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Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
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Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Kim G, Lee E, Kim K, Kim D, Kim S, Jin D, Song H, Mun S, Jeong H, Kim J, Choi B. Mitochondrial Genomes of Korean Native Black Goats Reveal Shared Phylogeographic Patterns and Demographic History. Animals (Basel) 2024; 14:2949. [PMID: 39457879 PMCID: PMC11503874 DOI: 10.3390/ani14202949] [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: 08/27/2024] [Revised: 10/01/2024] [Accepted: 10/11/2024] [Indexed: 10/28/2024] Open
Abstract
This study explores the phylogeny of Korean native black goats through analysis of their complete mitochondrial DNA. The National Institute of Animal Science has gathered genetic material on purebred goats from isolated regions such as Tongyeong, Dangjin, and Jangsu, and is actively breeding them on a national level. These populations, however, are small and exhibit high inbreeding rates, highlighting the urgent need to preserve genetic diversity. The haplotype diversity within this native group is 0.659, with 39 haplotypes identified. By contrast, including international breeds in the analysis increases the overall haplotype diversity to 0.925 with 203 haplotypes identified, highlighting the limited genetic diversity among native black goats. For phylogenetic assessment, a neighbor-joining tree and median-joining network were constructed using identified haplogroups (A, B, C, D, G, and F) from prior studies. The results pinpoint the native black goats as closely related to, but distinct from, Haplogroup A with a bootstrap value of 98, establishing them as a separate clade (A'). This supports the notion of a shared ancestry with various global populations. This research provides essential data on the origins and evolutionary history of Korean native black goats, supporting conservation and breeding efforts aimed at enhancing genetic diversity.
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Affiliation(s)
- Gaeun Kim
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
- Division of Animal Bioscience & Integrated Biotechnology, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Eundo Lee
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
| | - Kwanwoo Kim
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
| | - Dongkyo Kim
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
| | - Seungchang Kim
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
| | - Daehyeok Jin
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
| | - Huimang Song
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
| | - Seongsil Mun
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
| | - Hankyeol Jeong
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jaemin Kim
- Division of Animal Bioscience & Integrated Biotechnology, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Bonghwan Choi
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, 224, Hamyang 50000, Republic of Korea; (G.K.)
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Andaman local goat: mitochondrial genome characterization and lineage analysis. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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The whole mitochondrial genome signature of Teressa goat, an indigenous goat germplasm of Andaman and Nicobar Islands, India. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Baenyi Simon P, Owino Junga J, Tarekegn GM, Machuka E, Tiambo CK, Kabange D, Musale M. Dieudinné K, Vumilia Kizungu R, Ochieng JW, Pelle R. Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo. Ecol Evol 2022; 12:e8713. [PMID: 35342608 PMCID: PMC8928878 DOI: 10.1002/ece3.8713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 12/10/2021] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d-loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d-loop region (1169 bp d-loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor-joining (NJ) tree and median-joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (FST ) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p-value <.05) values for Fu's Fs (-20.418) and Tajima's (-2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long-term conservation of indigenous goats in DRC.
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Affiliation(s)
- Patrick Baenyi Simon
- Department of Animal ProductionUniversité Evangélique en AfriqueBukavuDemocratic Republic of Congo
- Department of Animal ProductionUniversity of NairobiNairobiKenya
- Institut National d'Etudes et des Recherches AgronomiquesINERA MulunguBukavuDemocratic Republic of Congo
| | | | - Getinet Mekuriaw Tarekegn
- Bioscience Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences UppsalaUppsalaSweden
- Department of Animal Production and TechnologyBahir Dar UniversityBahir DarEthiopia
| | - Eunice Machuka
- Bioscience Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | | | - Dorine Kabange
- Department of Veterinary MedicineUniversité de LubumbashiLubumbashiDemocratic Republic of Congo
| | | | - Roger Vumilia Kizungu
- Institut National d’Etudes et des Recherches AgronomiquesINERA, Gombe KinshasaKinshasaDemocratic Republic of Congo
| | | | - Roger Pelle
- Bioscience Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
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Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations. Animals (Basel) 2021; 11:ani11061510. [PMID: 34071004 PMCID: PMC8224610 DOI: 10.3390/ani11061510] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary In the local populations, the increase in inbreeding is a relevant problem for the reduction in production, reproduction, and adaptive traits. The application of genomic technologies has facilitated the assessment of inbreeding in these populations. The current study aims to investigate the patterns of homozygosity in five Italian local goat populations. The results showed the different selection histories and breeding schemes of these goat populations. The analysis also indicated the importance of this information to avoid future loss of diversity and to produce information for designing optimal breeding and conservation programs. Abstract The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.
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Gargano V, Blanda V, Gambino D, La Russa F, Di Cataldo S, Gentile A, Schirò G, Torina A, Millán J, Vicari D. Serological Survey and Molecular Characterization of Theileria annulata in Sicilian Cattle. Pathogens 2021; 10:pathogens10020101. [PMID: 33494377 PMCID: PMC7910905 DOI: 10.3390/pathogens10020101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Tropical theileriosis is a tick-borne disease caused by hemoprotozoan parasites with considerable veterinary and economic impact worldwide. Ticks transmitting the disease belong to the Haemaphysalis, Rhipicephalus, and Hyalomma genera. The Hyalomma genus is very common in Sicily (Italy) and represents the main Theileria annulata vector in the island. Data concerning the molecular epidemiology of this pathogen are missing in the region. In 2018-2019, blood and serum samples were collected from 480 cows in seven Sicilian farms from four different provinces. Seroprevalence in the farms ranged from 22% to 71%. Three farms were selected for molecular analysis consisting of real-time PCR targeting the almost complete 18S ribosomal RNA (rRNA). Four amplicons per farm were sequenced and phylogenetic analyses were carried out. The four sequences were identical within each farm and showed 92-99% identity with the other farms and with sequences from Genbank. According to the phylogenetic analysis, these three sequences and an additional one from a laboratory-cultured Theileria annulata strain obtained in 1999 belonged to a single T. annulata clade with good bootstrap support with other sequences from Italy, India, and Iran, indicating limited geographical and temporal genetic variability of the parasite. This study represents the first phylogenetic analysis of T. annulata in Sicily, which will be useful to improve the strategies for theileriosis control and prevention.
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Affiliation(s)
- Valeria Gargano
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (V.G.); (F.L.R.); (A.G.); (G.S.); (A.T.); (D.V.)
| | - Valeria Blanda
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (V.G.); (F.L.R.); (A.G.); (G.S.); (A.T.); (D.V.)
- Correspondence: (V.B.); (D.G.)
| | - Delia Gambino
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (V.G.); (F.L.R.); (A.G.); (G.S.); (A.T.); (D.V.)
- Correspondence: (V.B.); (D.G.)
| | - Francesco La Russa
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (V.G.); (F.L.R.); (A.G.); (G.S.); (A.T.); (D.V.)
| | - Sophia Di Cataldo
- Programa de Doctorado en Medicina de la Conservación, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile;
| | - Antonino Gentile
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (V.G.); (F.L.R.); (A.G.); (G.S.); (A.T.); (D.V.)
| | - Giorgia Schirò
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (V.G.); (F.L.R.); (A.G.); (G.S.); (A.T.); (D.V.)
| | - Alessandra Torina
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (V.G.); (F.L.R.); (A.G.); (G.S.); (A.T.); (D.V.)
| | - Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain;
- Fundación ARAID, 50018 Zaragoza, Spain
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Domenico Vicari
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (V.G.); (F.L.R.); (A.G.); (G.S.); (A.T.); (D.V.)
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Dettori ML, Petretto E, Pazzola M, Vidal O, Amills M, Vacca GM. Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers. Animals (Basel) 2020; 10:E2194. [PMID: 33255190 PMCID: PMC7761473 DOI: 10.3390/ani10122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022] Open
Abstract
A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The FST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations.
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Affiliation(s)
- Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Elena Petretto
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Oriol Vidal
- Departament de Biologia, Universitat de Girona, 17003 Girona, Spain;
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Department of Animal Genetics, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
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SHARMA ANURODH, SINGH KARANVEER, SIVALINGAM JAYAKUMAR, P MANIMOHAN, SAROHA VINITA, RAVIKUMAR D, KUMAR DINESH, DIXIT SP. Genetic diversity analysis among Indian goat breeds based on mitochondrial DNA. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i6.104994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
India ranks second in goat population with 34 genetically recognized and registered breeds. Information on their diversity and origin and ancestry is little known. Hence, the mtDNA based genetic diversity analysis of Indian goats; targeting mitochondrial HVR1 region from 21 Indian breeds belonging to different geographical regions was undertaken. A total of 124 haplotypes were identified and haplotype diversity estimate ranged from 0.67 to 1.0 with an average value of 0.99. The average nucleotide diversity was minimum (0.02) in Kanniadu and maximum in Surti breeds. Analysis of molecular variance revealed 5.16% variation among the breeds and 94.84% within breeds indicating weak phylogeographic structure. Neighbor-joining tree analysis revealed that the maximum number of individuals of Indian goats fall under A and few in B and C lineages. Principal component analyses of the Indian goat breeds revealed that Kanniadu goats clustered distantly from rest of the breeds of the country. Mantel test revealed a significant correlation between FST and geographical distance (r=0.29) among the goat breeds. The mismatch distribution analysis of the Indian goat breeds revealed bimodal distribution patterns. The analysis revealed that Kanniadu is highly distinct from the rest of the breeds.
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Li R, Sun J, Zhao Y, Xiao H, Chen S. Maternal origins, population structure and demographic history of ten Chinese indigenous goat breeds from Yunnan. J Anim Breed Genet 2020; 138:108-121. [PMID: 32658371 DOI: 10.1111/jbg.12492] [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: 12/31/2019] [Revised: 04/13/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
Abstract
Yunnan as a frontier zone that connects China with South and Southeast Asia, has 11 well-recognized goat breeds. However, the knowledge about maternal origins, population structure and demographic history of Chinese indigenous goats from Yunnan is limited. In this study, we analysed a 481-bp fragment of first hypervariable segment (HVSI) of the mitochondrial DNA (mtDNA) control region sequences of 749 individuals from 10 Yunnan indigenous goat breeds, of which 556 sequences were newly determined. There were 110 polymorphic sites that defined 158 haplotypes among all sequences. The haplotype and nucleotide diversity of these breeds ranged from 0.782 ± 0.079 to 0.982 ± 0.015 and from 0.028 ± 0.003 to 0.043 ± 0.005, respectively. Phylogenetic analysis identified two lineages A and B, of which the lineage A had higher frequency (68.1%) and distributed in all Yunnan breeds. We combined previously reported sequences with our sequences belonging to the lineage B and detected two subclades B1 and B2, in which the B1 subclade shared individuals from Eastern Asia, Southeast Asia and Southern Asia. Given higher level of diversity and more unique haplotypes, the B2 subclade probably originated from Southwestern China. The haplotype network, analysis of molecular variance (AMOVA) and a Mantel test revealed no significant phylogeographic structuring among Yunnan goat breeds. This can be explained by high gene flow and genetic admixture among these breeds from different geographic regions in Yunnan. Additionally, both the lineages A and B reflected different demographic histories. This study will provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.
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Affiliation(s)
- Rong Li
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China
| | - Jianshu Sun
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Yincheng Zhao
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Heng Xiao
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Shanyuan Chen
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
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Diwedi J, Singh AW, Ahlawat S, Sharma R, Arora R, Sharma H, Raja KN, Verma NK, Tantia MS. Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats. Gene 2020; 756:144910. [PMID: 32574758 DOI: 10.1016/j.gene.2020.144910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/01/2020] [Accepted: 06/17/2020] [Indexed: 11/18/2022]
Abstract
Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998 ± 0.001 and 0.028 ± 0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.
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Affiliation(s)
- Jyotsana Diwedi
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - 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
| | - Himani Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - K N Raja
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - N K Verma
- 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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Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations. Animals (Basel) 2020; 10:ani10061040. [PMID: 32560248 PMCID: PMC7341319 DOI: 10.3390/ani10061040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes and are known to be present in genomic regions that regulate important physiological functions. In this study, CNV detection was performed starting from genotypic data of 120 individuals, belonging to four Sicilian dairy goat breeds, genotyped with the Illumina GoatSNP50 BeadChip array. Using PennCNV software, a total of 702 CNVs were identified in 107 individuals. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair. Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs, which are involved in local adaptation, mild behaviour, immune response, reproduction, and olfactory receptors. This study provides insights into the genomic variations within these Italian goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits. Abstract Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell’Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour (ADAMTS20 and EDNRA), mild behaviour (NR3C2), immune response (EXOC3L4 and TNFAIP2), reproduction (GBP1 and GBP6), and olfactory receptors (OR7E24). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.
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Hermes TR, Frachetti MD, Voyakin D, Yerlomaeva AS, Beisenov AZ, Doumani Dupuy PN, Papin DV, Motuzaite Matuzeviciute G, Bayarsaikhan J, Houle JL, Tishkin AA, Nebel A, Krause-Kyora B, Makarewicz CA. High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor. PLoS One 2020; 15:e0233333. [PMID: 32437372 PMCID: PMC7241827 DOI: 10.1371/journal.pone.0233333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 05/01/2020] [Indexed: 12/23/2022] Open
Abstract
Goats were initially managed in the Near East approximately 10,000 years ago and spread across Eurasia as economically productive and environmentally resilient herd animals. While the geographic origins of domesticated goats (Capra hircus) in the Near East have been long-established in the zooarchaeological record and, more recently, further revealed in ancient genomes, the precise pathways by which goats spread across Asia during the early Bronze Age (ca. 3000 to 2500 cal BC) and later remain unclear. We analyzed sequences of hypervariable region 1 and cytochrome b gene in the mitochondrial genome (mtDNA) of goats from archaeological sites along two proposed transmission pathways as well as geographically intermediary sites. Unexpectedly high genetic diversity was present in the Inner Asian Mountain Corridor (IAMC), indicated by mtDNA haplotypes representing common A lineages and rarer C and D lineages. High mtDNA diversity was also present in central Kazakhstan, while only mtDNA haplotypes of lineage A were observed from sites in the Northern Eurasian Steppe (NES). These findings suggest that herding communities living in montane ecosystems were drawing from genetically diverse goat populations, likely sourced from communities in the Iranian Plateau, that were sustained by repeated interaction and exchange. Notably, the mitochondrial genetic diversity associated with goats of the IAMC also extended into the semi-arid region of central Kazakhstan, while NES communities had goats reflecting an isolated founder population, possibly sourced via eastern Europe or the Caucasus region.
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Affiliation(s)
- Taylor R. Hermes
- Graduate School “Human Development in Landscapes”, Kiel University, Kiel, Germany
- Institute of Prehistoric and Protohistoric Archaeology, Kiel University, Kiel, Germany
- * E-mail: (TRH); (CAM)
| | - Michael D. Frachetti
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Dmitriy Voyakin
- Archaeological Expertise, LLC, Almaty, Kazakhstan
- International Institute for Central Asian Studies, Samarkand, Uzbekistan
| | | | | | | | - Dmitry V. Papin
- The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Altai State University, Barnaul, Russia
- Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | - Jean-Luc Houle
- Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Alexey A. Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Cheryl A. Makarewicz
- Graduate School “Human Development in Landscapes”, Kiel University, Kiel, Germany
- Institute of Prehistoric and Protohistoric Archaeology, Kiel University, Kiel, Germany
- * E-mail: (TRH); (CAM)
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14
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Ganbold O, Lee SH, Paek WK, Munkhbayar M, Seo D, Manjula P, Khujuu T, Purevee E, Lee JH. Mitochondrial DNA variation and phylogeography of native Mongolian goats. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:902-912. [PMID: 32054227 PMCID: PMC7206382 DOI: 10.5713/ajas.19.0396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/15/2019] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Mongolia is one of a few countries that supports over 25 million goats, but genetic diversity, demographic history, and the origin of goat populations in Mongolia have not been well studied. This study was conducted to assess the genetic diversity, phylogenetic status and population structure of Mongolian native goats, as well as to discuss their origin together with other foreign breeds from different countries using hypervariable region 1 (HV1) in mtDNA. METHODS In this study, we examined the genetic diversity and phylogenetic status of Mongolian native goat populations using a 452 base-pair long fragment of HVI of mitochondrial DNA from 174 individuals representing 12 populations. In addition, 329 previously published reference sequences from different regions were included in our phylogenetic analyses. RESULTS Investigated native Mongolian goats displayed relatively high genetic diversities. After sequencing, we found a total of 109 polymorphic sites that defined 137 haplotypes among investigated populations. Of these, haplotype and nucleotide diversities of Mongolian goats were calculated as 0.997±0.001 and 0.0283±0.002, respectively. These haplotypes clearly clustered into four haplogroups (A, B, C, and D), with the predominance of haplogroup A (90.8%). Estimates of pairwise differences (Fst) and the analysis of molecular variance values among goat populations in Mongolia showed low genetic differentiation and weak geographical structure. In addition, Kazakh, Chinese (from Huanghuai and Leizhou), and Arabian (Turkish and Baladi breeds) goats had smaller genetic differentiation compared to Mongolian goats. CONCLUSION In summary, we report novel information regarding genetic diversity, population structure, and origin of Mongolian goats. The findings obtained from this study reveal that abundant haplogroups (A to D) occur in goat populations in Mongolia, with high levels of haplotype and nucleotide diversity.
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Affiliation(s)
- Onolragchaa Ganbold
- Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea.,Department of Biology, Mongolian National University of Education, Ulaanbaatar 210685, Mongolia
| | - Seung-Hwan Lee
- Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Woon Kee Paek
- Daegu National Science Museum of Korea, Daegu 43014, Korea
| | - Munkhbaatar Munkhbayar
- Department of Biology, Mongolian National University of Education, Ulaanbaatar 210685, Mongolia
| | - Dongwon Seo
- Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Prabuddha Manjula
- Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Tamir Khujuu
- Department of Biology, Mongolian National University of Education, Ulaanbaatar 210685, Mongolia
| | - Erdenetushig Purevee
- Department of Biology, Mongolian National University of Education, Ulaanbaatar 210685, Mongolia
| | - Jun Heon Lee
- Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea
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15
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Kamalakkannan R, Jose J, Thomas S, Prabhu VR, Nagarajan M. Genetic diversity and maternal lineages of south Indian goats. Mol Biol Rep 2018; 45:2741-2748. [PMID: 30145642 DOI: 10.1007/s11033-018-4322-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
In India, goats are considered to be one of the important livestock species that reinforce the rural economy. Even though India has 23 well-recognized goat breeds, the knowledge about their genetic diversity and domestication history is limited. In this study, we have analyzed the genetic diversity of 104 goats representing five different south Indian breeds using mtDNA D-loop region. The haplotype diversity of the breeds ranged from 0.9524 ± 0.0403 (Malabari) to 0.9921 ± 0.0154 (Kanni aadu). Analysis of molecular variance showed only 1.05% variation among breeds. On other hand, the variation within breed was remarkably high (98.95%) which suggested the weak phylogeographic structure of south Indian goats. The phylogenetic analysis revealed three haplogroups representing maternal lineages namely A, B and D. The analysis of 466 Indian goat sequences showed an additional lineage C. As reported in the previous studies, a major fraction of analyzed goats fell into haplogroup A. Our study confirms the presence of three maternal lineages for south Indian domestic goats.
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Affiliation(s)
- Ranganathan Kamalakkannan
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Jesna Jose
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Subhash Thomas
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Vandana R Prabhu
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Muniyandi Nagarajan
- Department of Genomic Science, School of Biological Science, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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16
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Daly KG, Maisano Delser P, Mullin VE, Scheu A, Mattiangeli V, Teasdale MD, Hare AJ, Burger J, Verdugo MP, Collins MJ, Kehati R, Erek CM, Bar-Oz G, Pompanon F, Cumer T, Çakırlar C, Mohaseb AF, Decruyenaere D, Davoudi H, Çevik Ö, Rollefson G, Vigne JD, Khazaeli R, Fathi H, Doost SB, Rahimi Sorkhani R, Vahdati AA, Sauer EW, Azizi Kharanaghi H, Maziar S, Gasparian B, Pinhasi R, Martin L, Orton D, Arbuckle BS, Benecke N, Manica A, Horwitz LK, Mashkour M, Bradley DG. Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science 2018; 361:85-88. [PMID: 29976826 DOI: 10.1126/science.aas9411] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/13/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
Abstract
Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
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Affiliation(s)
- Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Amelie Scheu
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,BioArCh, University of York, York YO10 5DD, UK
| | - Andrew J Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK.,Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| | - Ron Kehati
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Haifa, Israel
| | - François Pompanon
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Tristan Cumer
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Canan Çakırlar
- Groningen Institute of Archaeology, Groningen University, Groningen, Netherlands
| | - Azadeh Fatemeh Mohaseb
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Delphine Decruyenaere
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Hossein Davoudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Özlem Çevik
- Trakya Universitesi, Edebiyat Fakültesi, Arkeoloi Bölümü, Edirne, Turkey
| | - Gary Rollefson
- Department of Anthropology, Whitman College, Walla Walla, WA 99362, USA
| | - Jean-Denis Vigne
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Roya Khazaeli
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Homa Fathi
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Sanaz Beizaee Doost
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | | | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord, Iran
| | - Eberhard W Sauer
- School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Edinburgh EH8 9AG, UK
| | | | - Sepideh Maziar
- Institut für Archäologische Wissenschaften, Goethe Universität, Frankfurt am Main, Germany
| | - Boris Gasparian
- Institute of Archaeology and Ethnology, National Academy of Sciences of the Republic of Armenia, Yerevan 0025, Republic of Armenia
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Louise Martin
- Institute of Archeology, University College London, London, UK
| | - David Orton
- BioArCh, University of York, York YO10 5DD, UK
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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17
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Tarekegn GM, Tesfaye K, Mwai OA, Djikeng A, Dessie T, Birungi J, Osama S, Zergaw N, Alemu A, Achieng G, Tutah J, Mutai C, Njuguna J, Mwacharo JM. Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats. Ecol Evol 2018; 8:1543-1553. [PMID: 29435231 PMCID: PMC5792515 DOI: 10.1002/ece3.3710] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 10/30/2017] [Accepted: 11/10/2017] [Indexed: 01/19/2023] Open
Abstract
The Horn of Africa forms one of the two main historical entry points of domestics into the continent and Ethiopia is particularly important in this regard. Through the analysis of mitochondrial DNA (mtDNA) d-loop region in 309 individuals from 13 populations, we reveal the maternal genetic variation and demographic dynamics of Ethiopian indigenous goats. A total of 174 variable sites that generated 231 haplotypes were observed. They defined two haplogroups that were present in all the 13 study populations. Reference haplotypes from the six globally defined goat mtDNA haplogroups show the two haplogroups present in Ethiopia to be A and G, the former being the most predominant. Although both haplogroups are characterized by an increase in effective population sizes (Ne) predating domestication, they also have experienced a decline in Ne at different time periods, suggesting different demographic histories. We observed seven haplotypes, six were directly linked to the central haplotypes of the two haplogroups and one was central to haplogroup G. The seven haplotypes were common between Ethiopia, Kenya, Egypt, and Saudi Arabia populations, suggesting common maternal history and the introduction of goats into East Africa via Egypt and the Arabian Peninsula, respectively. While providing new mtDNA data from a historically important region, our results suggest extensive intermixing of goats mediated by human socio-cultural and economic interactions. These have led to the coexistence of the two haplogroups in different geographic regions in Ethiopia resulting in a large caprine genetic diversity that can be exploited for genetic improvement.
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Affiliation(s)
- Getinet Mekuriaw Tarekegn
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
- Department of Animal Production and Technology, Biotechnology Research InstituteBahir Dar UniversityBahir DarEthiopia
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
- Swedish University of Agricultural SciencesUppsalaSweden
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and HealthThe University of EdinburghEdinburghUK
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Josephine Birungi
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Sarah Osama
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Netsanet Zergaw
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Alubel Alemu
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Gloria Achieng
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Jack Tutah
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Collins Mutai
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Joram M. Mwacharo
- Small Ruminant Genetics and Genomics GroupInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
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18
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Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis. PLoS One 2017; 12:e0190235. [PMID: 29281717 PMCID: PMC5744987 DOI: 10.1371/journal.pone.0190235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 12/11/2017] [Indexed: 11/19/2022] Open
Abstract
The Sultanate of Oman has a complex mosaic of livestock species and production systems, but the genetic diversity, demographic history or origins of these Omani animals has not been expensively studied. Goats might constitute one of the most abundant and important domestic livestock species since the Neolithic transition. Here, we examined the genetic diversity, origin, population structure and demographic history of Omani goats. Specifically, we analyzed a 525-bp fragment of the first hypervariable region of the mitochondrial DNA (mtDNA) control region from 69 Omani individuals and compared this fragment with 17 mtDNA sequences from Somalia and Yemen as well as 18 wild goat species and 1,198 previously published goat sequences from neighboring countries. The studied goat breeds show substantial diversity. The haplotype and nucleotide diversities of Omani goats were found equal to 0.983 ± 0.006 and 0.0284 ± 0.014, respectively. The phylogenetic analyses allowed us to classify Omani goats into three mtDNA haplogroups (A, B and G): haplogroup A was found to be predominant and widely distributed and accounted for 80% of all samples, and haplogroups B and G exhibited low frequencies. Phylogenetic comparisons with wild goats revealed that five of the native Omani goat populations originate from Capra aegagrus. Furthermore, most comparisons of pairwise population FST values within and between these five Omani goat breeds as well as between Omani goats and nine populations from nearby countries were not significant. These results suggest strong gene flow among goat populations caused by the extensive transport of goats and the frequent movements of human populations in ancient Arabia. The findings improve our understanding of the migration routes of modern goats from their region of domestication into southeastern Arabia and thereby shed light on human migratory and commercial networks during historical times.
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19
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Al-Araimi NA, Al-Atiyat RM, Gaafar OM, Vasconcelos R, Luzuriaga-Neira A, Eisa MO, Amir N, Benaissa MH, Alfaris AA, Aljumaah RS, Elnakhla SM, Salem MM, Ishag IA, El Khasmi M, Beja-Pereira A. Maternal genetic diversity and phylogeography of native Arabian goats. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Deng J, Feng J, Li L, Zhong T, Wang L, Guo J, Ba G, Song T, Zhang H. Polymorphisms, differentiation, and phylogeny of 10 Tibetan goat populations inferred from mitochondrial D-loop sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:439-445. [PMID: 28358643 DOI: 10.1080/24701394.2017.1303491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
China has abundant population of Tibetan goats, but available information regarding genetic structure and phylogenetic status remains limited. Here, 130 mitochondrial D-loop sequences of individuals from 10 Tibetan goat populations located in distinct plateau areas were analyzed. Eighty-six haplotypes were defined, among which 97.7% were group-specific haplotypes. Haplotype and nucleotide diversity indices were 0.990 ± 0.003 and 0.0145 ± 0.0013, respectively. The pairwise Wright's F-statistics ranged from -0.028 to 0.385, and over half of them were greater than 0.05, indicating apparent genetic differentiation among the populations. AMOVA analysis (FST = 0.0858) manifested that the genetic structure has become weak. Phylogenetic trees revealed four haplogroups (A, B, C, and D), suggesting that Tibetan goats had four origins. Mismatch distribution analyses and neutrality tests indicated that at least one population expansion event occurred during the demographic history of Tibetan goat. These results will provide a more complete understanding of Tibetan goat genetic resources.
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Affiliation(s)
- Juan Deng
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Jing Feng
- b Institute of Animal Science , Tibet Academy of Agricultural & Animal Husbandry Science , Lhasa , P. R. China
| | - Li Li
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Tao Zhong
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Linjie Wang
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Jiazhong Guo
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Gui Ba
- b Institute of Animal Science , Tibet Academy of Agricultural & Animal Husbandry Science , Lhasa , P. R. China
| | - Tianzeng Song
- b Institute of Animal Science , Tibet Academy of Agricultural & Animal Husbandry Science , Lhasa , P. R. China
| | - Hongping Zhang
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province , Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
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21
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Mastrangelo S, Tolone M, Montalbano M, Tortorici L, Di Gerlando R, Sardina MT, Portolano B. Population genetic structure and milk production traits in Girgentana goat breed. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an15431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The aim of this work was to evaluate the genetic status of the Girgentana goat, an endangered breed from Sicily (Italy), using microsatellite markers. Furthermore, as the main purpose of the Girgentana breed is milk production, quantitative milk traits were investigated, including fatty acid profile. Molecular data from CSN1S1, CSN2, CSN1S2, and CSN3 casein genes were also used to infer haplotypes. A total of 264 individuals were collected. Samples of Maltese (n = 41) and Derivata di Siria (n = 33) goat breeds were also used to understand the genetic relationship among breeds. Test-day records for milk production were collected to determine daily milk yield, fat, protein, casein, lactose, and somatic cell count. Individual milk samples were also collected for fatty acid extraction. Wright’s statistics, gene flow, Nei genetic distance, factorial correspondence analysis, and Bayesian assignment test showed the existence of genetic variability and differentiation among breeds. The AMOVA results indicated that 89.96% of the total variance was partitioned within populations. The Girgentana breed appears to have a subdivided population, and has not experienced a recent bottleneck. A high variability in milk yield was observed. Mean morning milk yield was 1448 ± 404 g, with 4.30 ± 0.87% and 3.72 ± 0.44% of fat and protein percentages, respectively. The average somatic cell count found in Girgentana goat milk was higher than the threshold of 1 500 000 cells/mL advised in Europe for fresh milk. Gross milk and fatty acid composition were similar to that reported in the literature for other local goat breeds.
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Colli L, Lancioni H, Cardinali I, Olivieri A, Capodiferro MR, Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini F, Vahidi SMF, Agha S, Randi E, Battaglia V, Sardina MT, Portolano B, Rezaei HR, Lymberakis P, Boyer F, Coissac E, Pompanon F, Taberlet P, Ajmone Marsan P, Achilli A. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics 2015; 16:1115. [PMID: 26714643 PMCID: PMC4696231 DOI: 10.1186/s12864-015-2342-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/22/2015] [Indexed: 01/31/2023] Open
Abstract
Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Conclusions Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Rosario Capodiferro
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Pellecchia
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Marcin Rzepus
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Institute of Food Science and Nutrition - ISAN, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Wahid Zamani
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. .,Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, 46414-356, Iran.
| | - Saeid Naderi
- Natural Resources Faculty, University of Guilan, Guilan, 41335-1914, Iran.
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. .,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK.
| | | | - Saif Agha
- Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.
| | - Ettore Randi
- Laboratorio di Genetica, Istituto per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, 40064, Italy. .,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, DK-9000, Denmark.
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Hamid Reza Rezaei
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, 49138-15739, Iran.
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Iraklio, Crete, 71409, Greece.
| | - Frédéric Boyer
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Eric Coissac
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - François Pompanon
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Pierre Taberlet
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
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Othman OE, Pariset L, Balabel EA, Marioti M. Genetic characterization of Egyptian and Italian sheep breeds using mitochondrial DNA. J Genet Eng Biotechnol 2015; 13:79-86. [PMID: 30647570 PMCID: PMC6299800 DOI: 10.1016/j.jgeb.2014.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/06/2014] [Accepted: 12/23/2014] [Indexed: 11/30/2022]
Abstract
A 721-bp fragment from 15,541 to 16,261 bp (NC_001941.1) of the mtDNA control region from different Egyptian and Italian sheep breeds was amplified. The PCR products were purified and sequenced. From the amplified fragment of 721-bp, a region of 423 bp after excluding a central region rich in tandem repeats was analyzed. Within all tested breeds, the haplotype diversity and average number of pairwise differences were 0.97571 and 7.01484, respectively. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Laticauda and Italian Muflon followed by distance between Sarda and Italian Muflon while the highest distance was observed between Barki and Sarda followed by distance between Barki and Laticauda. Phylogenetic analysis showed the presence of three haplogroups - HapA, HapB and HapC - in the examined samples with the absence of other two haplogroups HapD and HapE. All Italian samples cluster with B haplogroup and also in the Egyptian breeds the most dominant haplogroup was B (62 out of 67 analyzed samples). In Egyptian Barki breed one individual clusters with A haplogroup and another individual with C haplogroup. In Ossimi breed two individuals cluster with C haplogroup and in Rahmani there is one sample belonging to A haplogroup. The matrix of pairwise differences among breeds was used to perform a Principal Component Analysis (PCA). This analysis showed that the Italian breeds are clearly separated from the Egyptian breeds; moreover the Egyptian Barki breed is separated from Ossimi and Rahmani.
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Affiliation(s)
| | - Lorraine Pariset
- Department for Innovation in Biological, Agro-Food and Forest System (DIBAF), Università degli Studi della Tuscia University, Viterbo, Italy
| | | | - Marco Marioti
- Department for Innovation in Biological, Agro-Food and Forest System (DIBAF), Università degli Studi della Tuscia University, Viterbo, Italy
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Kim JH, Byun MJ, Choi SB, Suh S, Kim YS, Kim MJ, Ko YG, Cho CY. Detection of a distinct variation site for geographical classification of mitochondrial DNA haplogroup A in the domestic goat (Capra hircus). Genes Genomics 2014. [DOI: 10.1007/s13258-014-0204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Akis I, Oztabak K, Mengi A, Un C. Mitochondrial DNA diversity of Anatolian indigenous domestic goats. J Anim Breed Genet 2014; 131:487-95. [PMID: 24942987 DOI: 10.1111/jbg.12096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 04/22/2014] [Indexed: 11/29/2022]
Abstract
Anatolia has been an important region for civilizations and agricultural revolution as a major domestication centre for livestock species. Goats (Capra hircus) were among the earliest domesticated animals in this region. In this study, genetic diversity of Anatolian goat breeds was characterized by comparison of mitochondrial DNA hypervariable region 1. A total of 295 individuals, including 99 Anatolian Black goats, 96 Angora goats and 100 Kilis goats, were used. Haplogroup A was found to be the dominant haplogroup in all three breeds. The highest haplogroup diversity, including haplogroups A, B2, C and G, was observed in the Anatolian Black breed. Haplogroup D was only observed in Kilis and Angora goats. Haplogroup G was found in Angora and Anatolian Black breeds. The Anatolian goat breeds had high genetic diversity values and a weak phylogeographical structure. The nucleotide diversity values were found to be higher than those in previously studied goat breeds. The fact that Anatolia is a domestication centre and its geographical position as a junction of trade routes may have caused the higher genetic diversity of Anatolian goat breeds.
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Affiliation(s)
- I Akis
- Faculty of Veterinary Medicine, Department of Biochemistry, Istanbul University, Istanbul, Turkey
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Hoda A, Biçoku Y, Dobi P. Genetic diversity of Albanian goat breeds revealed by mtDNA sequence variation. BIOTECHNOL BIOTEC EQ 2014; 28:77-81. [PMID: 26019491 PMCID: PMC4433870 DOI: 10.1080/13102818.2014.901672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Albanian farmers have a long tradition in goat farming. Recently, several studies were carried out to determine genetic diversity of local goat populations, using molecular markers such as SNP (Single Nucleotide Polymorphisms), microsatellites and AFLP (Amplified Fragment Length Polymorphism). In the present study 77 mtDNA D-loop sequences from six different goat breeds were analysed. The results revealed 67 different haplotypes, with haplotype diversity ranging from 0.864 to 1 and nucleotide diversity values ranging from 0.016 to 0.106. The results showed that the studied breed grouped only in lineage A. The FST analysis indicated that 98.7% of the variation was found within the goat breeds and only 1.3% among them.
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Affiliation(s)
- Anila Hoda
- Department of Animal Production, Faculty of Agriculture and Environment, Agricultural University of Tirana, Kodër Kamëz, Tirana, Albania
| | - Ylli Biçoku
- Department of Animal Production, Faculty of Agriculture and Environment, Agricultural University of Tirana, Kodër Kamëz, Tirana, Albania
| | - Petrit Dobi
- Department of Animal Production, Faculty of Agriculture and Environment, Agricultural University of Tirana, Kodër Kamëz, Tirana, Albania
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Cornale P, Renna M, Lussiana C, Bigi D, Chessa S, Mimosi A. The Grey Goat of Lanzo Valleys (Fiurinà): Breed characteristics, genetic diversity, and quantitative-qualitative milk traits. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2013.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhong T, Zhao QJ, Niu LL, Wang J, Jin PF, Zhao W, Wang LJ, Li L, Zhang HP, Ma YH. Genetic phylogeography and maternal lineages of 18 Chinese black goat breeds. Trop Anim Health Prod 2013; 45:1833-7. [DOI: 10.1007/s11250-013-0432-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
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Mariotti M, Valentini A, Marsan PA, Pariset L. Mitochondrial DNA of seven Italian sheep breeds shows faint signatures of domestication and suggests recent breed formation. ACTA ACUST UNITED AC 2013; 24:577-83. [DOI: 10.3109/19401736.2013.770493] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Hughes S, Fernández H, Cucchi T, Duffraisse M, Casabianca F, Istria D, Pompanon F, Vigne JD, Hänni C, Taberlet P. A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices. PLoS One 2012; 7:e30272. [PMID: 22299033 PMCID: PMC3267719 DOI: 10.1371/journal.pone.0030272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 12/14/2011] [Indexed: 12/02/2022] Open
Abstract
The goat (Capra hircus) is one of the earliest domesticated species ca. 10,500 years ago in the Middle-East where its wild ancestor, the bezoar (Capra aegagrus), still occurs. During the Neolithic dispersal, the domestic goat was then introduced in Europe, including the main Mediterranean islands. Islands are interesting models as they maintain traces of ancient colonization, historical exchanges or of peculiar systems of husbandry. Here, we compare the mitochondrial genetic diversity of both medieval and extant goats in the Island of Corsica that presents an original and ancient model of breeding with free-ranging animals. We amplified a fragment of the Control Region for 21 medieval and 28 current goats. Most of them belonged to the A haplogroup, the most worldwide spread and frequent today, but the C haplogroup is also detected at low frequency in the current population. Present Corsican goats appeared more similar to medieval goats than to other European goat populations. Moreover, 16 out of the 26 haplotypes observed were endemic to Corsica and the inferred demographic history suggests that the population has remained constant since the Middle Ages. Implications of these results on management and conservation of endangered Corsican goats currently decimated by a disease are addressed.
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Affiliation(s)
- Sandrine Hughes
- Paléogénomique et Evolution Moléculaire, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, INRA, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
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Siwek M, Finocchiaro R, Curik I, Portolano B. Hierarchical structure of the Sicilian goats revealed by Bayesian analyses of microsatellite information. Anim Genet 2011; 42:93-5. [PMID: 20497156 DOI: 10.1111/j.1365-2052.2010.02080.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic structure and relationship amongst the main goat populations in Sicily (Girgentana, Derivata di Siria, Maltese and Messinese) were analysed using information from 19 microsatellite markers genotyped on 173 individuals. A posterior Bayesian approach implemented in the program STRUCTURE revealed a hierarchical structure with two clusters at the first level (Girgentana vs. Messinese, Derivata di Siria and Maltese), explaining 4.8% of variation (amovaФ(ST) estimate). Seven clusters nested within these first two clusters (further differentiations of Girgentana, Derivata di Siria and Maltese), explaining 8.5% of variation (amovaФ(SC) estimate). The analyses and methods applied in this study indicate their power to detect subtle population structure.
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Affiliation(s)
- M Siwek
- Department SEnFiMiZo, University of Palermo, Viale delle Scienze Parco d'Orleans 90128 Palermo, Italy.
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Vacca GM, Daga C, Pazzola M, Carcangiu V, Dettori ML, Cozzi MC. D-loop sequence mitochondrial DNA variability of Sarda goat and other goat breeds and populations reared in the Mediterranean area. J Anim Breed Genet 2010; 127:352-60. [PMID: 20831559 DOI: 10.1111/j.1439-0388.2010.00863.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G M Vacca
- Department of Animal Biology, University of Sassari, Sassari, Italy Department of Animal Science, University of Milano, Milano, Italy
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Pereira F, Queirós S, Gusmão L, Nijman IJ, Cuppen E, Lenstra JA, Davis SJM, Nejmeddine F, Amorim A. Tracing the History of Goat Pastoralism: New Clues from Mitochondrial and Y Chromosome DNA in North Africa. Mol Biol Evol 2009; 26:2765-73. [PMID: 19729424 DOI: 10.1093/molbev/msp200] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Filipe Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
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Pariset L, Cuteri A, Ligda C, Ajmone-Marsan P, Valentini A. Geographical patterning of sixteen goat breeds from Italy, Albania and Greece assessed by Single Nucleotide Polymorphisms. BMC Ecol 2009; 9:20. [PMID: 19725964 PMCID: PMC2754418 DOI: 10.1186/1472-6785-9-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 09/02/2009] [Indexed: 12/01/2022] Open
Abstract
Background SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters. Results A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed. Conclusion Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean.
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Affiliation(s)
- Lorraine Pariset
- Dipartimento di Produzioni Animali, Università degli Studi della Tuscia, Viterbo, Italy.
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Amills M, Ramírez O, Tomàs A, Badaoui B, Marmi J, Acosta J, Sànchez A, Capote J. Mitochondrial DNA diversity and origins of South and Central American goats. Anim Genet 2009; 40:315-22. [DOI: 10.1111/j.1365-2052.2008.01837.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Royo LJ, Traoré A, Tambourá HH, Álvarez I, Kaboré A, Fernández I, Ouédraogo-Sanou G, Toguyeni A, Sawadogo L, Goyache F. Analysis of mitochondrial DNA diversity in Burkina Faso populations confirms the maternal genetic homogeneity of the West African goat. Anim Genet 2009; 40:344-7. [DOI: 10.1111/j.1365-2052.2008.01828.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Fan B, Han JL, Chen SL, Mburu DN, Hanotte O, Chen QK, Zhao SH, Li K. Individual-breed assignments in caprine populations using microsatellite DNA analysis. Small Rumin Res 2008. [DOI: 10.1016/j.smallrumres.2007.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Taberlet P, Valentini A, Rezaei HR, Naderi S, Pompanon F, Negrini R, Ajmone-Marsan P. Are cattle, sheep, and goats endangered species? Mol Ecol 2008; 17:275-84. [PMID: 17927711 DOI: 10.1111/j.1365-294x.2007.03475.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- P Taberlet
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 09, France.
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Fan B, Chen SL, Kijas JH, Liu B, Yu M, Zhao SH, Zhu MJ, Xiong TA, Li K. Phylogenetic relationships among Chinese indigenous goat breeds inferred from mitochondrial control region sequence. Small Rumin Res 2007. [DOI: 10.1016/j.smallrumres.2006.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Naderi S, Rezaei HR, Taberlet P, Zundel S, Rafat SA, Naghash HR, El-Barody MAA, Ertugrul O, Pompanon F. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS One 2007; 2:e1012. [PMID: 17925860 PMCID: PMC1995761 DOI: 10.1371/journal.pone.0001012] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Accepted: 09/17/2007] [Indexed: 11/29/2022] Open
Abstract
Background From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. Methodology/Principal Findings The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. Conclusions/Significance We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.
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Affiliation(s)
- Saeid Naderi
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
- Natural Resources Faculty, University of Guilan, Guilan, Iran
| | - Hamid-Reza Rezaei
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, Iran
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - Stéphanie Zundel
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | - Seyed-Abbas Rafat
- Animal Science Department, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Hamid-Reza Naghash
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | | | - Okan Ertugrul
- Department of Genetics, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - François Pompanon
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
- * To whom correspondence should be addressed. E-mail:
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Meadows JRS, Cemal I, Karaca O, Gootwine E, Kijas JW. Five ovine mitochondrial lineages identified from sheep breeds of the near East. Genetics 2006; 175:1371-9. [PMID: 17194773 PMCID: PMC1840082 DOI: 10.1534/genetics.106.068353] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Archaeozoological evidence indicates that sheep were first domesticated in the Fertile Crescent. To search for DNA sequence diversity arising from previously undetected domestication events, this survey examined nine breeds of sheep from modern-day Turkey and Israel. A total of 2027 bp of mitochondrial DNA (mtDNA) sequence from 197 sheep revealed a total of 85 haplotypes and a high level of genetic diversity. Six individuals carried three haplotypes, which clustered separately from the known ovine mtDNA lineages A, B, and C. Analysis of genetic distance, mismatch distribution, and comparisons with wild sheep confirmed that these represent two additional mtDNA lineages denoted D and E. The two haplogroup E sequences were found to link the previously identified groups A and C. The single haplogroup D sequence branched with the eastern mouflon (Ovis orientalis), urial (O. vignei), and argali (O. ammon) sheep. High sequence diversity (K = 1.86%, haplogroup D and O. orientalis) indicates that the wild progenitor of this domestic lineage remains unresolved. The identification in this study of evidence for additional domestication events adds to the emerging view that sheep were recruited from wild populations multiple times in the same way as for other livestock species such as goat, cattle, and pig.
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