• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.21
• /
• pp.9283-9289
• /
• 2014

Background: Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children and represents approximately 25% of cancer diagnoses among those younger than 15 years of age. Materials and Methods: This study investigated alterations in the displacement loop (d-loop) region of mitochondrial DNA (mtDNA) as a risk factor and diagnostic biomarker for early detection and diagnosis of acute lymphoblastic leukemia. Using mtDNA from 23 subjects diagnosed with acute lymphoblastic leukemia, the first 450 bp of the d-loop region were amplified and successfully sequenced. Results: This revealed 132 mutations at 25 positions in this region, with a mean of 6 alterations per subject. The d-loop alterations in mtDNA in subjects were all identified as single nucleotide polymorphisms in a homoplasmic distribution pattern. Mutant alleles were observed in all subjects with individual frequency rates of up to 95%. Thirteen mutant alleles in the d-loop region of mtDNA occurred with a high frequency. Novel alleles and locations were also identified in the d-loop of mtDNA as follows: 89 G insertions (40%), 95 G insertions (13%), 182 C/T substitutions (5%), 308 C insertions (19%), and 311 C insertions (80%). The findings of this study need to be replicated to be confirmed. Conclusions: Further investigation of the relationship between mutations in mitochondrial d-loop genes and incidence of acute lymphoblastic leukemia is recommended.

• Asian-Australasian Journal of Animal Sciences
• /
• v.25 no.7
• /
• pp.921-926
• /
• 2012

In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G), indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G). The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.

• Asian-Australasian Journal of Animal Sciences
• /
• v.22 no.7
• /
• pp.955-961
• /
• 2009

The aim of this study was to determine the specific polymorphic sites in cattle breeds and inter- and interbreed genetic variation among breeds and to develop a databank of Turkish native cattle mtDNA using sequence analysis. The entire D-loop region was analyzed based on DNA sequences in Turkish Grey, East Anatolian Red, South Anatolian Red, and Anatolian Black native breeds. In total, 68 nucleotide differences were observed at 26 different sites. The variable positions consisted of 22 transitions, two transversions, and two insertions, but no deletions. Haplotype number, haplotype diversity, nucleotide diversity, and mean number of pairwise difference values were found to be 17, 0.993, 0.00478, and 4.275, respectively. In addition, a phylogeny was developed by comparison among cattle populations for which the entire D-loop sequence was available. A high level of genetic variation was observed within and among the native cattle breeds.

• Asian-Australasian Journal of Animal Sciences
• /
• v.29 no.12
• /
• pp.1688-1695
• /
• 2016

The maternally inherited mitochondrial DNA (mtDNA) D-loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D-loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.4
• /
• pp.471-476
• /
• 2007

Little is known about the origin and genetic diversity of swamp buffaloes in China. To obtain more knowledge on genetics of the water buffalo in China, the complete mitochondrial D-loop sequences of 30 samples from 6 native types were investigated. The results revealed 12 mitochondrial haplotypes with 50 polymorphic sites. Among these polymorphic sites, there were 49 transitions and 1 transversion. The average nucleotide diversity and haplotype diversity estimated from mtDNA D-loop region in 6 Chinese water buffalo types were 0.00684 and 0.798, respectively, showing rather abundant mitochondrial genetic diversity. The Neighbor-Joining (NJ) tree of mtDNA of Chinese water buffaloes was constructed according to the 12 haplotypes. The NJ tree indicated two lineages being designated lineage A and lineage B, in which lineage A was predominant, and lineage B was at low frequency. The new lineage B was first discovered and defined in 6 Chinese water buffalo types. These results showed that two different maternal lineages were involved in the origin of domestic swamp buffaloes in China and the lineage B was probably an introgression from Southeast Asian buffaloes.

• Animal Bioscience
• /
• v.35 no.7
• /
• pp.949-954
• /
• 2022

Objective: The present study is aimed at phenotypic characterization and mitochondrial d-loop analysis of indigenous "Diara" buffalo population, which are mostly confined to the villages on the South and North Gangetic marshy plains in the Bihar state of India. These buffaloes are well adapted and are best suited for ploughing and puddling the wet fields meant for paddy cultivation. Methods: Biometric data on 172 buffaloes were collected using a standard flexible tape measure. Animals are medium in size; the typical morphometric features are long head with a broad forehead and moderately long and erect ears. Genomic DNA was isolated from unrelated animals. The mtDNA d-loop 358-bp sequence data was generated and compared with 338 sequences belonging to riverine and swamp buffaloes. Results: Based on the mitochondrial d-loop analysis the Diara buffaloes were grouped along with the haplotypes reported for riverine buffalo. Sequence analysis revealed the presence of 7 mitochondrial D loop haplotypes with haplotype diversity of 0.9643. Five of the haplotypes were shared with established swamp breeds and with Buffalo population of Orissa in India. Conclusion: Morphometric analyses clearly shows distinguishing features like long and broad forehead which may be useful in identification. The germplasm of Diara buffalo is much adapted to the marshy banks of river Ganga and its tributaries. It constitutes a valuable genetic resource which needs to be conserved on priority basis.

• Food Science of Animal Resources
• /
• v.25 no.2
• /
• pp.218-225
• /
• 2005

This study was performed to determine sequence variation and RFLP of the mt DNA D-loop region using Southern blot hybridization analysis and to develop mt DNA marker affecting milk production traits in Hanwoo cows. The PCR was used to amplify an 1142 bp fragment within the D-loop region of mt DNA using specific primers. Mt DNA were digested with seven restriction enzymes and hybridized using DIG-labeled D-loop probe. The mt DNA RFLP polymorphisms were observed in the four enzymes, BamHI, RsaI, XbaI and HpaII. Nucleotide substitutions were detected at positions 441 (G/C), 469 (T/C), 503 (C/T), 569 (G/A), 614 (C/A) and 644 (C/T) of the mt DNA D-loop region between two selected lines. Significant relationship between the XbaI RFLP type and breeding value was found(p<0.05). Cows with A type had higher estimated breeding values than those with B type (P<0.05) between high and low milk production lines. Therefore, the RFLP marker of mt DNA could be used as a selection assisted tool for individuals with high milk producing ability in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
• /
• v.17 no.11
• /
• pp.1484-1490
• /
• 2004

Mitochondrial DNA haplotypes from the displacement-loop (D-loop) region (436 bp) were genotyped and sequenced in Japanese Black beef cattle raised in the same herd. Correlation coefficients between mitochondrial DNA haplotypes, maternal lineage, birth weight, preweaning average daily gain, weaning weight, post weaning average daily gain and yearling weight were computed. The objective was to study the relationship between maternal and postnatal growth traits and to investigate if postnatal growth of calves to yearling age could be accurately predicted from mitochondrial DNA haplotypes. Results of the phylogenetic analysis revealed 17 maternal lineages and four mitochondrial DNA haplotypes. There were strong, positive and highly significant (p<0.001) correlations among maternal traits ranging from 0.52 to 0.98. Similarly, among postnatal growth traits, most of the correlations were also strong, positive and highly significant (p<0.001); the highest correlation of 0.94 was between preweaning average daily gain and weaning weight. However, correlations between mitochondrial DNA haplotypes and postnatal growth traits were very low, mostly negative and non-significant (p>0.05) ranging from -0.05 to 0.1. Prediction of postnatal growth from mitochondrial DNA yielded very low $R^{2}$ values ranging from 0.002 to 0.019. It was concluded that mitochondrial DNA polymorphism has no significant association with postnatal growth from birth to yearling age, and by implication, nuclear rather than cytoplasmic DNA, accounts for most of the genetic variation observed in postnatal growth of Japanese Black cattle. Therefore, mitochondrial DNA genotyping at an early age has no bearing on the accurate prediction of the future growth performance of calves.

• Journal of Life Science
• /
• v.20 no.12
• /
• pp.1859-1866
• /
• 2010

It is reported that about 80% of deer antlers (Cervi Pantotricuhum Cornu) produced in the world are consumed in Korea. Fraudulent replacement or mislabeling of costly deer antlers with cheaper ones, however, is one of the most common problems in the Korean deer antler market. Therefore, there is a continuous need for the development of genetic markers to discriminate between genuine and fraudulent deer antlers. This study was performed to develop a method for the identification and authentication of deer antlers using nucleotide sequence analysis against displacement loop of mitochondrial genome among four deer antlers, Cervus eleaphus sibericus, Cervus eleaphus bactrianus, Cervus eleaphus Canadensis, and Cervus eleaphus, originated from Russia, China, North America and New Zealand, respectively. As a result, multiple-alignment of mitochondrial displacement (D) loop region in 1.2 kb showed that, among the four deer antlers, a deleted sequence of about 70 bps was only found in Cervus elaphus bactrianus from China. Finally, Cervus elaphus bactrianus among nine samples of deer antlers were successfully identified by PCR using primer amplifying deleted D-loop. Cervus elaphus bactrianus was also confirmed from cloning the PCR products and their nucleotide sequence analyses were confirmed. However, no marker to identify Cervus eleaphus sibericus, Cervus eleaphus canadensis and Cervus eleaphus were found in the nucleotide sequences of mitochondrial D-loop. Our results suggest that PCR for deleted D-loop region of mitochondrial DNA are useful for identification and authentication of deer antlers of Cervus elaphus bactrianus originating from China.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.10
• /
• pp.1478-1484
• /
• 2007

To determine the origin and genetic diversity of Red Chittagong (RC) cattle in Bangladesh, we analyzed mitochondrial DNA displacement loop (D-loop) sequences of 48 samples along with 22 previously published sequences from Bos indicus and Bos taurus breeds. Twenty five haplotypes were identified in RC cattle that were defined by 44 polymorphic sites and nucleotide diversity was $0.0055{\pm}0.0026$. The estimated sequence divergence times between RC and other zebu cattle breeds studied ranged between 22,700-26,900 years before present (YBP) which, it is suggested, predate domestication of RC cattle. Furthermore, it is assumed that introgressions have occurred in this breed mainly from Indian zebu breeds in the recent millennia. The phylogenetic studies showed RC cattle clustered with Bos indicus lineage with two distinct haplogroups representing high genetic variability of this breed. These findings can be used for designing proper breeding and conservation strategies for RC cattle in Bangladesh.