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Yang L, Han J, Deng T, Li F, Han X, Xia H, Quan F, Hua G, Yang L, Zhou Y. Comparative analyses of copy number variations between swamp buffaloes and river buffaloes. Anim Genet 2023; 54:199-206. [PMID: 36683294 DOI: 10.1111/age.13288] [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: 11/24/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 01/24/2023]
Abstract
As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating FST for genome-wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.
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Affiliation(s)
- Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaotao Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fanfan Quan
- Livestock and Poultry Breeding Center of Hubei Province, Wuhan, China
| | - Guohua Hua
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
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2
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Ermetin O. Evaluation of the application opportunities of precision livestock farming (PLF) for water buffalo ( Bubalus bubalis) breeding: SWOT analysis. Arch Anim Breed 2023; 66:41-50. [PMID: 36756624 PMCID: PMC9901519 DOI: 10.5194/aab-66-41-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023] Open
Abstract
The use of technology in agriculture is increasing daily with the development of technology in all areas. With the help of PLF (precision livestock farming) technologies and efficient use of inputs, economic, environmentally friendly, and better-quality products are obtained. Significantly its use in dairy cattle is increasing daily, contributing to sustainable milk production in both economic and ecological terms. As the demand increased in the world for water buffalo meat, milk, and dairy products, different breeding systems have been applied for more and higher-quality production purposes. This way the number of water buffalo farms breeding in intensive conditions is increasing. It is necessary to investigate the possibilities of using PLF technologies, which are still widespread in dairy cattle, in water buffalo breeding, and to benefit from the advanced technology in this regard. This study aims to discuss the applicability of PLF technologies by surveying buffalo breeders. With the data obtained from the survey results made with the water buffalo breeders, the strengths, opportunities, threats, and effects of the weaknesses were discussed with the SWOT analysis.
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3
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Pineda PS, Flores EB, Herrera JRV, Low WY. Opportunities and Challenges for Improving the Productivity of Swamp Buffaloes in Southeastern Asia. Front Genet 2021; 12:629861. [PMID: 33828581 PMCID: PMC8021093 DOI: 10.3389/fgene.2021.629861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/26/2021] [Indexed: 11/18/2022] Open
Abstract
The swamp buffalo is a domesticated animal commonly found in Southeast Asia. It is a highly valued agricultural animal for smallholders, but the production of this species has unfortunately declined in recent decades due to rising farm mechanization. While swamp buffalo still plays a role in farmland cultivation, this species' purposes has shifted from draft power to meat, milk, and hide production. The current status of swamp buffaloes in Southeast Asia is still understudied compared to its counterparts such as the riverine buffaloes and cattle. This review discusses the background of swamp buffalo, with an emphasis on recent work on this species in Southeast Asia, and associated genetics and genomics work such as cytogenetic studies, phylogeny, domestication and migration, genetic sequences and resources. Recent challenges to realize the potential of this species in the agriculture industry are also discussed. Limited genetic resource for swamp buffalo has called for more genomics work to be done on this species including decoding its genome. As the economy progresses and farm mechanization increases, research and development for swamp buffaloes are focused on enhancing its productivity through understanding the genetics of agriculturally important traits. The use of genomic markers is a powerful tool to efficiently utilize the potential of this animal for food security and animal conservation. Understanding its genetics and retaining and maximizing its adaptability to harsher environments are a strategic move for food security in poorer nations in Southeast Asia in the face of climate change.
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Affiliation(s)
- Paulene S. Pineda
- Philippine Carabao Center National Headquarters and Genepool, Science City of Muñoz, Philippines
| | - Ester B. Flores
- Philippine Carabao Center National Headquarters and Genepool, Science City of Muñoz, Philippines
| | | | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia
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4
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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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5
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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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6
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Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel. Animal 2017; 12:464-471. [PMID: 28735584 DOI: 10.1017/s1751731117001719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Buffalo (Bubalus bubalis) is an important livestock species in many tropical and subtropical regions. In recent decades, the interest in buffalo's milk have expanded and intensive buffalo farms start to emerge. However, breeding programs and population genetics information for this species is scarce or inexistent. The present study aims to test the suitability of the commercial high-density single nucleotide polymorphisms (SNP) genotyping panel, the Illumina BovineHD BeadChip, to estimate population genetics parameters, pedigree control and identification of common variants in major production candidate genes. From a total of 777 962 SNPs included in the panel, 20 479 were polymorphic in water buffalo at a call rate of 86% and an average expected heterozygosity (HE) of 0.306. From these, 357 were mapped within or around the flanking regions of several major candidate genes. A principal components analysis identified three different clusters, each representing pure swamp buffalo type, pure river buffalo type and admixed river buffalo. The hybrids between swamp and river buffalo were clearly identified as an intermediary cluster. The suitability of these SNPs data set for parentage and identity testing demonstrated that the combination of just 30 to 50 SNPs were enough to attain high probabilities of parentage exclusion (0.9999) in both types and identity (2.3×10-5 and 2.0×10-7) for river and swamp buffalo, respectively. Our analysis confirms the suitability of the BovineHD BeadChip to assess population structure, hybridization and identity of the water buffalo populations.
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7
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de Camargo GMF, Aspilcueta-Borquis RR, Fortes MRS, Porto-Neto R, Cardoso DF, Santos DJA, Lehnert SA, Reverter A, Moore SS, Tonhati H. Prospecting major genes in dairy buffaloes. BMC Genomics 2015; 16:872. [PMID: 26510479 PMCID: PMC4625573 DOI: 10.1186/s12864-015-1986-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 10/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Asian buffaloes (Bubalus bubalis) have an important socio-economic role. The majority of the population is situated in developing countries. Due to the scarce resources in these countries, very few species-specific biotechnology tools exist and a lot of cattle-derived technologies are applied to buffaloes. However, the application of cattle genomic tools to buffaloes is not straightforward and, as results suggested, despite genome sequences similarity the genetic polymorphisms are different. RESULTS The first SNP chip genotyping platform designed specifically for buffaloes has recently become available. Herein, a genome-wide association study (GWAS) and gene network analysis carried out in buffaloes is presented. Target phenotypes were six milk production and four reproductive traits. GWAS identified SNP with significant associations and suggested candidate genes that were specific to each trait and also genes with pleiotropic effect, associated to multiple traits. CONCLUSIONS Network predictions of interactions between these candidate genes may guide further molecular analyses in search of disruptive mutations, help select genes for functional experiments and evidence metabolism differences in comparison to cattle. The cattle SNP chip does not offer an optimal coverage of buffalo genome, thereafter the development of new buffalo-specific genetic technologies is warranted. An annotated reference genome would greatly facilitate genetic research, with potential impact to buffalo-based dairy production.
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Affiliation(s)
- G M F de Camargo
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
| | - R R Aspilcueta-Borquis
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
| | - M R S Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - R Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, Brisbane, QLD, 4072, Australia.
| | - D F Cardoso
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
| | - D J A Santos
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
| | - S A Lehnert
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, Brisbane, QLD, 4072, Australia.
| | - A Reverter
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St Lucia, Brisbane, QLD, 4072, Australia.
| | - S S Moore
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4067, Australia.
| | - H Tonhati
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Professor Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil.
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8
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Hirayama H, Kageyama S, Moriyasu S, Sawai K, Minamihashi A. Embryo sexing and sex chromosomal chimerism analysis by loop-mediated isothermal amplification in cattle and water buffaloes. J Reprod Dev 2014; 59:321-6. [PMID: 23965599 PMCID: PMC3944364 DOI: 10.1262/jrd.2013-028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In domestic animals of the family Bovidae, sex preselection of offspring has been
demanded for convenience of milk/beef production and animal breeding. Development of the
nonsurgical embryo transfer technique and sexing methods of preimplantation embryos made
it possible. Sexing based on detection of Y chromosome-specific DNA sequences is
considered the most reliable method to date. PCR enables amplification of a target
sequence from a small number of blastomeres. However, it requires technical skill and is
time consuming. Furthermore, PCR has the risk of false positives because of DNA
contamination during handling of the PCR products in duplicate PCR procedures and/or
electrophoresis. Therefore, for embryo sexing to become widely used in the cattle embryo
transfer industry, a simple, rapid and precise sexing method needs to be developed.
Loop-mediated isothermal amplification (LAMP) is a novel DNA amplification method, and the
reaction is carried out under isothermal conditions (range, 60 to 65 C) using DNA
polymerase with strand displacement activity. When the target DNA is amplified by LAMP, a
white precipitate derived from magnesium pyrophosphate (a by-product of the LAMP reaction)
is observed. It is noteworthy that LAMP does not need special reagents or electrophoresis
to detect the amplified DNA. This review describes the development and application of an
embryo sexing method using LAMP in cattle and water buffaloes.
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Affiliation(s)
- Hiroki Hirayama
- Animal Biotechnology Group, Animal Research Center, Hokkaido Research Organization, Hokkaido 081-0038, Japan
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9
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Dubey PK, Goyal S, Kumari N, Mishra SK, Arora R, Kataria RS. Genetic diversity within 5'upstream region of Toll-like receptor 8 gene reveals differentiation of riverine and swamp buffaloes. Meta Gene 2013; 1:24-32. [PMID: 25606371 PMCID: PMC4205041 DOI: 10.1016/j.mgene.2013.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 08/30/2013] [Accepted: 08/30/2013] [Indexed: 12/20/2022] Open
Abstract
In this study the nucleotide diversity in the 5'untranslated region (UTR) of TLR8 gene in riverine as well as swamp buffaloes has been described. Analysis of the 5'UTR of TLR8 gene showed presence of two SNPs in this region, g.-139G>T and g.-128A>G. A PCR-RFLP assay designed for genotyping of g.-139G>T SNP across 667 samples from 2 buffalo populations revealed a striking difference in allele frequency distribution across the swamp and riverine buffaloes. The frequency of T allele was higher in swamp buffalo as compared to riverine buffalo, ranging from 0.71 to 1. The G allele on the other hand exhibited a higher frequency across all the Indian riverine buffalo breeds/populations. The principal component analysis revealed separate clusters for the riverine and swamp buffaloes, as expected; however, the riverine type Assamese buffalo population of eastern India formed a distinct cluster. Since most of the buffalo populations in the eastern region are swamp type, this demarcation may be related to the difference in immune response in riverine and swamp buffaloes. These preliminary results indicate that the genetic variation observed in 5'upstream region of TLR8 gene, which differentiates swamp and riverine buffalo, needs to be further explored for association with disease susceptibility in buffalo, an important dairy and meat animal of Southeast Asia.
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Affiliation(s)
- P K Dubey
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - S Goyal
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - N Kumari
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - S K Mishra
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R Arora
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R S Kataria
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
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10
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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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11
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Kumar S, Nagarajan M, Sandhu JS, Kumar N, Behl V, Nishanth G. Mitochondrial DNA analyses of Indian water buffalo support a distinct genetic origin of river and swamp buffalo. Anim Genet 2007; 38:227-32. [PMID: 17459014 DOI: 10.1111/j.1365-2052.2007.01602.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water buffalo (Bubalus bubalis) is broadly classified into river and swamp categories, but it remains disputed whether these two types were independently domesticated, or if they are the result of a single domestication event. In this study, we sequenced the mitochondrial D-loop region and cytochrome b gene of 217 and 80 buffalo respectively from eight breeds/locations in northern, north-western, central and southern India and compared our results with published Mediterranean and swamp buffalo sequences. Using these data, river and swamp buffalo were distinguished into two distinct clades. Based upon the existing knowledge of cytogenetic, ecological and phenotypic parameters, molecular data and present-day distribution of the river and swamp buffalo, we suggest that these two types were domesticated independently, and that classification of the river and swamp buffalo as two related subspecies is more appropriate.
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Affiliation(s)
- S Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
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12
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Hirayama H, Kageyama S, Takahashi Y, Moriyasu S, Sawai K, Onoe S, Watanabe K, Kojiya S, Notomi T, Minamihashi A. Rapid sexing of water buffalo (Bubalus bubalis) embryos using loop-mediated isothermal amplification. Theriogenology 2006; 66:1249-56. [PMID: 16672158 DOI: 10.1016/j.theriogenology.2006.03.036] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Accepted: 03/19/2006] [Indexed: 11/23/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a novel DNA amplification method that amplifies a target sequence specifically under isothermal conditions. The objective of this study was to identify a Y chromosome-specific sequence in water buffalo and to establish an efficient procedure for embryo sexing by LAMP. The homologues of a Y chromosome-specific sequence, bovine repeat Y-associated.2, in swamp and river buffalo were cloned, and designated swamp buffalo repeat Y-associated.2 and river buffalo repeat Y-associated.2, respectively. Sexing by LAMP was performed using primers for swamp buffalo repeat Y-associated.2. A 12S rRNA was also amplified by LAMP as a control reaction in both male and female. The minimal amount of the template DNA required for LAMP appeared to be 0.1-10 pg. The sensitivity was further examined using swamp buffalo fibroblasts as templates. When fibroblasts were lysed with NaOH, the minimal cell number required for detection of both male-specific and male-female common DNA appeared to be two cells, whereas correct determination of sex could not be achieved using fibroblasts lysed by heat denaturation. Embryo sexing was also performed using blastomeres from interspecies nuclear transfer embryos. The sex determined by LAMP for blastomeres corresponded with the sex of nuclear donor cells in analyses using four or five blastomeres as templates. The LAMP reaction required only about 45 min, and the total time for embryo sexing, including DNA extraction, was about 1 h. In conclusion, the present procedure without thermal cycling and electrophoresis was reliable and applicable for water buffalo embryos.
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Affiliation(s)
- Hiroki Hirayama
- Hokkaido Animal Research Center, Shintoku, Hokkaido 081-0038, Japan.
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