Polymorphism of mitochondrial DNA (mtDNA) in cattle and buffaloes

Bhat, P. N.; Mishra, Bina

doi:10.1007/bf02401421

Cited by 26 publications

(24 citation statements)

References 10 publications

(5 reference statements)

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“…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%

Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

Chung¹

2013

OJGen

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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.

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Section: Discussionmentioning

confidence: 99%

Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

Chung¹

2013

OJGen

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“…Most previous studies examining differences in bovine mtDNA, with the exception of studies such as those by Loftus et al (1994a), Mannen et al (1998Mannen et al ( , 2000 and Cymbron et al (1999), have traditionally used polymorphism in restriction enzyme cleavage pattern (e.g., Watanabe et al 1985Watanabe et al , 1989Bhat et al 1990;Kikkawa et al 1995;Parfitt and Huismans 1998). These studies were successful in revealing breed differences but, as RFLP analysis cannot identify variation that is present at sites other than those specific for restriction enzyme cleavage, a fair amount of variation was probably missed by these studies.…”

Section: Discussionmentioning

confidence: 99%

“…The Holstein cattle were only recognized as a separate breed from the Friesian nearly 80 yr ago; therefore the variability between the two breeds was expected to be narrow. Bhat et al (1990) and Watanabe et al (1985) characterized variations in mtDNA restriction enzyme cleavage patterns within and between various European, North American, Indian and Asian cattle breeds. Similarly, Loftus et al (1994a, b) have demonstrated, using both restriction fragment length polymorphism (RFLP) analysis of mtDNA and mtDNA D-loop sequence variation, that while numerous differences among and within breeds can be identified, sequence variation between European and African (Bos taurus) cattle breeds is not significant enough to point to more than one major mitochondrial lineage.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity among Canadienne, Brown Swiss, Holstein and Jersey cattle based on mitochondrial D-loop sequence variation

Hansen

Shrestha²,

Parker³

et al. 2003

Can. J. Anim. Sci.

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[39][40][41][42][43][44]. Polymorphisms creating 36 unique haplotypes were observed within breeds at 55 sites in the displacement loop (Dloop) region of the mitochondrial DNA (mtDNA) consisting of 814 bp. The majority (56%) of the differences observed were the result of nucleotide substitution events with 19 transitions, 12 transversions, 11 deletions, 12 insertions and 1 inversion. In all cases, the insertions and deletions were of a single nucleotide. Canadienne cattle were found to have 60% unique haplotypes within the population compared to 89% in Brown Swiss, 90% in Holstein and 100% in Jersey cattle, possibly reflecting the narrow genetic base in the Canadienne breed. The degree of sequence divergence in the D-loop region of mtDNA was based on samples from 20 Canadienne, 9 Brown Swiss, 10 Holstein and 10 Jersey cattle and a phylogenetic analysis showed that these cattle (Bos taurus) were not evolutionarily distinct. All four breeds grouped together when a strict consensus tree was generated. Intra-breed variability proved to be high for the Canadienne, Holstein and Jersey breeds (57-73%) but not the Brown Swiss breed (29%). The Canadienne and Brown Swiss (45%), and Brown Swiss and Holstein (43%) showed the lowest degree of inter-breed variability. The greatest variability among the four breeds was between Canadienne and Jersey (80%) cattle. These findings question the validity of phenotypic assessment of genetic diversity, such as Canadienne cattle being described as "Black Jersey". Les auteurs ont dénombré 36 haplotypes uniques attribuables au polymorphisme intra-racial à 55 endroits de la boucle D de l'ADN mitochondrial (ADNmt), sur laquelle on retrouve 814 paires de bases. La plupart des variations (56 %) observées résul-tent de la substitution de nucléotides, en l'occurrence une transition (19 cas), une transversion (12 cas), une suppression (11 cas), une insertion (12 cas) ou une inversion (1 cas). Les insertions et les suppressions n'affectent toujours qu'un nucléotide. La race Canadienne présente 60 % d'haplotypes uniques au sein de sa population, contre 89 % pour les Suisse brune, 90 % pour les Holstein et 100 % pour les Jersey, ce qui illustre peut-être son étroite base génétique. Le degré de divergence des séquences sur la boucle D de l'ADNmt a été établi au moyen des échantillons prélevés de 20 sujets Canadienne, 9 Suisse brune, 10 Holstein et 10 Jersey. Une analyse phylogéné-tique révèle que les animaux (Bos taurus) ne sont pas distincts sur le plan de l'évolution. En effet, les quatre races se retrouvent ensemble quand on produit un arbre de consensus strict. Il existe bien une forte variation intra-raciale pour les sujets Canadienne, Holstein et Jersey (de 57 à 73 %), mais pas pour ceux de la race Suisse brune (29 %). Les sujets Canadienne et Suisse brune (45 %) ainsi que Suisse brune et Holstein (43 %) présentent le plus faible degré de variation inter-raciale. Des quatre races, ce sont les races Canadienne et Jersey qui montrent la plus grande variabilité entre elles (80 %). Ces résultats ...

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“…It can also act as a weak transcriptional regulator in the absence of Gal3p [11]. When grown on a medium, where galactose is present as a sole carbon source, null mutants for GAL1 are unable to metabolize galactose and grow [12, 13]. This protein shares a high similarity of 90% in amino acids with Gal3p [12].…”

Section: Introductionmentioning

confidence: 99%

Comparative modeling and genomics for galactokinase (Gal1p) enzyme

Sharma¹,

Malakar²

2011

Bioinformation

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The Gal1p (Galactokinase) protein is known for regulation of D-galactose metabolism. It catalyzes the formation of galactose -1-phosphate from alpha – D-galactose, which is an important step in galactose catabolism. The knowledge of Gal1p protein structure, its protein interacting partners and enumeration of functional site residues will provide great insight in understanding the functional role of Gal1p. These studies are lacking in case of the Gal11p kinase enzyme. Structure of this enzyme has already been determined in S. cerevisiae, however, no structural information for this protein is available for K. lactis and E. coli. We used the homology modeling based approach to model the structures of Gal1p for K. lactis and E. coli. Furthermore, functional residues were predicted for these Gal1 proteins and the strength of interaction between Gal1p and other Gal proteins was determined by protein–protein interaction studies via patchdock software. The interaction studies revealed that the affinity for Gal1p for other Gal proteins varies in different organisms. Sequence and structural based comparison of Gal1p kinase enzyme showed that the orthologs in K.lactis and S. cervisiae are more similar to each other as compared to the ortholog in E. coli. These studies carried out by us will help in better understanding of the galactose metabolism. Our sequence and structure comparison studies revealed that Human Gal1p shows more homology for Gal1p protein of E. coli. The above studies may be applied to Human Gal1p, where it can help in gaining useful insight into Galactosemia disease.

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Polymorphism of mitochondrial DNA (mtDNA) in cattle and buffaloes

Cited by 26 publications

References 10 publications

Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle

Genetic diversity among Canadienne, Brown Swiss, Holstein and Jersey cattle based on mitochondrial D-loop sequence variation

Comparative modeling and genomics for galactokinase (Gal1p) enzyme

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