotes in Chitarangi sheep. The population revealed presence of substantial genetic diversity and the typical L-type distribution of allelic frequencies indicated the absence of any recent bottlenecks in Chitarangi sheep and no mode shift was detected in this population. Majority of haplotypes identified through mitochondrial DNA based analysis of Chitarangi sheep grouped with major haplogroup A that is predominantly of Asian origin. The genetic characterization of Chitarangi sheep will help in devising suitable strategies for its genetic improvement, management and recognition at National level.
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Dudu A, Ghiţă E, Costache M, Georgescu SE. Origin and genetic diversity of Romanian Racka sheep using mitochondrial markers. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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