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Haplotype Diversity of Swamp Buffalo and River Buffalo Based on Cytochrome B Gene: A Study of Meta-Analysis

Tropical Animal Science Journal · Vol. 44 No. 4 (2021) · hlm. 399–407

DOI
10.5398/tasj.2021.44.4.399
ISSN
2615-790X, 2615-787X
Terbit
2021-11-12
Penerbit
Faculty of Animal Science, IPB University
Bahasa
eng

Abstrak

Buffalo (Bubalus bubalis) is well known as a domesticated buffalo in Asia. The genetic diversity of buffaloes in Asia needs to be studied to ensure a proper breeding program. A meta-analysis study on the cytochrome b gene of the mitochondrial genome from various published data was conducted to evaluate genetic variation and haplo-geography of Asian buffaloes. A meta-analysis is used to provide a comprehensive view of the data. A total of 1369 swamp buffaloes Cytochrome B sequences (from Indonesia (79), Bangladesh (98), China (909), India (4), Laos (96), Taiwan (29), Thailand (54), and Vietnam (100)) and 91 river buffaloes (from China (42), Nepal (42), and Pakistan (7)) were used in this study. Cytochrome B sequences (678 bp) of Syncerus caffer, Bubalus arnee, Bubalus depressicornis, Bubalus quarlesi, Bubalus mindorensis, swamp buffalo, and river buffalo were determined for their haplotypes using DnaSP v6 program. Haplotypes were analyzed by Principal Coordinate Analysis (PCoA) using Adegenet Package and Hierarchical Clustering on Principal Components (HCPC) methods using Factoextra and FactoMineR Package in R-4.0.0 program. Bayesian analysis of genetic differentiation was implemented in BAPS 6.0. Furthermore, we found 56 haplotypes for swamp buffaloes in eight Asian countries and 5 haplotypes for river buffaloes in Pakistan. We also found 5 haplotypes for outgroup (B. arnee, S. caffer, B. depressicornis, B. quarlesi, B. mindorensis). Therefore, we found 66 haplotypes in total with outgroup sequences. Based on the PCoA results, three clusters were found. However, the HCPC found eight clusters. Based on HCPC, countries in East and South Asia have four maternal lineages. This is evidence that buffalo domestication has first occurred in East-South Asia. In conclusion, we found four maternal lineages of swamp buffalo and two maternal lineages of river buffalo from ten countries. We also found one maternal lineage for Syncerus caffer and one maternal lineage for B. depressicornis, B. quarlesi, and B. mindorensis.

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  • IPB University
  • Universitas Halu Oleo
  • National Research and Innovation Agency
  • Indonesian Agency for Agricultural Instruments Standardization
  • Universitas Djuanda
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  • Organisasi berbeda
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Rekan penulisOrganisasiArtikel bersama
Asep GunawanIPB University16
Jakaria JakariaIPB University12
Ronny Rachman NoorIPB University10
La Ode NafiuUniversitas Halu Oleo8
Anneke AnggraeniNational Research and Innovation Agency8
Achmad FarajallahIPB University8
Eryk AndreasIPB University7
Sri MurtiniIPB University6
Isyana KhaerunnisaNational Research and Innovation Agency6
Muhammad Amrullah PagalaUniversitas Halu Oleo5
Kasita ListyariniIPB University5
Niken UlupiIPB University5
Ratna Sholatia HarahapIPB University4
Ismeth InounuIPB University4
Iman SupriatnaIPB University4
SubandriyoUniversitas Djuanda4
Eko HandiwirawanNational Research and Innovation Agency4
Dedy Duryadi SolihinIPB University4
Achmad Selamet AkuUniversitas Halu Oleo3
Arief BoedionoIPB University3
Irma Isnafia AriefIPB University3
Raden Iis ArifiantiniIPB University3
Tike SartikaNational Research and Innovation Agency3
Takdir SailiUniversitas Halu Oleo2
Deki ZulkarnainUniversitas Halu Oleo2
Dewi Apri AstutiIPB University2
Sri DarwatiIPB University2
Musram AbadiUniversitas Halu Oleo2
Yamin YaddiAfiliasi tidak diketahui2
Surahmanto SurahmantoAfiliasi tidak diketahui2
Takdir SailiAfiliasi tidak diketahui2
Rusli BadaruddinUniversitas Halu Oleo2
Astriana NapirahUniversitas Halu Oleo2
Rahim AkaUniversitas Halu Oleo2

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Sumber metadata: OAI-PMH (metadata jurnal) https://journal.ipb.ac.id/index.php/tasj/oai, pertama di-harvest 10 Nov 2026, terakhir terlihat 10 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en">Haplotype Diversity of Swamp Buffalo and River Buffalo Based on Cytochrome B Gene: A Study of Meta-Analysis</dc:title>
	<dc:creator xml:lang="en">Saputra, F.</dc:creator>
	<dc:creator xml:lang="en">Anggraeni, A.</dc:creator>
	<dc:creator xml:lang="en">Ishak, A. B. L.</dc:creator>
	<dc:creator xml:lang="en">Hafid, A.</dc:creator>
	<dc:creator xml:lang="en">Rusdin, M.</dc:creator>
	<dc:creator xml:lang="en">Sumantri, C.</dc:creator>
	<dc:subject xml:lang="en">haplotype diversity</dc:subject>
	<dc:subject xml:lang="en">swamp buffalo</dc:subject>
	<dc:subject xml:lang="en">cytochrome b</dc:subject>
	<dc:subject xml:lang="en">meta-analysis</dc:subject>
	<dc:description xml:lang="en">Buffalo (Bubalus bubalis) is well known as a domesticated buffalo in Asia. The genetic diversity of buffaloes in Asia needs to be studied to ensure a proper breeding program. A meta-analysis study on the cytochrome b gene of the mitochondrial genome from various published data was conducted to evaluate genetic variation and haplo-geography of Asian buffaloes. A meta-analysis is used to provide a comprehensive view of the data. A total of 1369 swamp buffaloes Cytochrome B sequences (from Indonesia (79), Bangladesh (98), China (909), India (4), Laos (96), Taiwan (29), Thailand (54), and Vietnam (100)) and 91 river buffaloes (from China (42), Nepal (42), and Pakistan (7)) were used in this study. Cytochrome B sequences (678 bp) of Syncerus caffer, Bubalus arnee, Bubalus depressicornis, Bubalus quarlesi, Bubalus mindorensis, swamp buffalo, and river buffalo were determined for their haplotypes using DnaSP v6 program. Haplotypes were analyzed by Principal Coordinate Analysis (PCoA) using Adegenet Package and Hierarchical Clustering on Principal Components (HCPC) methods using Factoextra and FactoMineR Package in R-4.0.0 program. Bayesian analysis of genetic differentiation was implemented in BAPS 6.0. Furthermore, we found 56 haplotypes for swamp buffaloes in eight Asian countries and 5 haplotypes for river buffaloes in Pakistan. We also found 5 haplotypes for outgroup (B. arnee, S. caffer, B. depressicornis, B. quarlesi, B. mindorensis). Therefore, we found 66 haplotypes in total with outgroup sequences. Based on the PCoA results, three clusters were found. However, the HCPC found eight clusters. Based on HCPC, countries in East and South Asia have four maternal lineages. This is evidence that buffalo domestication has first occurred in East-South Asia. In conclusion, we found four maternal lineages of swamp buffalo and two maternal lineages of river buffalo from ten countries. We also found one maternal lineage for Syncerus caffer and one maternal lineage for B. depressicornis, B. quarlesi, and B. mindorensis.</dc:description>
	<dc:publisher xml:lang="en">Faculty of Animal Science, IPB University</dc:publisher>
	<dc:date>2021-11-12</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://journal.ipb.ac.id/tasj/article/view/32724</dc:identifier>
	<dc:identifier>10.5398/tasj.2021.44.4.399</dc:identifier>
	<dc:source xml:lang="en">Tropical Animal Science Journal; Vol. 44 No. 4 (2021): Tropical Animal Science Journal; 399-407</dc:source>
	<dc:source>2615-790X</dc:source>
	<dc:source>2615-787X</dc:source>
	<dc:source>10.5398/tasj.2021.44.4</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://journal.ipb.ac.id/tasj/article/view/32724/22485</dc:relation>
	<dc:rights xml:lang="en">Copyright (c) 2021 Tropical Animal Science Journal</dc:rights>
</oai_dc:dc>