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Ahlawat S, Sharma U, Chhabra P, Arora R, Sharma R, Singh KV, Vijh RK. Maternal genetic diversity and phylogenetic analysis of Indian riverine and swamp buffaloes: insights from complete mitochondrial genomes. Mamm Genome 2024; 35:390-398. [PMID: 38888811 DOI: 10.1007/s00335-024-10048-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
This study explored the genetic diversity and evolutionary history of riverine and swamp buffaloes in India, utilizing complete mitochondrial genome sequences. Through comprehensive sampling across varied agro-climatic zones, including 91 riverine buffaloes from 12 breeds and 6 non-descript populations, along with 16 swamp buffaloes of the Luit breed, this study employed next-generation sequencing techniques to map the mitogenomic landscape of these subspecies. Sequence alignments were performed with the buffalo mitochondrial reference genome to identify mitochondrial DNA (mtDNA) variations and distinct maternal haplogroups among Indian buffaloes. The results uncovered the existence of 212 variable sites in riverine buffaloes, yielding 67 haplotypes with high haplotype diversity (0.991), and in swamp buffaloes, 194 variable sites resulting in 12 haplotypes, displaying haplotype diversity of 0.950. Phylogenetic analyses elucidated the genetic relationships between Indian buffaloes and the recognized global haplogroups, categorizing Indian swamp buffaloes predominantly into the SA haplogroup. Intriguingly, the haplogroup SB2b was observed for the first time in swamp buffaloes. Conversely, riverine buffaloes conformed to established sub-haplogroups RB1, RB2, and RB3, underscoring the notion of Northwestern India as a pivotal domestication site for riverine buffaloes. The study supports the hypothesis of independent domestication events for riverine and swamp buffaloes, highlighting the critical role of genetic analysis in unraveling the complex evolutionary pathways of domestic animals. This investigation contributes to the global understanding of buffalo mitogenome diversity, offering insights into this important livestock species' domestication and dispersal patterns.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - R K Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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El Sabry M, Almasri O. Space allowance: a tool for improving behavior, milk and meat production, and reproduction performance of buffalo in different housing systems-a review. Trop Anim Health Prod 2022; 54:266. [PMID: 35970907 PMCID: PMC9378332 DOI: 10.1007/s11250-022-03247-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/29/2022] [Indexed: 11/26/2022]
Abstract
Buffalo population has dramatically increased during the last two decades, especially in tropical and subtropical regions. Although buffalo are important milk and meat-producing animal, still practices of buffalo farming and welfare aspects are not well established. Housing system and stocking density are significant factors that affect the welfare and production of animals; however, no space allowance standards have been demonstrated for buffalo at different ages. This review article presents the following: (1) an overview of buffalo subtypes and the geographical distribution of buffalo populations and their production; (2) the effect of housing systems and space allowance on the social behavior and welfare indices; (3) the effects of space allowance on milk production and growth performance of buffalo; and (4) the relationship between space allowance and reproductive performance. Although the limited data in this area of research, it can be driven that a larger space allowance with access to a pool, especially during the hot season, maintains buffalo production at optimal levels. Moreover, optimal floor space improves the welfare and social indices of buffalo; however, there are discrepancies in aggressive and agonistic behavior results. Surprisingly, the reproductive performance of buffalo was not affected by space allowance. Therefore, further research is needed to identify the impact of the housing aspects, including space allowance and enrichment tools, on the productive performance, and welfare indices of buffalo. This would assist in implementing welfare-economic standards for buffalo production and reveal the potentiality of this eco-friendly animal.
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Affiliation(s)
- Mohamed El Sabry
- Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamma street, Giza, 12613, Egypt.
| | - Obaida Almasri
- Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamma street, Giza, 12613, Egypt.,General Commission for Scientific Agricultural Research, Damascus, Syria
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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: 53] [Impact Index Per Article: 13.3] [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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Sun T, Wang S, Hanif Q, Chen N, Chen H, Lei C. Genetic diversity of mitochondrial cytochrome b gene in swamp buffalo. Anim Genet 2020; 51:977-981. [PMID: 32910515 DOI: 10.1111/age.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/12/2020] [Accepted: 08/18/2020] [Indexed: 11/26/2022]
Abstract
The swamp buffalo (Bubalus carabanensis) is mainly bred for meat, transport and rice cultivation in China and Southeast Asian countries. In the current study, we investigated the genetic diversity, maternal origin and phylogenetic relationship of swamp buffalo by analyzing 1,786 mitochondrial cytochrome b (cytb) sequences from China, Vietnam, Laos, Thailand, India and Bangladesh. Our results indicated that the swamp buffalo can be divided into two major lineages (SA and SB with the sublineages) and three rare lineages (SC, SD and SE), which showed strong geographic differentiation. The SA1 lineage represented a major domestication event, which involved population expansion. Regions III and V showed higher haplotype diversity than the other regions, indicating that the regions of Southwest China and IndoChina are potential domestication centers for the swamp buffalo. In addition, the swamp buffalo showed a closer phylogenetic relationship to tamaraw. In conclusion, our findings revealed a high level of genetic diversity and the phylogenetic pattern of the swamp buffalo.
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Affiliation(s)
- T 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
| | - S 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
| | - Q Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 577, Pakistan.,Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - N 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
| | - H 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
| | - C 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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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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7
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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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Harun-Or-Rashid M, Sarkar AK, Hasan MMI, Hasan M, Juyena NS. Productive, reproductive, and estrus characteristics of different breeds of buffalo cows in Bangladesh. J Adv Vet Anim Res 2019; 6:553-560. [PMID: 31819886 PMCID: PMC6882708 DOI: 10.5455/javar.2019.f382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/02/2019] [Accepted: 09/09/2019] [Indexed: 11/30/2022] Open
Abstract
Objective: The objective of this research work is to know the productive and reproductive performances and problems of local, crossbred, Nilli, and Murrah buffalo cows in selected study areas in Bangladesh. Methodology: A total of 1,241 local, crossbred, Nilli, and Murrah buffalo cows were surveyed in the selected areas with a pre-set questionnaire. Among 1,241 buffalo cows, 112 buffalo cows were randomly selected at day 0 of the estrus cycle for studying ovarian features. Results: Results showed that the average age, body condition score, and body weight were significantly (p < 0.05) different among the studied breeds. Milk production in Murrah and lactation length in Nilli cows were significantly (p < 0.05) higher than indigenous, crossbred, Nilli, and indigenous, crossbred, Murrah buffalo cows, respectively. Results also illustrated that sexual maturity, estrus cycle length, insemination time after the onset of estrus, and gestation length insignificantly (p > 0.05) varied among the surveyed breed. But, the fallout of the study denoted that estrus duration, first calving age, parity number, number of service per conception, calving interval, and voluntary waiting period varied significantly (p < 0.05) in different breeds. Ovarian physiological characteristics such as vaginal electrical resistance, average number of follicles in two ovaries, and largest follicular diameter, estrogen, and progesterone at day 0 of the estrus cycle of local, crossbred, Nilli, and Murrah buffalo cows showed insignificantly (p > 0.05) differences. Conclusion: The study will help the veterinarian and researcher to identify the constraints for the reproductive efficiency of buffalo in Bangladesh.
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Affiliation(s)
- Mohammad Harun-Or-Rashid
- Department of Surgery and Obstetrics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Anup Kumar Sarkar
- Department of Surgery and Obstetrics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mir Md Iqbal Hasan
- Department of Surgery and Obstetrics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Moinul Hasan
- Department of Surgery and Obstetrics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Nasrin Sultana Juyena
- Department of Surgery and Obstetrics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
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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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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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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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12
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Ren M, Wu F, Zou Y, Tu Y, Wang D, Li LY, Zhang HJ, Wang JM, Lin Q. Molecular characterization of Sarcocystis species isolated from Chinese buffaloes in Guizhou province based on 18S rRNA and cox1 sequences. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1507630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Mei Ren
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province, People’s Republic of China
| | - Fei Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
| | - Yong Zou
- Animal Diseases Control & Prevention Centre of Guanling Autonomous County, Anshun, Guizhou province, People’s Republic of China
| | - Ya Tu
- Animal Diseases Control & Prevention Centre of Guanling Autonomous County, Anshun, Guizhou province, People’s Republic of China
| | - Dan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
| | - Lu-Yao Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
| | - Hui-Jun Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
| | - Jia-Ming Wang
- Animal Diseases Control & Prevention Centre of Qiannan, Duyun, Guizhou province, People’s Republic of China
| | - Qing Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province, People’s Republic of China
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13
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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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14
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Abstract
Null hypothesis significance testing (NHST) is the most common statistical framework used by scientists, including archaeologists. Owing to increasing dissatisfaction, however, Bayesian inference has become an alternative to these methods. In this article, we review the application of Bayesian statistics to archaeology. We begin with a simple example to demonstrate the differences in applying NHST and Bayesian inference to an archaeological problem. Next, we formally define NHST and Bayesian inference, provide a brief historical overview of their development, and discuss the advantages and limitations of each method. A review of Bayesian inference and archaeology follows, highlighting the applications of Bayesian methods to chronological, bioarchaeological, zooarchaeological, ceramic, lithic, and spatial analyses. We close by considering the future applications of Bayesian statistics to archaeological research.
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Affiliation(s)
| | - Melissa G. Torquato
- Department of Anthropology, Purdue University, West Lafayette, Indiana 47907, USA;,
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15
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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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16
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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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17
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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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18
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Deng T, Pang C, Lu X, Zhu P, Duan A, Tan Z, Huang J, Li H, Chen M, Liang X. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PLoS One 2016; 11:e0147132. [PMID: 26766209 PMCID: PMC4713091 DOI: 10.1371/journal.pone.0147132] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/29/2015] [Indexed: 01/11/2023] Open
Abstract
The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.
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Affiliation(s)
- Tingxian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Chunying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xingrong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Peng Zhu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Anqin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Zhengzhun Tan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Jian Huang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Hui Li
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Mingtan Chen
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xianwei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
- * E-mail:
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19
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Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle. DIVERSITY-BASEL 2014. [DOI: 10.3390/d6010178] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Li LF, Wang HY, Zhang C, Wang XF, Shi FX, Chen WN, Ge XJ. Origins and domestication of cultivated banana inferred from chloroplast and nuclear genes. PLoS One 2013; 8:e80502. [PMID: 24260405 PMCID: PMC3832372 DOI: 10.1371/journal.pone.0080502] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Cultivated bananas are large, vegetatively-propagated members of the genus Musa. More than 1,000 cultivars are grown worldwide and they are major economic and food resources in numerous developing countries. It has been suggested that cultivated bananas originated from the islands of Southeast Asia (ISEA) and have been developed through complex geodomestication pathways. However, the maternal and parental donors of most cultivars are unknown, and the pattern of nucleotide diversity in domesticated banana has not been fully resolved. METHODOLOGY/PRINCIPAL FINDINGS We studied the genetics of 16 cultivated and 18 wild Musa accessions using two single-copy nuclear (granule-bound starch synthase I, GBSS I, also known as Waxy, and alcohol dehydrogenase 1, Adh1) and two chloroplast (maturase K, matK, and the trnL-F gene cluster) genes. The results of phylogenetic analyses showed that all A-genome haplotypes of cultivated bananas were grouped together with those of ISEA subspecies of M. acuminata (A-genome). Similarly, the B- and S-genome haplotypes of cultivated bananas clustered with the wild species M. balbisiana (B-genome) and M. schizocarpa (S-genome), respectively. Notably, it has been shown that distinct haplotypes of each cultivar (A-genome group) were nested together to different ISEA subspecies M. acuminata. Analyses of nucleotide polymorphism in the Waxy and Adh1 genes revealed that, in comparison to the wild relatives, cultivated banana exhibited slightly lower nucleotide diversity both across all sites and specifically at silent sites. However, dramatically reduced nucleotide diversity was found at nonsynonymous sites for cultivated bananas. CONCLUSIONS/SIGNIFICANCE Our study not only confirmed the origin of cultivated banana as arising from multiple intra- and inter-specific hybridization events, but also showed that cultivated banana may have not suffered a severe genetic bottleneck during the domestication process. Importantly, our findings suggested that multiple maternal origins and a reduction in nucleotide diversity at nonsynonymous sites are general attributes of cultivated bananas.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
| | - Hua-Ying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Cui Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Xin-Feng Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Feng-Xue Shi
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Wen-Na Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
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