• Journal of Animal Reproduction and Biotechnology
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• v.35 no.2
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• pp.198-206
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• 2020

Food and agricultural production sector, especially livestock production is vital for Mongolia's economic and social development. Domestic sheep play key roles for Mongolians, providing food (meat, milk) and raw materials (wool, sheepskin), but genetic diversity, origin of sheep populations in Mongolia have not been well studied. Studies of population genetic diversity is important research field in conservation and restoration of animal breeds and genetic resources. Therefore, this study aimed to investigate genetic characteristics and estimate origin through the analysis of mitochondrial DNA control region D-loop and Cytochrome b of Mongolian indigenous sheep (Mongolian native, Orkhon and Altanbulag) and one Europe sheep (Suffolk). As a result of there were found, 220 SNPs (Single nucleotide polymorphism) in the D-loop region, 28 SNPs in the Cytochrome B region, furthermore, 77 Haplotypes. The nucleotide diversity was only found in D-loop region (n = 0.0184). Phylogenetic analysis showed that 3 (A, B, and C) of 5 haplogroups of sheep have been identified in our research. Haplogroup C was only found in Mongolian indigenous sheep. Haplogroup D and E were not observed. As a result of haplogroups, haplogroup A was dominant (n = 46 of 94 sheeps), followed by haplogroup B (n = 36) and haplogroup C (n = 12). Sequence analysis showed that T deletion, insertion and heteroplasmy in D-loop region occurred at a high rate in Mongolian indigenous sheep population (T insertion = 47, T deletion = 83). The heteroplasmy, which has never been found in Mongolian sheep, has been newly discovered in this study. As a result, the Mongolian sheep varieties, which mainly derived from Asia, were in hybridization with European sheep varieties.

• Fisheries and Aquatic Sciences
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• v.25 no.3
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• pp.158-166
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• 2022

The complete mitochondrial genome of Tremoctopus violaceus was sequenced to analyze its organization and phylogenetic status within the order Octopoda. The mitochondrial genome of T. violaceus had a structure and organization similar to that of other Octopoda. The content of the nucleotides A, C, G, and T was 31.68 %, 7.71 %, 20.02 %, and 40.58 %, respectively. All protein-coding genes (PCG) began with the ATG codon, excluding ND4 and ATP6, which began with ATC and ATT, respectively, and terminated with TAG, TAA, TA, or T. Codons for isoleucine were the most used codons, whereas those for arginine were used the least. Two extra tRNAs, trnN and trnL, were found in the control region. These tRNAs have a D-armless structure. The control region had excess A + T content (83.16 %) and a stem-loop structure with two elements, which is reported for the first time in Octopoda by our study. Bayesian inference using 13 PCG revealed that Octopus and Octopodidae were polyphyletic, and that Tremoctopodidae diverged relatively earlier within Octopoda. The mitochondrial genome of T. violaceus and its characteristics may help to understand the evolutionary history of Octopoda and establish a marine biodiversity conservation strategy.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.313-315
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• 2007

Seventeen haplotypes were detected from the complete mitochondrial DNA control region sequences analyzed from eighty individuals of two Tibetan domestic sheep breeds. The nucleotide composition of all the sequences was 33.0% A, 29.7%T, 22.9%C and 14.4%G; G+C was 37.3%. The length of the sequences ranged from 1,107 bp to 1,259 bp. The difference between them was primarily due to 3-5 copy numbers of a 75 bp tandem repeat sequence. The NJ phylogenetic tree (the number of replications of bootstrap test is 1,000) presented three major domestic sheep lineages, which suggested that modern Tibetan sheep breeds are derived from three maternal sources.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.4
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• pp.531-538
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• 2020

Objective: Evidence from previous reports indicates that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River. Further research identified two new origin centers for domestic pigs in the Tibetan Plateau and the islands of Southeast Asia. However, due to the small sample size of Tibetan pigs, details of the origin and spread of Tibetan pigs has not yet been established. Methods: We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces. Comprehensive Tibetan pig samples were taken to perform the most detailed analysis of Tibetan pigs to date. Results: The result indicate that Rkaze pigs had the lowest level of diversity, while Changdu pigs had the highest diversity. Interestingly, these two populations were both in the Tibetan Plateau area. If we calculate diversity in terms of each province, the Tibetan Plateau area had the lowest diversity, while the Chinese province of Gansu had the highest diversity. Diversity gradient analysis of major haplotypes suggested three domestication centers of Tibetan pigs in the Tibetan Plateau and the Chinese provinces of Gansu and Yunnan. Conclusion: We found two new domestication centers for Tibetan pigs. One is in the Chinese province of Gansu, which lies in the upstream region of the Yellow River, and the other is in the Chinese province of Yunnan.

• Animal Systematics, Evolution and Diversity
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• v.25 no.3
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• pp.325-329
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• 2009

Lepomis macrochirus from the family Centrarchidae, commonly known as Bluegill sunfish, is an introduced freshwater fish in Korea that thrives in lakes, ponds, reservoirs and rivers. Since its introduction into Korea in 1969, Lepomis macrochirus has rapidly dispersed out and increased in number almost all over the freshwater ecosystems in Korea. Consequently this species causes a severe ecological problem, threatening native fishes due to its omnivorous foraging behaviors upon fish juveniles and many freshwater invertebrates. To address population genetic structure of L. macrochirus, 74 fish samples from 10 populations were collected and compared for their mitochondrial D-loop control region. As the result we found that the genetic diversity of L. macrochirus is extremely low such as resulting only four haplotypes with a few nucleotide differences among them. Analysis of molecular variance (AMOVA) revealed that the source of population genetic variation is largely retained in the comparisons among individuals within populations, while it is relatively low with slight significance at the highest hierarchical group. This distribution pattern differs from what is expected when biogeography is under the influence of natural geographic barriers such as mountain ranges in Korea. Instead the result is accord with the influential role of random spreading events facilitated by local people for aquaculture and fishing, and subsequent dispersals since its single point of introduction into Korea.

• Molecules and Cells
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• v.20 no.1
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• pp.151-156
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• 2005

The phylogeny and geography of the medaka (Oryzias latipes) populations of Korea were investigated by analyzing sequence data for the mitochondrial control region. From the 41 haplotypes including 25 Korean haplotypes detected in 64 Korean specimens and data for the Japanese and Chinese populations, phylogenetic and nested clade analyses were executed to examine the phylogeny of haplogroups and the relation of the genetic architecture of the haplotypes to the historical geography of the Korean medaka fish. The analyses suggest that there are two very distinct lineages of Korean medaka, and that these result from reproductive isolation mechanisms due to geographic barriers. The southeastern lineage has experienced recent range expansion to the western region. The northwestern lineage, sister to Chinese populations, showed evidence of internal range expansion with shared haplotypes.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.5
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• pp.631-639
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• 2016

China has a long history of sheep (Ovis aries [O. aries]) breeding and an abundance of sheep genetic resources. Knowledge of the complete O. aries mitogenome should facilitate the study of the evolutionary history of the species. Therefore, the complete mitogenome of O. aries was sequenced and annotated. In order to characterize the mitogenomes of 3 Chinese sheep breeds (Altay sheep [AL], Shandong large-tailed sheep [SD], and small-tailed Hulun Buir sheep [sHL]), 19 sets of primers were employed to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) sequence of each breed. The sizes of the complete mitochondrial genomes of the sHL, AL, and SD breeds were 16,617 bp, 16,613 bp, and 16,613 bp, respectively. The mitochondrial genomes were deposited in the GenBank database with accession numbers KP702285 (AL sheep), KP981378 (SD sheep), and KP981380 (sHL sheep) respectively. The organization of the 3 analyzed sheep mitochondrial genomes was similar, with each consisting of 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and 1 control region (D-loop). The NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes were encoded on the light strand, whereas the rest of the mitochondrial genes were encoded on the heavy strand. The nucleotide skewness of the coding strands of the 3 analyzed mitogenomes was biased toward A and T. We constructed a phylogenetic tree using the complete mitogenomes of each type of sheep to allow us to understand the genetic relationships between Chinese breeds of O. aries and those developed and utilized in other countries. Our findings provide important information regarding the O. aries mitogenome and the evolutionary history of O. aries inside and outside China. In addition, our results provide a foundation for further exploration of the taxonomic status of O. aries.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.12
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• pp.1905-1911
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• 2020

Objective: Tibetan pigs, an excellent species unique to China, face serious threats, which in turn affects the development and utilization of the outstanding advantages of plateau hypoxia adaptability and reduces their genetic diversity. Therefore, a discussion of measures to conserve this genetic resource is necessary. The method, based on genetic diversity, genetic divergence and total genetic contribution rate of population, reflects the priority conservation order and varies depending on the three different purposes of conservation. Methods: We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces and downloaded 564 mtDNA D-loop sequences from three indigenous pig breeds in Qinghai, Sichuan, and Yunnan Provinces distributed near the Tibetan pigs. Results: We analyzed three different aspects: Changdu Tibetan pigs have the highest genetic diversity, and from the perspective of genetic diversity, the priority conservation is Changdu Tibetan pigs. Hezuo Tibetan pigs have the highest genetic contribution, so the priority conservation is Hezuo Tibetan pigs in the genetic contribution aspect. Rkaze Tibetan pigs were severely affected by indigenous pig breeds, so if considering from the perspective of introgression, the priority conservation is Rkaze Tibetan pigs. Conclusion: This study evaluated genetic diversity and comprehensively assessed conservation priority from three different aspects in nine Tibetan pig populations.

• Korean Journal of Poultry Science
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• v.41 no.4
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• pp.235-240
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• 2014

Recently, the consumption of duck meat has been gradually increased in Korea. However, most of the duck breeds in Korea were imported from overseas. Based on the large demands for the breeding stocks of native ducks, a new project for the commercial use of the Korean native ducks has been launched. For the initial investigation of the relationships between Korean native duck (KND) with other duck breeds, the sequences from D-loop control region in mitochondrial DNA (mtDNA) was used. The results from phylogenetic analysis indicated that both KND and White Commercial Duck (WCD) breeds were classified well with wild duck breeds. However, mallard duck was not discriminated well with KND. The haplotype analysis indicated that KND and WCD have eight different haplotypes with eleven SNPs. Three haplotypes (haplotype 1, 3, 4) were shared both in KND and WCD. On the other hand, haplotype 1 was appeared only KND and haplotype 5, 6, 7, 8 were identified only in WCD population. With further verifications, the results presented here can be used for the conservation and commercialization of the Korean native ducks.

• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.937-946
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• 2004

Duroc is widely used to improve the meat quality and productivity. To elucidate the phylogenetic relation and the sequence specificity for the maternal property, the complete sequence of mitochondrial genome was determined and the population diversity of Duroc was investigated in this study. The length of mtDNA tested is 16,584-bp. There are several insertion/deletion mutations in the control region and coding regions for tRNA and rRNA, respectively, but not in peptide-coding regions. Four peptide-coding genes(COⅡ, COⅢ, ND3 and ND4) showed incomplete termination codon sequences such as T--, and two(ND2 and ND4L) did alternative initiation codons(AIC), respectively. Especially, the initiation codon sequences of ND2 gene were polymorphic in this population. Polymorphisms were detected in 11-bp duplication motif within control region as well as ND2 and CYTB. Variation patterns observed from the tests on three mtDNA regions were linked completely and then two haplotypes obtained from combining the data dividing this population. Duroc mtDNA is observed at the European pig cluster in the phylogenetic tree, however, the results from the population analyses supported previous opinions. This study suggests that the breed Duroc was mainly originated from the European pig lineage, and Asian lineage was also used to form the pig breed Duroc as maternal progenitors.