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Singh KV, Das R, Sodhi M, Kataria RS. Genetic characterization and diversity assessment in 'Bhangor' indigenous swamp buffalo population using heterologous microsatellite markers. Anim Biotechnol 2023; 34:4380-4386. [PMID: 36519776 DOI: 10.1080/10495398.2022.2154220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
'Bhangor' newly identified swamp buffalo population from North East Indian, was characterized using microsatellite markers. Genomic DNA was isolated from blood samples of 76 unrelated animals, 15 microsatellite markers (CSSM33, BM1818, CSRM60, HEL13, ILSTS019, ILSTS025, ILSTS028, ILSTS029, ILSTS033, ILSTS036, ILSTS056, ILSTS058, ILSTS061, ILSTS089 and ETH003) were found to be highly polymorphic in the population of the selected markers. A total of 114 alleles were observed, which ranged from 3 in CSRM60 and ILSTS025 locus to 12 in ILSTS056 and ILSTS061. The mean effective number of alleles across all polymorphic loci was found to be 3.76. The overall mean expected heterozygosity and unbiased expected heterozygosity values were 0.67 and 0.68, ranging from 0.067 (ILSTS025) to 0.85 (ILSTS058) and 0.068 (ILSTS025) to 0.86 (ILSTS058), respectively. Within the population, the inbreeding estimates (FIS) ranged between -0.4352 and 0.804, with an average FIS of 0.114 ± 0.033. The outcome for infinite allele model (IAM), two-phase model (TPM) and test for mode shift revealed the absence of any recent bottleneck in the investigated buffalo population. The population was found to be in optimum diversity based on polymorphic microsatellite markers. With fast changing agro-climatic conditions; there is an urgent need to characterize the nondescript livestock populations.
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Affiliation(s)
- Karan Veer Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Ramendra Das
- Animal Resources Development Department, Tripura Livestock Development Agency (TLDA), Agartala, Tripura, India
| | - Monika Sodhi
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - R S Kataria
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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Curaudeau M, Rozzi R, Hassanin A. The genome of the lowland anoa (Bubalus depressicornis) illuminates the origin of river and swamp buffalo. Mol Phylogenet Evol 2021; 161:107170. [PMID: 33798669 DOI: 10.1016/j.ympev.2021.107170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Two types of domestic water buffalo are currently recognized: the river buffalo from the Indian subcontinent and Mediterranean countries and the swamp buffalo from China and Southeast Asia. To test the hypothesis of two separate species of water buffalo, we sequenced the genome of the lowland anoa, Bubalus depressicornis, which is a dwarf wild buffalo endemic to Sulawesi, and two genomes of swamp buffalo, and made comparisons with 12 additional genomes. Three genomic data sets were constructed to infer phylogenetic relationships: the mitochondrial genome (15,468 bp; maternal transmission), two concatenated Y-chromosomal genes, AMELY and DDX3Y (20,036 bp; paternal transmission), and a selection of 30 nuclear genes representing all cattle chromosomes (364,887 bp; biparental transmission). The comparisons between our 30 nuclear gene sequences obtained by read mapping and those directly extracted from Bos taurus and Bubalus bubalis genome assemblies show that the mapping approach revealed higher levels of heterozygosity at both nucleotide sites and indels (insertions and deletions) (0.09-0.15%), as well as several sequence errors (0.07%). Our phylogenetic and molecular dating analyses provide strong evidence that the lowland anoa, river buffalo, and swamp buffalo are three distinct taxa which separated rapidly from each other during the Pleistocene epoch. We therefore conclude that two species of domestic water buffalo should be distinguished: Bubalus bubalis for the river buffalo and Bubalus kerabau for the swamp buffalo. The new classification can have deep implications for understanding the evolution and selection of domesticated forms and for the conservation and management of wild buffalo populations in South and Southeast Asia.
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Affiliation(s)
- Manon Curaudeau
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - Roberto Rozzi
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Synthesis Centre for Biodiversity Sciences (sDiv), Puschstr. 4, D-04103 Leipzig, Germany; Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France.
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Rehman SU, Hassan FU, Luo X, Li Z, Liu Q. Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges. Animals (Basel) 2021; 11:904. [PMID: 33809937 PMCID: PMC8004149 DOI: 10.3390/ani11030904] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/17/2022] Open
Abstract
The buffalo was domesticated around 3000-6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.
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Affiliation(s)
- Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
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Minervino AHH, Zava M, Vecchio D, Borghese A. Bubalus bubalis: A Short Story. Front Vet Sci 2020; 7:570413. [PMID: 33335917 PMCID: PMC7736047 DOI: 10.3389/fvets.2020.570413] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
The domestic buffalo (Bubalus bubalis), also known as water buffalo or Asian buffalo to prevent confusion with the American bison (Bison bison), wrongly named buffalo in North America, comprises two subspecies: the river buffalo (B. bubalis bubalis) and the swamp buffalo (B. bubalis kerebau). The swamp buffalo has a consistent phenotype and is considered as one type, even if many breeds are recognized within it; conversely, the river buffalo subspecies has many breeds. We found limited information available regarding the worldwide distribution of buffaloes. The best estimate is that 208,098,759 buffalo head are distributed in 77 countries in five continents. In this review, we presented the basic aspects of the water buffalo and unraveled the buffalo path followed from the origin of the species to its current global distribution. We reviewed several data sources to provide a better estimate of the world buffalo count and distribution.
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Affiliation(s)
| | - Marco Zava
- Argentine Buffalo Breeders Association, Buenos Aires, Argentina
| | - Domenico Vecchio
- Italian National Reference Centre on Water Buffalo Farming and Productions Hygiene and Technologies (CReNBuf), Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Antonio Borghese
- International Buffalo Federation - IBF, FAO/ESCORENA Buffalo Network, Animal Production Research Institute, Rome, Italy
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SINGH KARANVEER, VERMA UMAKANT, ARORA MANISHA, KATARIA RS, NIRANJAN SAKET. Cytogenetic analysis reveals existence of swamp buffalo population in Meghalaya. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i6.104989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The present study aimed at assessing the status of the Meghalaya buffalo population from North-East India employing cytogenetic studies. So far buffaloes of the northeastern states of India have been studied except for Tripura and Meghalaya and are generally considered to be of swamp type based on their phenotypic resemblance to swamp type buffaloes. A pilot survey was conducted in the Indian State of Meghalaya for collection of morphometric data from adult animals. The Meghalaya buffaloes investigated cytogenetically possessed a somatic chromosome count of 2N=48, identical to that of typical swamp buffalo, 23 pairs of autosomes and a pair of sex chromosomes. The distinctive karyotypic feature of swamp buffalo observed was due to the distinct size of the fourth pair of metacentric chromosome. No morphological or chromosomal abnormality was observed in any of the populations. This is the first confirmed documentation of existence of pure swamp type buffaloes in Meghalaya state of India.
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Singh R, Lava Kumar S, Mishra SK, Gurao A, Niranjan SK, Vohra V, Dash SK, Rajesh C, Kataria RS. Mitochondrial sequence-based evolutionary analysis of riverine-swamp hybrid buffaloes of India indicates novel maternal differentiation and domestication patterns. Anim Genet 2020; 51:476-482. [PMID: 32281135 DOI: 10.1111/age.12938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2020] [Indexed: 11/29/2022]
Abstract
In this study, mitochondrial D-loop sequence data on riverine, swamp and hybrid buffaloes from India have been generated and compared with other reported Indian riverine, Chinese and Bangladeshi swamp buffalo populations. Sequence analysis revealed the presence of 132 haplotypes, with a haplotype diversity of 0.9611 ± 0.0045 and a nucleotide diversity of 0.04801 ± 0.00126. For the first time, the existence of riverine-swamp hybrids among the Indian Chilika buffalo population has been recorded, having 49 chromosomes, which was also confirmed by mitochondrial haplotype sharing between Chilika and Indian swamp as well as Chinese swamp buffalo populations in the network analysis. Phylogenetic analysis documents the sharing of reported pre-domestication haplogroups 'SA1', 'SA2', 'SA3' and 'SB1' between the Chilika and swamp buffalo populations of India, China and Bangladesh, an indication of the migration of swamp buffaloes towards Bangladesh and adjoining lower parts of India and north towards Chinese domestication sites. The results have also been supplemented by multidimension scaling, grouping Indian and Chinese swamp buffaloes more closely together with Bangladeshi buffaloes, but into a separate quadrant, whereas Chilika grouped away from other riverine as well as swamp buffaloes. These findings thus confirm the previous reports that the northeast region of India, close to the Indo-China border, is the point of evolution of swamp buffaloes with multiple sites of domestication.
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Affiliation(s)
- R Singh
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.,Department of Biotechnology, SGGSWU, Fatehgarh Sahib, Punjab, 140407, India
| | - S Lava Kumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - S K Mishra
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - A Gurao
- Department of Veterinary Microbiology and Biotechnology, College of Veterinary and Animal Sciences, Rajasthan University of Veterinary and Animal Sciences, Bikaner, Rajasthan, 334001, India
| | - S K Niranjan
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - V Vohra
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - S K Dash
- Department of Animal Breeding and Genetics, OUAT, Bhubaneshwar, Odisha, 751003, India
| | - C Rajesh
- Department of Biotechnology, SGGSWU, Fatehgarh Sahib, Punjab, 140407, India
| | - R S Kataria
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
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Sun T, Huang G, Sun J, Wang Z, Teng S, Cao Y, Hanif Q, Chen N, Lei C, Liao Y. Mitogenome Diversity and Maternal Origins of Guangxi Buffalo Breeds. Animals (Basel) 2020; 10:ani10040547. [PMID: 32218165 PMCID: PMC7222400 DOI: 10.3390/ani10040547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 11/16/2022] Open
Abstract
Guangxi Province, in the southwest of China, is one of the putative migratory corridors or domestication centers for swamp buffalo. In this study, we investigated the evolutionary status of two Guangxi native buffalo breeds (Fuzhong buffalo, n = 15; Xilin buffalo, n = 25) based on the complete mitogenome sequencing. Our results revealed rich genetic diversity in the two buffalo breeds. We detected five haplogroups (SA1, SA2, SB1, SB2, SB3) in the two Guangxi buffalo breeds, and the haplogroup SB3 in the Fuzhong buffalo. Our results showed that the haplogroup SA1 was associated with the major domestication event that involved population expansion in Guangxi buffalo. In conclusion, our findings revealed a high level of maternal genetic diversity and the phylogenetic pattern of the two Guangxi buffalo breeds.
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Affiliation(s)
- Ting Sun
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning 530001, China; (T.S.); (G.H.); (J.S.); (Z.W.); (S.T.); (Y.C.)
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Guangyun Huang
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning 530001, China; (T.S.); (G.H.); (J.S.); (Z.W.); (S.T.); (Y.C.)
| | - Junli Sun
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning 530001, China; (T.S.); (G.H.); (J.S.); (Z.W.); (S.T.); (Y.C.)
| | - Zihao Wang
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning 530001, China; (T.S.); (G.H.); (J.S.); (Z.W.); (S.T.); (Y.C.)
| | - Shaohua Teng
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning 530001, China; (T.S.); (G.H.); (J.S.); (Z.W.); (S.T.); (Y.C.)
| | - Yanhong Cao
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning 530001, China; (T.S.); (G.H.); (J.S.); (Z.W.); (S.T.); (Y.C.)
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad 577, Pakistan;
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (N.C.); (C.L.)
| | - Yuying Liao
- Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning 530001, China; (T.S.); (G.H.); (J.S.); (Z.W.); (S.T.); (Y.C.)
- Correspondence: ; Tel.: +86-135-729-92159
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Lu XR, Duan AQ, Li WQ, Abdel-Shafy H, Rushdi HE, Liang SS, Ma XY, Liang XW, Deng TX. Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk production traits in Chinese buffalo breeds. J Dairy Sci 2020; 103:4545-4556. [PMID: 32147265 DOI: 10.3168/jds.2019-17364] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/13/2020] [Indexed: 11/19/2022]
Abstract
The water buffalo is an important dual-purpose livestock that is widespread throughout central and southern China. However, there has been no characterization of the population genetics of Chinese buffalo. Using an Axiom buffalo genotyping array (Thermo Fisher Scientific, Wilmington, DE), we analyzed the genetic diversity, linkage disequilibrium pattern, and signature of selection in 176 Chinese buffaloes from 13 breeds. A total of 35,547 SNP passed quality control and were used for further analyses. Population genetic analysis revealed a clear separation between swamp and river types. Ten Chinese indigenous breeds were clustered into the swamp group, the Murrah and Nili-Ravi breeds were clustered into the river group, and the crossbred breed was closer to the river group. Genetic diversity analysis showed that the swamp group had a lower average expected heterozygosity. Linkage disequilibrium decay distance was much shorter in the swamp group compared with the river group, with an average square of correlation coefficient value of 0.2 of approximately 50 kb. Analysis of runs of homozygosity indicated extensive remote and recent inbreeding within swamp and river groups, respectively. Moreover, one genomic region under selection was detected between the river and swamp groups. Our findings contribute to our understanding of the characterization of population genetics in Chinese buffaloes, which in turn may be used in buffalo breeding programs.
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Affiliation(s)
- X R Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - A Q Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - W Q Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - H Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - H E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - S S Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - X Y Ma
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - X W Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - T X Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
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Sun T, Shen J, Achilli A, Chen N, Chen Q, Dang R, Zheng Z, Zhang H, Zhang X, Wang S, Zhang T, Lu H, Ma Y, Jia Y, Capodiferro MR, Huang Y, Lan X, Chen H, Jiang Y, Lei C. Genomic analyses reveal distinct genetic architectures and selective pressures in buffaloes. Gigascience 2020; 9:giz166. [PMID: 32083286 PMCID: PMC7033652 DOI: 10.1093/gigascience/giz166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/26/2019] [Accepted: 12/27/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The domestic buffalo (Bubalus bubalis) is an essential farm animal in tropical and subtropical regions, whose genomic diversity is yet to be fully discovered. RESULTS In this study, we describe the demographic events and selective pressures of buffalo by analyzing 121 whole genomes (98 newly reported) from 25 swamp and river buffalo breeds. Both uniparental and biparental markers were investigated to provide the final scenario. The ancestors of swamp and river buffalo diverged ∼0.23 million years ago and then experienced independent demographic histories. They were domesticated in different regions, the swamp buffalo at the border between southwest China and southeast Asia, while the river buffalo in south Asia. The domestic stocks migrated to other regions and further differentiated, as testified by (at least) 2 ancestral components identified in each subspecies. Different signals of selective pressures were also detected in these 2 types of buffalo. The swamp buffalo, historically used as a draft animal, shows selection signatures in genes associated with the nervous system, while in river dairy breeds, genes under selection are related to heat stress and immunity. CONCLUSIONS Our findings substantially expand the catalogue of genetic variants in buffalo and reveal new insights into the evolutionary history and distinct selective pressures in river and swamp buffalo.
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Affiliation(s)
- Ting Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiafei Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani,” Università di Pavia, Pavia 27100, Italy
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuqing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hucai Zhang
- Key Laboratory of Plateau Lake Ecology and Environment Change, Yunnan University, Kunming 650504, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shaoqiang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Zhang
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Hongzhao Lu
- School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Yun Ma
- Agricultural College, Ningxia University, Yinchuan 750021, China
| | - Yutang Jia
- Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei 230001, China
| | | | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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Zhang Y, Colli L, Barker JSF. Asian water buffalo: domestication, history and genetics. Anim Genet 2020; 51:177-191. [PMID: 31967365 DOI: 10.1111/age.12911] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
Abstract
The domestic Asian water buffalo (Bubalus bubalis) is found on all five continents, with a global population of some 202 million. The livelihoods of more people depend on this species than on any other domestic animal. The two distinct types (river and swamp) descended from different wild Asian water buffalo (Bubalus arnee) populations that diverged some 900 kyr BP and then evolved in separate geographical regions. After domestication in the western region of the Indian subcontinent (ca. 6300 years BP), the river buffalo spread west as far as Egypt, the Balkans and Italy. Conversely, after domestication in the China/Indochina border region ca. 3000-7000 years BP, swamp buffaloes dispersed through south-east Asia and China as far as the Yangtze River valley. Molecular and morphological evidence indicates that swamp buffalo populations have strong geographic genetic differentiation and a lack of gene flow, but strong phenotypic uniformity. In contrast, river buffalo populations show a weaker phylogeographic structure, but higher phenotypic diversity (i.e. many breeds). The recent availability of a high-quality reference genome and of a medium-density marker panel for genotyping has triggered a number of genome-wide investigations on diversity, evolutionary history, production traits and functional elements. The growing molecular knowledge combined with breeding programmes should pave the way to improvements in production, environmental adaptation and disease resistance in water buffalo populations worldwide.
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Affiliation(s)
- Y Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - L Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - J S F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
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Kumar De A, Ponraj P, Malakar D, Muthiyan R, Kundu A, Bhattacharya D. Complete mitogenome sequencing of Andaman buffalo: an endangered germplasm of Andaman and Nicobar Islands, India. J Genet 2019. [DOI: 10.1007/s12041-019-1140-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Sun T, Wang S, Chanthakhoun V, Dang R, Huang Y, Chen H, Lei C. Multiple domestication of swamp buffalo in China and South East Asia. J Anim Breed Genet 2019; 137:331-340. [PMID: 31588618 DOI: 10.1111/jbg.12445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 11/28/2022]
Abstract
The domestication of swamp buffalo (Bubalus bubalis carabanesis) has been discussed for years and still remained unclear. To obtain a better understanding of where, when and how the swamp buffaloes were domesticated, the complete mitochondrial DNA D-loop sequences of 1,788 individuals from China, Vietnam, Laos, Thailand, Burma, Bangladesh and India were investigated. Our results revealed swamp buffalo with abundant genetic diversity. The lineage SA of swamp buffalo may be first domesticated in Lower Yangtze and then migrated following two different routes: one migrated along the Upper Yangtze to Southwest China (L1); the other migrated to Southeast China to Southeast Asia through Guangxi province (L2). During the migration process several later domestication events may be inspired in the Upper Yangtze (SB3), Southwest China and North of Southeast Asia (SB1 and SB2). In this study, we proposed a non-independent multiple domestication pattern in swamp buffalo.
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Affiliation(s)
- Ting Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shaoqiang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Vongprasith Chanthakhoun
- Department of Animal Science, Faculty of Agriculture and Forest Resource, Souphanouvong University, Luangprabang, Lao People's Democratic Republic
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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13
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Young R, Lefevre L, Bush SJ, Joshi A, Singh SH, Jadhav SK, Dhanikachalam V, Lisowski ZM, Iamartino D, Summers KM, Williams JL, Archibald AL, Gokhale S, Kumar S, Hume DA. A Gene Expression Atlas of the Domestic Water Buffalo ( Bubalus bubalis). Front Genet 2019; 10:668. [PMID: 31428126 PMCID: PMC6689995 DOI: 10.3389/fgene.2019.00668] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/19/2022] Open
Abstract
The domestic water buffalo (Bubalus bubalis) makes a major contribution to the global agricultural economy in the form of milk, meat, hides, and draught power. The global water buffalo population is predominantly found in Asia, and per head of population more people depend upon the buffalo than on any other livestock species. Despite its agricultural importance, there are comparatively fewer genomic and transcriptomic resources available for buffalo than for other livestock species. We have generated a large-scale gene expression atlas covering multiple tissue and cell types from all major organ systems collected from three breeds of riverine water buffalo (Mediterranean, Pandharpuri and Bhadawari) and used the network analysis tool Graphia Professional to identify clusters of genes with similar expression profiles. Alongside similar data, we and others have generated for ruminants as part of the Functional Annotation of Animal Genomes Consortium; this comprehensive transcriptome supports functional annotation and comparative analysis of the water buffalo genome.
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Affiliation(s)
- Rachel Young
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Akshay Joshi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Velu Dhanikachalam
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Zofia M. Lisowski
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Alan L. Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Suresh Gokhale
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Satish Kumar
- Centre for Cellular and Molecular Biology, Hyderabad, India
- School of Life Science, Central University of Haryana, Mahendergargh, India
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
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14
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Shaari N'AL, Jaoi-Edward M, Loo SS, Salisi MS, Yusoff R, Ab Ghani NI, Saad MZ, Ahmad H. Karyotypic and mtDNA based characterization of Malaysian water buffalo. BMC Genet 2019; 20:37. [PMID: 30909863 PMCID: PMC6434848 DOI: 10.1186/s12863-019-0741-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 03/19/2019] [Indexed: 11/26/2022] Open
Abstract
Background In Malaysia, the domestic water buffaloes (Bubalus bubalis) are classified into the swamp and the murrah buffaloes. Identification of these buffaloes is usually made via their phenotypic appearances. This study characterizes the subspecies of water buffaloes using karyotype, molecular and phylogenetic analyses. Blood of 105 buffaloes, phenotypically identified as swamp, murrah and crossbred buffaloes were cultured, terminated and harvested using conventional karyotype protocol to determine the number of chromosomes. Then, the D-loop of mitochondrial DNA of 10 swamp, 6 crossbred and 4 murrah buffaloes which were identified earlier by karyotyping were used to construct a phylogenetic tree was constructed. Results Karyotypic analysis confirmed that all 93 animals phenotypically identified as swamp buffaloes with 48 chromosomes, all 7 as crossbreds with 49 chromosomes, and all 5 as murrah buffaloes with 50 chromosomes. The D-loop of mitochondrial DNA analysis showed that 10 haplotypes were observed with haplotype diversity of 0.8000 ± 0.089. Sequence characterization revealed 72 variables sites in which 67 were parsimony informative sites with sequence diversity of 0.01906. The swamp and murrah buffaloes clearly formed 2 different clades in the phylogenetic tree, indicating clear maternal divergence from each other. The crossbreds were grouped within the swamp buffalo clade, indicating the dominant maternal swamp buffalo gene in the crossbreds. Conclusion Thus, the karyotyping could be used to differentiate the water buffaloes while genotypic analysis could be used to characterize the water buffaloes and their crossbreds.
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Affiliation(s)
- Nor ' Ammar Liyana Shaari
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Marilyn Jaoi-Edward
- Agro-Biotechnology Institute (ABI), National Institutes of Biotechnology Malaysia (NIBM), c/o MARDI Headquarters, 43400, Serdang, Malaysia
| | - Shu San Loo
- Agro-Biotechnology Institute (ABI), National Institutes of Biotechnology Malaysia (NIBM), c/o MARDI Headquarters, 43400, Serdang, Malaysia
| | - Mohd Shahrom Salisi
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Rosnina Yusoff
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Nurul Izza Ab Ghani
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Mohd Zamri Saad
- Research Centre for Ruminant Diseases, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Hafandi Ahmad
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Malaysia.
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15
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Deng T, Liang A, Liu J, Hua G, Ye T, Liu S, Campanile G, Plastow G, Zhang C, Wang Z, Salzano A, Gasparrini B, Cassandro M, Riaz H, Liang X, Yang L. Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations. Front Genet 2019; 9:688. [PMID: 30671082 PMCID: PMC6332145 DOI: 10.3389/fgene.2018.00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/11/2018] [Indexed: 02/04/2023] Open
Abstract
Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for the purebred (Mediterranean buffalo; n = 411) and crossbred [Mediterranean × Jianghan × Nili-Ravi buffalo, n = 9; Murrah × Nili-Ravi × local (Xilin or Fuzhong) buffalo, n = 36] buffalo populations using the 90K Buffalo SNP genotyping array. The results showed that the average square of correlation coefficient (r 2) between adjacent SNP was 0.13 ± 0.19 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the most rapid decline in LD was observed over the first 200 kb. Estimated r 2 ≥ 0.2 extended up to ~50 kb in crossbred and 170 kb in purebred populations, while average r 2 values ≥0.3 were respectively observed in the ~10 and 60 kb in the crossbred and purebred populations. The largest phase correlation (R P, C = 0.47) was observed at the distance of 100 kb, suggesting that this phase was not actively preserved between the two populations. Estimated Ne for the purebred and crossbred population at the current generation was 387 and 113 individuals, respectively. These findings may provide useful information to guide the GS and GWAS in buffaloes.
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Affiliation(s)
- Tingxian Deng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Aixin Liang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jiajia Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Guohua Hua
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Tingzhu Ye
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shenhe Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Giuseppe Campanile
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy
| | - Graham Plastow
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Chunyan Zhang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Angela Salzano
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy
| | - Bianca Gasparrini
- Department of Veterinary Medicine and Animal Productions, University of Naples "Federico II", Naples, Italy
| | - Martino Cassandro
- Department of Agronomy Food Natural Resources Animal Environmental, University of Padova, Legnaro, Italy
| | - Hasan Riaz
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan
| | - Xianwei Liang
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
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16
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Wang S, Xia X, Zhang T, Sun T, Dang R, Huang Y, Lan X, Chen H, Lei C. Y-chromosome haplotype analysis revealing multiple paternal origins in swamp buffaloes of China and Southeast Asia. J Anim Breed Genet 2018; 135:442-449. [DOI: 10.1111/jbg.12364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Shaoqiang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Tao Zhang
- School of Bioscience and Engineering; Shaanxi University of Technology; Hanzhong Shaanxi China
| | - Ting Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi China
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17
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Colli L, Milanesi M, Vajana E, Iamartino D, Bomba L, Puglisi F, Del Corvo M, Nicolazzi EL, Ahmed SSE, Herrera JRV, Cruz L, Zhang S, Liang A, Hua G, Yang L, Hao X, Zuo F, Lai SJ, Wang S, Liu R, Gong Y, Mokhber M, Mao Y, Guan F, Vlaic A, Vlaic B, Ramunno L, Cosenza G, Ahmad A, Soysal I, Ünal EÖ, Ketudat-Cairns M, Garcia JF, Utsunomiya YT, Baruselli PS, Amaral MEJ, Parnpai R, Drummond MG, Galbusera P, Burton J, Hoal E, Yusnizar Y, Sumantri C, Moioli B, Valentini A, Stella A, Williams JL, Ajmone-Marsan P. New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data. Front Genet 2018; 9:53. [PMID: 29552025 PMCID: PMC5841121 DOI: 10.3389/fgene.2018.00053] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/02/2018] [Indexed: 01/14/2023] Open
Abstract
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.
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Affiliation(s)
- Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Centro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA), Piacenza, Italy
| | - Marco Milanesi
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil.,International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Elia Vajana
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Daniela Iamartino
- PTP Science Park, Lodi, Italy.,LGS-AIA Associazione Italiana Allevatori, Cremona, Italy
| | - Lorenzo Bomba
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Francesco Puglisi
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Università degli Studi di Parma, Parma, Italy
| | - Marcello Del Corvo
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | - Sahar S E Ahmed
- Cell Biology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, Egypt
| | | | | | - Shujun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Aixin Liang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Guohua Hua
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xingjie Hao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Fuyuan Zuo
- Department of Animal Husbandry, Southwest University, Chongqing, China
| | - Song-Jia Lai
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Shuilian Wang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Ruyu Liu
- College of Animal Science, Guizhou University, Guiyang, China
| | | | - Mahdi Mokhber
- Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Feng Guan
- College of Life Science, China Jiliang University, Hangzhou, China
| | - Augustin Vlaic
- Department of Animal Genetics, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
| | - Bogdan Vlaic
- Department of Animal Genetics, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
| | - Luigi Ramunno
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Gianfranco Cosenza
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Ali Ahmad
- COMSATS Institute of Information Technology, Sahiwal, Pakistan
| | - Ihsan Soysal
- Department of Animal Science, Faculty of Agriculture, Namik Kemal University, Tekirdag, Turkey
| | - Emel Ö Ünal
- Department of Animal Science, Faculty of Agriculture, Namik Kemal University, Tekirdag, Turkey
| | - Mariena Ketudat-Cairns
- School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - José F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil.,International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp.), São Paulo, Brazil
| | - Yuri T Utsunomiya
- International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp.), São Paulo, Brazil
| | - Pietro S Baruselli
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Maria E J Amaral
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, Brazil
| | - Rangsun Parnpai
- School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | | | - Peter Galbusera
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - James Burton
- IUCN SSC Asian Wild Cattle Specialist Group and Chester Zoo, Upton by Chester, United Kingdom.,Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Roslin, United Kingdom
| | - Eileen Hoal
- NRF/DST Centre of Excellence for Biomedical TB Research, MRC Centre for TB Research, and Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Yulnawati Yusnizar
- Research Centre for Biotechnology, Indonesian Institute of Sciences, Jalan Raya, Indonesia.,Indonesian Buffalo Conservation and Breeding Centre, Ciapus-Bogor, Indonesia
| | - Cece Sumantri
- Department of Animal Production and Technology, Bogor Agricultural University (IPB), Bogor, Indonesia
| | - Bianca Moioli
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Monterotondo, Italy
| | - Alessio Valentini
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, DIBAF, Università della Tuscia, Viterbo, Italy
| | | | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Science, University of Adelaide, Roseworthy, SA, Australia
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Centro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA), Piacenza, Italy
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18
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Whole Mitogenomes Reveal the History of Swamp Buffalo: Initially Shaped by Glacial Periods and Eventually Modelled by Domestication. Sci Rep 2017; 7:4708. [PMID: 28680070 PMCID: PMC5498497 DOI: 10.1038/s41598-017-04830-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/22/2017] [Indexed: 11/08/2022] Open
Abstract
The newly sequenced mitochondrial genomes of 107 Asian swamp buffalo (Bubalus bubalis carabensis) allowed the reconstruction of the matrilineal divergence since ~900 Kya. Phylogenetic trees and Bayesian skyline plots suggest a role of the glacial periods in the demographic history of swamp buffalo. The ancestral swamp-buffalo mitogenome is dated ~232 ± 35 Kya. Two major macro-lineages diverged during the 2nd Pleistocene Glacial Period (~200-130 Kya), but most (~99%) of the current matrilines derive from only two ancestors (SA1'2 and SB) that lived around the Last Glacial Maximum (~26-19 Kya). During the late Holocene optimum (11-6 Kya) lineages differentiated further, and at least eight matrilines (SA1, SA2, SB1a, SB1b, SB2a, SB2b, SB3 and SB4) were domesticated around 7-3 Kya. Haplotype distributions support an initial domestication process in Southeast Asia, while subsequent captures of wild females probably introduced some additional rare lineages (SA3, SC, SD and SE). Dispersal of domestic buffaloes created local population bottlenecks and founder events that further differentiated haplogroup distributions. A lack of maternal gene flow between neighboring populations apparently maintained the strong phylogeography of the swamp buffalo matrilines, which is the more remarkable because of an almost complete absence of phenotypic differentiation.
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19
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Zhang Y, Lu Y, Yindee M, Li K, Kuo H, Ju Y, Ye S, Faruque MO, Li Q, Wang Y, Cuong VC, Pham LD, Bouahom B, Yang B, Liang X, Cai Z, Vankan D, Manatchaiworakul W, Kowlim N, Duangchantrasiri S, Wajjwalku W, Colenbrander B, Zhang Y, Beerli P, Lenstra JA, Barker JSF. Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Mol Ecol 2016; 25:1530-50. [DOI: 10.1111/mec.13518] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/30/2015] [Accepted: 12/10/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Yi Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yongfang Lu
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Marnoch Yindee
- Department of Clinical Science and Public Health Faculty of Veterinary Science Mahidol University Kanchanaburi Campus Kanchanaburi 71150 Thailand
| | - Kuan‐Yi Li
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Hsiao‐Yun Kuo
- Livestock Research Institute Council of Agriculture Tainan 71246 Taiwan
| | - Yu‐Ten Ju
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Shaohui Ye
- College of Animal Science and Technology Yunnan Agricultural University Kunming 650201 China
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics Bangladesh Agricultural University Mymensingh 2202 Bangladesh
| | - Qiang Li
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Vu Chi Cuong
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Lan Doan Pham
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Bounthong Bouahom
- National Agriculture and Forestry Research Institute P.O. Box 811 Vientiane Capital Lao P.D.R
| | - Bingzhuang Yang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Xianwei Liang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Zhihua Cai
- College of Animal Science Anhui Science and Technology University Fengyang 233100 China
| | - Dianne Vankan
- The School of Veterinary Science University of Queensland, Gatton Campus Gatton Qld 4343 Australia
| | - Wallaya Manatchaiworakul
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Nonglid Kowlim
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Somphot Duangchantrasiri
- Khao‐Nang‐Ram Wildlife Research Station Department of National Parks Wildlife and Plant Conservation Bangkok 10900 Thailand
| | - Worawidh Wajjwalku
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Ben Colenbrander
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - Yuan Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Peter Beerli
- Department of Scientific Computing Florida State University Tallahassee FL 32306‐4120 USA
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - J. Stuart F. Barker
- School of Environmental and Rural Science University of New England Armidale NSW 2351 Australia
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Han H, Zhang Q, Gao K, Yue X, Zhang T, Dang R, Lan X, Chen H, Lei C. Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1066-74. [PMID: 26104513 PMCID: PMC4478473 DOI: 10.5713/ajas.14.0784] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/16/2014] [Accepted: 03/04/2015] [Indexed: 11/27/2022]
Abstract
In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10(-4)) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.
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Affiliation(s)
- Haoyuan Han
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kexin Gao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangpeng Yue
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Zhang
- Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Ruihua Dang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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21
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Mishra BP, Dubey PK, Prakash B, Kathiravan P, Goyal S, Sadana DK, Das GC, Goswami RN, Bhasin V, Joshi BK, Kataria RS. Genetic analysis of river, swamp and hybrid buffaloes of north-east India throw new light on phylogeography of water buffalo (Bubalus bubalis). J Anim Breed Genet 2015; 132:454-66. [PMID: 25780854 DOI: 10.1111/jbg.12141] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/22/2015] [Indexed: 11/27/2022]
Abstract
This study analysed buffaloes from north-east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South-East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north-east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise FST revealed the clustering of all swamp-type buffaloes of north-east India with Lower Assamese (significantly hybrid type) buffaloes in one plane and all the mainland river buffaloes in another plane while the upper Assamese buffaloes being distinct from both these clusters. Analysis of mtDNA D-loop region of 530-bp length was performed on 345 sequences belonging to 23 buffalo populations from various geographical regions to establish the phylogeography of Indian water buffalo. The swamp buffaloes of north-east India clustered with both the lineages of Chinese swamp buffalo. Multidimensional scaling display of pairwise FST derived from mitochondrial DNA data showed clustering of upper Assamese, Chilika and Mediterranean buffaloes distinctly from all the other Indian buffalo populations. Median-joining network analysis further confirmed the distinctness and ancestral nature of these buffaloes. The study revealed north-east region of India forming part of the wider hybrid zone of water buffalo that may probably extend from north-east India to South-East Asia.
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Affiliation(s)
- B P Mishra
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - P K Dubey
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - B Prakash
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - P Kathiravan
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - S Goyal
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - D K Sadana
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - G C Das
- Assam Agricultural University, Khanapara, Guwahati, Assam, India
| | - R N Goswami
- Assam Agricultural University, Khanapara, Guwahati, Assam, India
| | - V Bhasin
- Animal Science Division, Indian Council of Agricultural Research, New Delhi, India
| | - B K Joshi
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - R S Kataria
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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Joshi J, Salar RK, Banerjee P, S U, Tantia MS, Vijh RK. Genetic variation and phylogenetic relationships of Indian buffaloes of uttar pradesh. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1229-36. [PMID: 25049904 PMCID: PMC4093408 DOI: 10.5713/ajas.2012.12669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/05/2013] [Accepted: 02/17/2013] [Indexed: 11/27/2022]
Abstract
India possesses a total buffalo population of 105 million out of which 26.1% inhabit Uttar Pradesh. The buffalo of Uttar Pradesh are described as nondescript or local buffaloes. Currently, there is no report about the genetic diversity, phylogenetic relationship and matrilineal genetic structure of these buffaloes. To determine the origin and genetic diversity of UP buffaloes, we sequenced and analysed the mitochondrial DNA D-loop sequences in 259 samples from entire Uttar Pradesh. One hundred nine haplotypes were identified in UP buffaloes that were defined by 96 polymorphic sites. We implemented neutrality tests to assess signatures of recent historical demographic events like Tajima’s D test and Fu’s Fs test. The phylogenetic studies revealed that there was no geographic differentiation and UP buffaloes had a single maternal lineage while buffaloes of Eastern UP were distinctive from rest of the UP buffaloes.
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Affiliation(s)
- Jyoti Joshi
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - R K Salar
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - Priyanka Banerjee
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - Upasna S
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - M S Tantia
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - R K Vijh
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
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23
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Yue XP, Li R, Xie WM, Xu P, Chang TC, Liu L, Cheng F, Zhang RF, Lan XY, Chen H, Lei CZ. Phylogeography and domestication of Chinese swamp buffalo. PLoS One 2013; 8:e56552. [PMID: 23437167 PMCID: PMC3577850 DOI: 10.1371/journal.pone.0056552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 01/14/2013] [Indexed: 11/19/2022] Open
Abstract
To further probe into whether swamp buffaloes were domesticated once or multiple times in China, this survey examined the mitochondrial DNA (mtDNA) Control Region (D-loop) diversity of 471 individuals representing 22 populations of 455 Chinese swamp buffaloes and 16 river buffaloes. Phylogenetic analysis revealed that Chinese swamp buffaloes could be divided into two distinct lineages, A and B, which were defined previously. Of the two lineages, lineage A was predominant across all populations. For predominant lineage A, Southwestern buffalo populations possess the highest genetic diversity among the three hypothesized domestication centers (Southeastern, Central, and Southwestern China), suggesting Southwestern China as the most likely location for the domestication of lineage A. However, a complex pattern of diversity is detected for the lineage B, preventing the unambiguous pinpointing of the exact place of domestication center and suggesting the presence of a long-term, strong gene flow among swamp buffalo populations caused by extensive migrations of buffaloes and frequent human movements along the Yangtze River throughout history. Our current study suggests that Southwestern China is the most likely domestication center for lineage A, and may have been a primary center of swamp buffalo domestication. More archaeological and genetic evidence is needed to show the process of domestication.
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Affiliation(s)
- Xiang-Peng Yue
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Ran Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Wen-Mei Xie
- Department of Basic Medicine, Pingliang Medical College, Pingliang, Gansu, China
| | - Ping Xu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Ti-Cheng Chang
- Department of Dairy and Animal Science, The Center for Reproductive Biology and Health, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Li Liu
- Department of East Asian Languages and Cultures, Stanford University, Stanford, California, United States of America
| | - Feng Cheng
- Animal Science Department, Xinyang Agricultural College, Xinyang, Henan, China
| | - Run-Feng Zhang
- College of Life Science, Hubei Normal University, Huangshi, Hubei, China
| | - Xian-Yong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Chu-Zhao Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail:
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24
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Babar ME, Hussain T, Imran M, Nagarajan M, Kumar S. Mitochondrial DNA diversity patterns in Pakistani buffalo. Anim Genet 2011; 43:315-7. [DOI: 10.1111/j.1365-2052.2011.02250.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Lei CZ, Zhang CM, Weining S, Campana MG, Bower MA, Zhang XM, Liu L, Lan XY, Chen H. Genetic diversity of mitochondrial cytochrome b gene in Chinese native buffalo. Anim Genet 2011; 42:432-6. [PMID: 21749426 DOI: 10.1111/j.1365-2052.2011.02174.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
The origins of the domestic water buffalo remain contentious. To better understand the origins of Chinese water buffalo, we sequenced the complete mitochondrial cytochrome b (MT-CYB) gene from 270 individuals representing 13 Chinese domestic swamp buffalo populations. We found genetic evidence of introgression of river buffalo into Chinese swamp buffalo herds. Swamp buffalo haplotypes can be divided into two highly divergent lineages (A and B), suggesting that Chinese native swamp buffalo have two maternal origins. We found that the A→G transition in the buffalo MT-CYB gene stop codon resulted in buffalo haplotypes being terminated by one of two stop codons: AGA or AGG. AGA is common to river buffalo and lineage A of swamp buffalo, while AGG is specific to lineage B of swamp buffalo. Lineage A appears to have been domesticated in China. Further genetic evidence is required to clarify the origins of lineage B.
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Affiliation(s)
- C Z Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
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26
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Zhang Y, Vankan D, Zhang Y, Barker JSF. Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo. Anim Genet 2011; 42:366-77. [DOI: 10.1111/j.1365-2052.2010.02166.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Michelizzi VN, Dodson MV, Pan Z, Amaral MEJ, Michal JJ, McLean DJ, Womack JE, Jiang Z. Water buffalo genome science comes of age. Int J Biol Sci 2010; 6:333-49. [PMID: 20582226 PMCID: PMC2892297 DOI: 10.7150/ijbs.6.333] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 06/14/2010] [Indexed: 12/30/2022] Open
Abstract
The water buffalo is vital to the lives of small farmers and to the economy of many countries worldwide. Not only are they draught animals, but they are also a source of meat, horns, skin and particularly the rich and precious milk that may be converted to creams, butter, yogurt and many cheeses. Genome analysis of water buffalo has advanced significantly in recent years. This review focuses on currently available genome resources in water buffalo in terms of cytogenetic characterization, whole genome mapping and next generation sequencing. No doubt, these resources indicate that genome science comes of age in the species and will provide knowledge and technologies to help optimize production potential, reproduction efficiency, product quality, nutritional value and resistance to diseases. As water buffalo and domestic cattle, both members of the Bovidae family, are closely related, the vast amount of cattle genetic/genomic resources might serve as shortcuts for the buffalo community to further advance genome science and biotechnologies in the species.
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Affiliation(s)
- Vanessa N Michelizzi
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 297] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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[Screening and polymorphism of Y chromosome microsatellite markers in swamp buffalo]. YI CHUAN = HEREDITAS 2010; 32:242-7. [PMID: 20233701 DOI: 10.3724/sp.j.1005.2010.00242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To understand the genetic diversity of buffalo Y chromosome, 14 microsatellite markers specific for cattle Y chromosomes were used to analyze 31 male buffaloes of three populations (i.e., HH, BN, and PR) originating from southeastern Yunnan Province, P. R. China. The aim of this study was to examine the practicability of cattle Y chromosome-specific microsatellite markers in studying genetic diversity of buffalo Y chromosome. Three markers (INRA008, UMN0103, and UMN0504) produced single allele, and three (UMN1113, UMN0304, and BC1.2) produced three alleles. But these markers were all monomorphic. Another three markers (UMN0920, UMN0307, and UMN3008) amplified irregular ladder-like bands. These markers were not suitable for investigating the swamp buffalo Y chromosome genetic diversity. The remaining five microsatellites (INRA124, INRA189, BM861, PBR1F1, and UMN2001) were polymorphic, which can be used to study the swamp buffalo Y chromosome genetic diversity. The mean number of alleles (Na), expected heterozygosity (He), genetic diversity (GD), polymorphism information content (PIC), and Shannon's information index (SI) across these five polymorphic loci in the buffalo population samples studied were 2.8000, 0.3998, 0.4144, 0.3245, and 0.5849, respectively, demonstrating a moderate degree of polymorphism in the Y chromosome of the buffalo population.
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Yindee M, Vlamings BH, Wajjwalku W, Techakumphu M, Lohachit C, Sirivaidyapong S, Thitaram C, Amarasinghe AAAWK, Alexander PABDA, Colenbrander B, Lenstra JA. Y-chromosomal variation confirms independent domestications of swamp and river buffalo. Anim Genet 2010; 41:433-5. [PMID: 20219068 DOI: 10.1111/j.1365-2052.2010.02020.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Y-chromosomal variation in the water buffalo was analysed by sequencing of DBY, ZFY and SRY gene segments. A clear separation of the paternal lineages of the river and swamp types parallels the differences between their maternal lineages and nuclear DNA. Sequence divergence was found to be comparable to the divergence of taurine cattle and zebu, and this divergence predated domestication, confirming that river and swamp buffalo originated from different wild populations. Within a sample of 23 Thai swamp buffaloes, we identified four haplotypes with different geographical distributions, two of which were shared by Thai wild buffaloes.
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Affiliation(s)
- M Yindee
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
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31
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Hassan A, El Nahas S, Kumar S, Godithala P, Roushdy K. Mitochondrial D-loop nucleotide sequences of Egyptian river buffalo: Variation and phylogeny studies. Livest Sci 2009. [DOI: 10.1016/j.livsci.2009.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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MacEachern S, McEwan J, Goddard M. Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae). BMC Genomics 2009; 10:177. [PMID: 19393045 PMCID: PMC2694835 DOI: 10.1186/1471-2164-10-177] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 04/24/2009] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The Bovinae subfamily incorporates an array of antelope, buffalo and cattle species. All of the members of this subfamily have diverged recently. Not surprisingly, a number of phylogenetic studies from molecular and morphological data have resulted in ambiguous trees and relationships amongst species, especially for Yak and Bison species. A partial phylogenetic reconstruction of 13 extant members of the Bovini tribe (Bovidae, Bovinae) from 15 complete or partially sequenced autosomal genes is presented. RESULTS We identified 3 distinct lineages after the Bovini split from the Boselaphini and Tragelaphini tribes, which has lead to the (1) Buffalo clade (Bubalus and Syncerus species) and a more recent divergence leading to the (2) Banteng, Gaur and Mithan and (3) Domestic cattle clades. A fourth lineage may also exist that leads to Bison and Yak. However, there was some ambiguity as to whether this was a divergence from the Banteng/Gaur/Mithan or the Domestic cattle clade. From an analysis of approximately 30,000 sites that were amplified in all species 133 sites were identified with ambiguous inheritance, in that all trees implied more than one mutation at the same site. Closer examination of these sites has identified that they are the result of ancient polymorphisms that have subsequently undergone lineage sorting in the Bovini tribe, of which 53 have remained polymorphic since Bos and Bison species last shared a common ancestor with Bubalus between 5-8 million years ago (MYA). CONCLUSION Uncertainty arises in our phylogenetic reconstructions because many species in the Bovini diverged over a short period of time. It appears that a number of sites with ambiguous inheritance have been maintained in subsequent populations by chance (lineage sorting) and that they have contributed to an association between Yak and Domestic cattle and an unreliable phylogenetic reconstruction for the Bison/Yak clade. Interestingly, a number of these aberrant sites are in coding sections of the genome and their identification may have important implications for studying the neutral rate of mutation at nonsynonymous sites. The presence of these sites could help account for the apparent contradiction between levels of polymorphism and effective population size in domesticated cattle.
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Affiliation(s)
- Sean MacEachern
- Primary Industries Research Victoria, Animal Genetics and Genomics, Attwood VIC 3049, Australia
- Latrobe University, Department of Genetics, Bundoora VIC 3086, Australia
- Avian Disease and Oncology Laboratory 3606 E Mt Hope Rd, East Lansing, Mi. 48823, USA
| | - John McEwan
- Animal Genomics, AgResearch, Private Bag 50034, Mosgiel, New Zealand
| | - Mike Goddard
- Primary Industries Research Victoria, Animal Genetics and Genomics, Attwood VIC 3049, Australia
- Melbourne University, School of Agriculture and Food Systems, Melbourne VIC 3000, Australia
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Mishra B, Kataria R, Bulandi S, Prakash B, Kathiravan P, Mukesh M, Sadana D. Riverine status and genetic structure of Chilika buffalo of eastern India as inferred from cytogenetic and molecular marker-based analysis. J Anim Breed Genet 2009; 126:69-79. [DOI: 10.1111/j.1439-0388.2008.00759.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
The domestic buffalo is an indispensable livestock resource to millions of smallholder farmers in developing countries, particularly in Asia. Although its reproductive biology is basically similar to that of cattle, there are important differences and unique characteristics that need to be considered in order to apply modern reproductive technologies to improve its productivity. Under most smallholder production systems, the reproductive efficiency of buffalo is compromised by factors related to climate, management, nutrition and diseases. However, when managed and fed properly, buffalo can have good fertility and provide milk, calves and draught power over a long productive life. The basic technical problems associated with artificial insemination in buffalo were largely overcome two decades ago, but the technology has not had the expected impact in some developing countries, because largely of infrastructural and logistic problems. Approaches involving the use of hormones for treating anoestrus and for synchronizing oestrus have had varying rates of success, depending on the protocols used and the incidence of underlying problems that cause infertility. Embryo technologies such as multiple ovulation embryo transfer, in vitro embryo production, cryopreservation and cloning are being intensively studied but have had far lower success rates than in cattle. Improving the productivity of buffalo requires an understanding of their potential and limitations under each farming system, development of simple intervention strategies to ameliorate deficiencies in management, nutrition and healthcare, followed by judicious application of reproductive technologies that are sustainable with the resources available to buffalo farmers.
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Affiliation(s)
- B M A O Perera
- Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka.
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35
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He DQ, Zhu Q, Chen SY, Wang HY, Liu YP, Yao YG. A homogenous nature of native Chinese duck matrilineal pool. BMC Evol Biol 2008; 8:298. [PMID: 18957137 PMCID: PMC2586638 DOI: 10.1186/1471-2148-8-298] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 10/29/2008] [Indexed: 11/22/2022] Open
Abstract
Background China, with around 30 unique breeds, has a diverse duck genetic pool. Currently, there is no systematic report which investigates the genetic diversity, phylogenetic relationship, and matrilineal genetic structure of these domestic breeds and wild mallards (Anas platyrhynchos). Results In this study, we sequenced the mitochondrial DNA (mtDNA) control region segments in 278 domestic ducks (Anas platyrhynchos domestica) from 19 indigenous breeds/populations and 70 wild mallard samples and analyzed them together with the 101 control region sequences from published sources. Fifty-two samples were then sequenced for a cytochrome b (Cyt b) gene fragment to solidify the pattern emerged from the control region sequences. All domestic duck and wild mallard haplotypes were essentially indistinguishable and were clustered together in the phylogenetic tree. There was no geographic differentiation and breed/population-specific distribution of duck lineages. Conclusion Our results showed that unlike other domesticated farm animals in China such as chicken, cattle, goat, and yak with multiple matrilineal components, the matrilineal pool of Chinese ducks was homogenous.
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Affiliation(s)
- Da-Qian He
- College of Animal Science and Technology, Sichuan Agriculture University, Ya'an, Sichuan, PR China.
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Zhang Y, Sun D, Yu Y, Zhang Y. Genetic diversity and differentiation of Chinese domestic buffalo based on 30 microsatellite markers. Anim Genet 2007; 38:569-75. [DOI: 10.1111/j.1365-2052.2007.01648.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kumar S, Nagarajan M, Sandhu JS, Kumar N, Behl V. Phylogeography and domestication of Indian river buffalo. BMC Evol Biol 2007; 7:186. [PMID: 17915036 PMCID: PMC2140268 DOI: 10.1186/1471-2148-7-186] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 10/04/2007] [Indexed: 05/17/2023] Open
Abstract
Background The water buffalo- Bubalus bubalis holds tremendous potential in livestock sector in many Asian countries, particularly India. The origin, domestication and genetic structure of the Indian river buffalo are poorly understood. Therefore, to understand the relationship among the maternal lineages of Indian river buffalo breeds and their domestication process, we analysed mitochondrial D-loop region of 217 animals representing eight breeds from eight different locations in India along with published sequences of Mediterranean buffalo. Results The maximum parsimony tree showed one major clade with six internal branches. Reduced median network revealed expansion from more than one set of haplotypes indicating complex domestication events for this species. In addition, we found several singleton haplotypes. Using rho statistics, we obtained a time estimate of 6300 years BP for the expansion of one set of hapltoypes of the Indian domestic buffalo. A few breed specific branches in the network indicated an ancient time depth of differentiation of some of the maternal lineages of river buffalo breeds. The multidimensional display of breed pairwise FST values showed significant breed differentiation. Conclusion Present day river buffalo is the result of complex domestication processes involving more than one maternal lineage and a significant maternal gene flow from the wild populations after the initial domestication events. Our data are consistent with the available archaeological information in supporting the proposition that the river buffalo was likely to be domesticated in the Western region of the Indian subcontinent, specifically the present day breeding tracts of the Mehsana, Surati and Pandharpuri breeds.
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Affiliation(s)
- Satish Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
| | - Muniyandi Nagarajan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
| | - Jasmeet S Sandhu
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
| | - Niraj Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
| | - Vandana Behl
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
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