Genetic variants of ribosomal DNA and mitochondrial DNA between swamp and river buffaloes

Amano, Takashi; Miyakoshi, Yasuyuki; Takada, Toyoyuki; Kikkawa, Yoshiaki; Suzuki, Hitoshi

doi:10.1111/j.1365-2052.1994.tb00400.x

Cited by 34 publications

(26 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Therefore, finding genetic markers have been focused on mtDNA, improving availabilities of abundant mutation sites to perform population studies and identifying individuals as well as breeds. Before applying SNP in genetic studies, RFLP (restriction fragment length polymorphism) analysis using restriction enzymes [10][11][12][13] was firstly reported as genetic variants by Laipis et al [14]. After development of sequencing technology, SNP are the most major markers to differentiate individual characterizations.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

Chung¹

2013

OJGen

View full text Add to dashboard Cite

This study was aimed to preserve mitochondria from liver tissues of Korean native cattle (KNC) as genetic resources and to analyze phylogenetic relationships among cattle breeds using the whole sequences of mtDNA. Mitochondria of KNC has been isolated with the alkaline lysis procedure using 1 g of liver tissues, and measurements showed numbers of cells (2.64 × 10 10 ), concentration (114.6 ug/ml), proteins (0.278 ug/ml), and absorbance (0.029) in 260 nm. Mitochondrial DNAs (mtDNA) were extracted from the isolated mitochondria to determine whole sequences that can be used to estimate genetic distances among cattle breeds. Designing of primers based on the bovine mtDNA sequence was resulted in 16 primer sets covering the whole mtDNA regions. The analysis of 40 KNC mtDNA sequences revealed 69 polymorphic sites that were less than the average number of SNP (single nucleotide polymorphism) for other populations (82 sites) in this study. As expected, the highest observation of SNPs was found in the D-loop region, and a total of 29 SNPs were shared between cattle populations. The haplotype analysis, which used 13 SNPs located in D-loop, COX2, ND5, CYTB, and non coding regions, revealed that KNC showed clearly different haplotypes that may be used to distinguish KNC from other breeds as well as to characterize individual identifications. The phylogenetic analysis revealed that KNC showed a relatively close genetic distance with Japanese black cattle (JBC) comparing with other breeds. Estimations of the average nucleotide diversity (0.0008) and the ratio of transition/ transversion (0.1050) of KNC were placed somewhere in the middle of genetic diversity among cattle breeds. The identified genetic variants and results of phylogenetic analysis will help understanding the phylogenetic relationships of KNC and provide useful genetic information for further studies regarding SNPs in mtDNA regions.

show abstract

Section: Discussionmentioning

confidence: 99%

“…Individual sequences were aligned to find genetic variants with the Seqman program of DNAstar version 6.0. The haplotype analysis was conducted to find genetic differences and to distinguish breed specificities using commonly observed 13 …”

Section: Sequencing and Phylogenetic Analysismentioning

confidence: 99%

Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

Chung¹

2013

OJGen

View full text Add to dashboard Cite

show abstract

“…5). (Buckland 1985;Allard et al 1992;Amano et al 1994) of the common ancestors of the Bovini (domestic cow, the water buffalo, and other catflelike species), the Bovidae (cattle, water buffalo, sheep, and goat), and the Ruminantia (Bovidae, deer, giraffe, and chevrotain, but not the camels).…”

Section: Satellitesmentioning

confidence: 99%

Evolution and recombination of bovine DNA repeats

et al. 1995

View full text Add to dashboard Cite

The history of the abundant repeat elements in the bovine genome has been studied by comparative hybridization and PCR. The Bov-A and Bov-B SINE elements both emerged just after the divergence of the Camelidae and the true ruminants. A 31-bp subrepeat motif in satellites of the Bovidae species cattle, sheep, and goat is also present in Cervidae (deer) and apparently predates the Bovidae. However, the other components of the bovine satellites were amplified after the divergence of the cattle and the Caprinae (sheep and goat). A 23-bp motif, which as subrepeat of two major satellites occupies 5% of the cattle genome, emerged only after the split of the water buffalo and other cattle species. During the evolution of the Bovidae the satellite repeat units were shaped by recombination events involving subrepeats, other satellite components, and SINE elements. Differences in restriction sites of homologous satellites indicate a continuing rapid horizontal spread of new sequence variants.

show abstract

“…Domestication of river buffalo most likely took place in the Indian subcontinent 15 , whereas swamp buffalo was proposed to originate from the border region between south China and north Indochina 6, 17 . However, the fragmentary buffalo mtDNA sequences from rDNA, COII, and cytochrome b loci reported to date 5–7, 18 , confound quantitative inferences of population history. So far two swamp buffalo mitogenomes (NC006295/AY702618 and JN632607) and one river buffalo mitogenome (AF547270) were deposited in GenBank.…”

Section: Introductionmentioning

confidence: 99%

Whole Mitogenomes Reveal the History of Swamp Buffalo: Initially Shaped by Glacial Periods and Eventually Modelled by Domestication

Wang

Chen

Capodiferro

et al. 2017

Sci Rep

View full text Add to dashboard Cite

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.

show abstract

Genetic variants of ribosomal DNA and mitochondrial DNA between swamp and river buffaloes

Cited by 34 publications

References 22 publications

Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

Evolution and recombination of bovine DNA repeats

Whole Mitogenomes Reveal the History of Swamp Buffalo: Initially Shaped by Glacial Periods and Eventually Modelled by Domestication

Contact Info

Product

Resources

About