1
|
Belay S, Belay G, Nigussie H, Ahbara AM, Tijjani A, Dessie T, Tarekegn GM, Jian-Lin H, Mor S, Woldekiros HS, Dobney K, Lebrasseur O, Hanotte O, Mwacharo JM. Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats. Sci Rep 2024; 14:14908. [PMID: 38942813 PMCID: PMC11213886 DOI: 10.1038/s41598-024-65303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.
Collapse
Affiliation(s)
- Shumuye Belay
- Tigray Agricultural Research Institute, Mekelle, Ethiopia.
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helen Nigussie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abulgasim M Ahbara
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Department of Zoology, Misurata University, Misurata, Libya
| | - Abdulfatai Tijjani
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Getinet M Tarekegn
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Institute of Biotechnology (IoB), Addis Ababa University, Addis Ababa, Ethiopia
| | - Han Jian-Lin
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Siobhan Mor
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Helina S Woldekiros
- Department of Anthropology, Washington University in St. Louis, St. Louis, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- University of Sydney, Sydney, Australia
| | - Ophelie Lebrasseur
- Palaeogenomics and Bioarchaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.
| |
Collapse
|
2
|
Masila EM, Ogada SO, Ogali IN, Kennedy GM, Too EK, Ommeh CS. Mitochondrial DNA D-Loop Polymorphisms among the Galla Goats Reveals Multiple Maternal Origins with Implication on the Functional Diversity of the HSP70 Gene. Genet Res (Camb) 2024; 2024:5564596. [PMID: 38348366 PMCID: PMC10861283 DOI: 10.1155/2024/5564596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Despite much attention given to the history of goat evolution in Kenya, information on the origin, demographic history, dispersal route, and genetic diversity of Galla goats remains unclear. Here, we examined the genetic background, diversity, demographic history, and population genetic variation of Galla goats using mtDNA D-loop and HSP70 single-nucleotide polymorphism markers. The results revealed 90 segregating sites and 68 haplotypes in a 600-bp mtDNA D-loop sequence. The overall mean mitochondrial haplotype diversity was 0.993. The haplotype diversities ranged between 0.8939 ± 0.0777 and 1.0000 ± 0.0221 in all populations supporting high genetic diversity. Mitochondrial phylogenetic analysis revealed three Galla goat haplogroups (A, G, and D), supporting multiple maternal ancestries, of which haplogroup A was the most predominant. Analysis of molecular variance (AMOVA) showed considerable variation within populations at 94.39%, evidence of high genetic diversity. Bimodal mismatch distribution patterns were observed while most populations recorded negative results for Tajima and Fu's Fs neutrality tests supporting population expansion. Genetic variation among populations was also confirmed using HSP70 gene fragment sequences, where six polymorphic sites which defined 21 haplotypes were discovered. Analysis of molecular variance revealed a significant FST index value of 0.134 and a high FIS index value of 0.746, an indication of inbreeding. This information will pave the way for conservation strategies and informed breeding to improve Galla or other goat breeds for climate-smart agriculture.
Collapse
Affiliation(s)
- Ednah M. Masila
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Juja, Kenya
- Veterinary Science Research Institute (VSRI), Kenya Agricultural Livestock and Research Organization (KALRO), P.O. Box 32-00902, Nairobi, Kenya
| | - Stephen O. Ogada
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Juja, Kenya
| | - Irene N. Ogali
- Veterinary Science Research Institute (VSRI), Kenya Agricultural Livestock and Research Organization (KALRO), P.O. Box 32-00902, Nairobi, Kenya
| | - Grace M. Kennedy
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Juja, Kenya
| | - Eric K. Too
- Veterinary Science Research Institute (VSRI), Kenya Agricultural Livestock and Research Organization (KALRO), P.O. Box 32-00902, Nairobi, Kenya
| | - Cecily S. Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Juja, Kenya
| |
Collapse
|
3
|
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.
Collapse
Affiliation(s)
- Patrick Baenyi Simon
- Department of Animal Production Université Evangélique en Afrique Bukavu Democratic Republic of Congo.,Department of Animal Production University of Nairobi Nairobi Kenya.,Institut National d'Etudes et des Recherches Agronomiques INERA Mulungu Bukavu Democratic Republic of Congo
| | | | - Getinet Mekuriaw Tarekegn
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya.,Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Uppsala Sweden.,Department of Animal Production and Technology Bahir Dar University Bahir Dar Ethiopia
| | - Eunice Machuka
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya
| | | | - Dorine Kabange
- Department of Veterinary Medicine Université de Lubumbashi Lubumbashi Democratic Republic of Congo
| | - Katunga Musale M Dieudinné
- Institut National d'Etudes et des Recherches Agronomiques INERA Mulungu Bukavu Democratic Republic of Congo
| | - Roger Vumilia Kizungu
- Institut National d'Etudes et des Recherches Agronomiques INERA, Gombe Kinshasa Kinshasa Democratic Republic of Congo
| | | | - Roger Pelle
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya
| |
Collapse
|
4
|
Nguluma A, Kyallo M, Tarekegn GM, Loina R, Nziku Z, Chenyambuga S, Pelle R. Mitochondrial DNA D-loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations. Ecol Evol 2021; 11:15961-15971. [PMID: 34824803 PMCID: PMC8601934 DOI: 10.1002/ece3.8265] [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: 02/27/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
The Small East African (SEA) goat are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (H d = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were observed from a total of 389 haplotypes. The majority of the haplotypes (n = 334) belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B, and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.
Collapse
Affiliation(s)
- Athumani Nguluma
- Tanzania Livestock Research Institute (TALIRI)DodomaTanzania
- Sokoine University of AgricultureMorogoroTanzania
| | - Martina Kyallo
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Getinet Mekuriaw Tarekegn
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
- Department of Animal Production and TechnologyBahir Dar UniversityBahir DarEthiopia
| | - Rose Loina
- Tanzania Livestock Research Institute (TALIRI)DodomaTanzania
| | - Zabron Nziku
- Tanzania Livestock Research Institute (TALIRI)DodomaTanzania
| | | | - Roger Pelle
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| |
Collapse
|
5
|
Alaqeely R, Alhajeri BH, Almathen F, Alhaddad H. Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types. Front Genet 2021; 12:723964. [PMID: 34527024 PMCID: PMC8435798 DOI: 10.3389/fgene.2021.723964] [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: 06/11/2021] [Accepted: 08/12/2021] [Indexed: 11/22/2022] Open
Abstract
Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.
Collapse
Affiliation(s)
- Randa Alaqeely
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| | - Bader H Alhajeri
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia.,The Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Hasan Alhaddad
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| |
Collapse
|
6
|
Tarekegn GM, Khayatzadeh N, Liu B, Osama S, Haile A, Rischkowsky B, Zhang W, Tesfaye K, Dessie T, Mwai OA, Djikeng A, Mwacharo JM. Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats. Evol Appl 2021; 14:1716-1731. [PMID: 34295359 PMCID: PMC8287980 DOI: 10.1111/eva.13118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/15/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
Collapse
Affiliation(s)
- Getinet M. Tarekegn
- Department of Animal Production and TechnologySchool of Animal Sciences and Veterinary MedicineBahir Dar UniversityBahir DarEthiopia
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural SystemsDivision of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bin Liu
- Inner Mongolia Agricultural UniversityHohhotChina
| | - Sarah Osama
- The University of QueenslandSaint LuciaQLDAustralia
| | - Aynalem Haile
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | - Barbara Rischkowsky
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | | | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| | - Joram M. Mwacharo
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| |
Collapse
|
7
|
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.
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Tabata R, Kawaguchi F, Sasazaki S, Yamamoto Y, Rakotondraparany F, Ratsoavina FM, Yonezawa T, Mannen H. Phylogeographic Analysis of Madagascan Goats Using mtDNA Control Region and SRY Gene Sequences. Zoolog Sci 2019; 36:294-298. [DOI: 10.2108/zs180184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/21/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Risa Tabata
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Yoshio Yamamoto
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Felix Rakotondraparany
- Mention Zoologie et Biodiversité Animale, Faculty of Sciences, Antananarivo University, BP 906 Ankatso, Antananarivo 101, Madagascar
| | - Fanomezana Mihaja Ratsoavina
- Mention Zoologie et Biodiversité Animale, Faculty of Sciences, Antananarivo University, BP 906 Ankatso, Antananarivo 101, Madagascar
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa 243-0034, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| |
Collapse
|
11
|
Tarekegn GM, Wouobeng P, Jaures KS, Mrode R, Edea Z, Liu B, Zhang W, Mwai OA, Dessie T, Tesfaye K, Strandberg E, Berglund B, Mutai C, Osama S, Wolde AT, Birungi J, Djikeng A, Meutchieye F. Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics. PLoS One 2019; 14:e0214843. [PMID: 31002664 PMCID: PMC6474588 DOI: 10.1371/journal.pone.0214843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/21/2019] [Indexed: 11/18/2022] Open
Abstract
Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.
Collapse
Affiliation(s)
- Getinet Mekuriaw Tarekegn
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- * E-mail: (GMT); (FM)
| | - Patrick Wouobeng
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Faculty of Agronomy and Agriculture, University of Dschang, Dschang, Cameroon
| | - Kouam Simo Jaures
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Faculty of Agronomy and Agriculture, University of Dschang, Dschang, Cameroon
| | - Raphael Mrode
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju, Korea
| | - Bin Liu
- Nei Mongol BioNew Technology Co.Ltd, Hohhot, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Britt Berglund
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Collins Mutai
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Sarah Osama
- The University of Queensland, Queensland, Australia
| | - Asaminew Tassew Wolde
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Josephine Birungi
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Appolinaire Djikeng
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health, The University of Edinburgh, Scotland, United Kingdom
| | - Félix Meutchieye
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Faculty of Agronomy and Agriculture, University of Dschang, Dschang, Cameroon
- * E-mail: (GMT); (FM)
| |
Collapse
|
12
|
E G, Zhao Y, Chen L, Ma Y, Chu M, Li X, Hong Q, Li L, Guo J, Zhu L, Han Y, Gao H, Zhang J, Jiang H, Jiang C, Wang G, Ren H, Jin M, Sun Y, Zhou P, Huang Y. Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA. Ecol Evol 2018; 8:5111-5123. [PMID: 29876086 PMCID: PMC5980450 DOI: 10.1002/ece3.4100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/21/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D-loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high-frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low-frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.
Collapse
Affiliation(s)
- Guang‐Xin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Yong‐Ju Zhao
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Li‐Peng Chen
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yue‐Hui Ma
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Ming‐Xing Chu
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiang‐Long Li
- College of Animal Science and TechnologyHebei Normal University of Science & TechnologyQinghuangdaoChina
| | - Qiong‐Hua Hong
- Yunnan Animal Scinence and Veterinary InstituteKunmingChina
| | - Lan‐Hui Li
- College of Animal Science and TechnologyAgricultural University of HebeiBaoding, HebeiChina
| | - Ji‐Jun Guo
- Animal Husbandry Station of Qinghai ProvinceXining, QinghaiChina
| | - Lan Zhu
- Yunnan Animal Scinence and Veterinary InstituteKunmingChina
| | - Yan‐Guo Han
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Hui‐Jiang Gao
- Institute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Jia‐Hua Zhang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Huai‐Zhi Jiang
- Animal Science and Technology CollegeJilin Agriculture UniversityChangchun, JilinChina
| | - Cao‐De Jiang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Gao‐Fu Wang
- Chongqing Academy of Animal SciencesChongqingChina
| | | | - Mei‐Lan Jin
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| | - Yuan‐Zhi Sun
- Wuhan Tianyi Huiyuan Bioscience & Technology IncWuhanChina
| | - Peng Zhou
- Chongqing Academy of Animal SciencesChongqingChina
| | - Yong‐Fu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & HerbivoreChongqing Engineering Research Centre for Herbivores Resource Protection and UtilizationSouthwest UniversityChongqingChina
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
|
15
|
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]
|
16
|
New insights into mitogenomic phylogeny and copy number in eight indigenous sheep populations based on the ATP synthase and cytochrome c oxidase genes. Animal 2017; 12:1341-1349. [PMID: 29143714 DOI: 10.1017/s175173111700297x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0.944 and 0.00322, respectively. We identified a correlation between the lineages distribution and the genetic distance, whereby Valley-type Tibetan sheep had a closer genetic relationship with introduced breeds (Dorper, Poll Dorset and Suffolk) than with other indigenous breeds. Similarly, the Median-joining profile of haplotypes revealed the distribution of clusters according to genetic differences. Moreover, copy number analysis based on the five mitochondrial coding genes was affected by the genetic distance combining with genetic phylogeny; we also identified obvious non-synonymous mutations in ATP6 between the different levels of copy number expressions. These results imply that differences in mitogenomic compositions resulting from geographical separation lead to differences in mitochondrial function.
Collapse
|