• 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.

• Journal of Life Science
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• v.23 no.1
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• pp.24-30
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• 2013

The purpose of this study was to identify genetic polymorphisms of the mitochondrial cytochrome b (mtDNA cyt b) gene in Korean black (KB) cattle breed and to analyze the genetic relationship between the KB and other breeds. We determined the complete sequence of the mtDNA cyt b gene in 38 KB cattle. We also analyzed their genetic diversity, and phylogenetic analysis was performed by comparison with Korean cattle (KC, called Hanwoo) and breeds from China and Japan. A nucleotide substitution was detected in the KB cattle, and two haplotypes were defined. In the neighbor-joining (NJ) tree, the haplotypes of KB were located in Bos taurus lineage with those of KC, Japanese black (JB), Yanbian and Zaosheng breeds. However, the haplotypes of Chinese breeds, excluding Yanbian and Zaosheng, were separated into B. taurus and B. indicus lineages. In the NJ tree of breeds based on Dxy genetic distances, Chinese breeds mixed with B. taurus and B. indicus lineages were located between B. indicus and B. taurus lineages. KB was contained within B. taurus lineage and was determined to be genetically more closely related to two Chinese (Yanbian and Zaosheng) breeds than to KC and JB. The haplotype distribution and the results of the phylogenetic analysis suggest that KB and KC have genetic differences in their mtDNA cyt b gene sequences.

• Korean Journal of Plant Taxonomy
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• v.45 no.3
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• pp.254-261
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• 2015

Genetic variations of Abies koreana and Abies nephrolepis were assessed using two mitochondrial DNA regions (nad5 intron 4 and nad5 intron 1) for 16 natural populations to understand their phylogeographical history. Seven polymorphic sites of the two combined regions resulted in the resolution of four haplotypes (M1-M4). The average gene diversity within the population ($H_S$) was 0.098, the total gene diversity ($H_T$) was 0.620, and the interpopulation differentiation was $G_{ST}=0.841$, $N_{ST}=0.849$. The populations were divided into three groups (northern area, central area, southern area) according to their geographic locations. The populations of the northern and southern areas were mostly fixed for M1 and M2, respectively. The populations of the central area showed the highest levels of gene diversity ($H_T=0.654$) due to introgression from the northern area and southern area. The presence of a single mtDNA haplotype in the southern area suggests that current widespread populations have expanded to the central area from a specific refugium population after the last glacial period.

• Parasites, Hosts and Diseases
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• v.51 no.1
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• pp.55-59
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• 2013

Twelve 924 bp cytochrome c oxidase subunit 1 (cox1) mitochondrial DNA sequences from Taenia asiatica isolates from Thailand were aligned and compared with multiple sequence isolates from Thailand and 6 other countries from the GenBank database. The genetic divergence of T. asiatica was also compared with Taenia saginata database sequences from 6 different countries in Asia, including Thailand, and 3 countries from other continents. The results showed that there were minor genetic variations within T. asiatica species, while high intraspecies variation was found in T. saginata. There were only 2 haplotypes and 1 polymorphic site found in T. asiatica, but 8 haplotypes and 9 polymorphic sites in T.saginata. Haplotype diversity was very low, 0.067, in T. asiatica and high, 0.700, in T. saginata. The very low genetic diversity suggested that T. asiatica may be at a risk due to the loss of potential adaptive alleles, resulting in reduced viability and decreased responses to environmental changes, which may endanger the species.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.8
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• pp.1048-1052
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• 2011

The Chinese Holstein cattle breed, an introduced breed in China, has been crossbred with native cattle breeds. We hypothesised that the Chinese Holstein local population in Beijing share haplotypes with native Asian cattle breeds, the result of a sudden population expansion in the recent past. We also hypothesised that crossbreeding and population expansion left traces that shaped the genetic makeup of the breed. Evaluation of this was performed by mitochondrial DNA (mtDNA) sequence analysis of Chinese Holstein cattle from Beijing (n = 41) and a comparison of them with the published mtDNA sequences (n = 293) of 14 Asian breeds with an emphasis on Chinese native cattle breeds. Three shared common haplotypes between Chinese Holstein cattle and native Asian cattle were found. Moreover, a high level of haplotype diversity in Chinese Holstein cattle (h = 0.9557) and low nucleotide diversity (${\pi}$ = 0.0052) was found, indicating a past population bottleneck followed by rapid population growth. These findings are supported by the significantly negative deviation of Tajima's D (-1.82085), the star-like pattern of dominant haplotypes and the pairwise mismatch distribution analysis, which showed a unimodal pattern.

• Fisheries and Aquatic Sciences
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• v.15 no.1
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• pp.49-56
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• 2012

Genetic variation in the Asian shore crab Hemigrapsus sanguineus was determined from partial mitochondrial DNA (mtDNA) sequences of the cytochrome b (Cytb) gene. Samples included 143 crabs from six localities along three coastlines in South Korea. A nucleotide sequence analysis revealed 38 variable sites in a 470-bp sequence, which defined 37 haplotypes. The haplotypes were not associated geographically and had a shallow genealogy. Pairwise $F_{ST}$ tests and a two-dimensional scaling analysis revealed no significant genetic differentiation among most of the populations. The low pairwise comparison values, but significant genetic differentiation of a northeastern population from all other populations, might have been influenced by a restriction in gene flow caused by hydrographic conditions such as ocean boundaries. The high haplotype diversity, low nucleotide diversity, and time since H. sanguineus expansion in Korean coastal waters indicate rapid population growth and a recent, sudden expansion in the Late Pleistocene.

• Animal cells and systems
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• v.14 no.3
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• pp.197-206
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• 2010

The population structure of brown sole was examined in a total of 308 samples collected from three geographical groups: one locality (Gangneung) on the east side of the Korean Peninsula, two localities (Erimo and Tomakomai) on the southeastern side and four localities (Onishika, Teshio, Tomamae and Yoichi) on the northwestern side of Hokkaido Island, Japan, by using sequences of 484 bp from the 5' end of the control region of mtDNA. We detected 225 haplotypes, but 183 of them were unique to an individual. A total of 116 nucleotide sites were variable. Haplotype diversity (h) was very high, ranging from 0.989 to 1.000, and nucleotide diversity (${\pi}$) was detected between 0.015 and 0.022. Genetic distances (${\Phi}_{ST}$) within populations, among populations and among geographical groups were low (0.0002 to 0.0014). No significant difference was detected by the AMOVA test (P < 0.05). Pairwise $F_{ST}$ values between sampling localities were also low and not significant. Genetic differentiation was not detected among sampling localities.

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

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.216-216
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• 2022

The starch-branching enzymes (BEs) are responsible for synthesizing the amylopectin, which plays an important role in determining the structural and physical properties of starch granules. BE has two differently functioning isoforms (BEI and BEIIa/b) based on their difference in the chain-length pattern by the degree of polymerization (DP), which mainly contributes to the amylopectin chain length distribution in starch biosynthesis. In this study, we investigated functional haplotypes and evolutionary analyses of SBE1 in 374 rice accessions (320 Korean bred and 54 wild). The analyses were performed based on the classified subpopulations. Haplotype analysis generates a total of 8 haplotypes, of which only four haplotypes were functional carrying four functional SNPs in four different exons of SBE1 on chromosome 6. Nucleotide diversity analysis showed a highest pi-value in aromatic group (0.0029), while the lowest diversity value was in temperate japonica (0.0002), indicating the signal of this gene evolution origin. Different directional selections could be estimated by negative Tajima's D value of temperate japonica (-1.1285) and positive Tajima's D value of tropical japonica (0.9456), where the selective sweeps were undergone by both positive purifying and balancing selections. Phylogenetic analysis indicates a closer relationship of the wild with most of the cultivated subgroups indicating a common ancestor for SBE1 gene. FST-values indicate distant genetic relationships of temperate japonica from all other classified groups. PCA and population structure analysis show an admixed structure of wild and cultivated subpopulations in some proportions.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.217-217
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• 2022

Pullulanase (PUL), a debranching enzyme, has been utilized in hydrolyzing the a-1,6 glucosidic linkages in starch, amylopectin, pullulan, as well as related oligosaccharides. It has also been indicated that PUL is a novel indicator of inherent RS (Resistant Starch) formation in rice. In this study, we performed haplotype analysis on 320 bred rice accessions, and additional 54 wild accessions were added to study genetic diversity along with other population-based analyses of the PUL gene. Through these investigations, we summarized a total of 10 functional (non-synonymous) SNPs from 7 different exons on chromosome 4. There were 10 haplotypes, of which only six haplotypes were functional, implicating different subpopulations. Diversity reduction was noticed in temperate japonica (0.0005) compared to the highest one (aus, 0.0154), illustrating their higher genetic differentiation by F_ST-value (0.926). The highest Tajima^ D value was observed in indica (3.6613), indicating PUL gene domestication signature under balancing selection, while the lowest Tajima's D value was found in temperate japonica (-2.2191) which might have undergone under positive selection and purified due to the excess of rare alleles. PCA, population structure, and phylogenetic analyses provide information on the genetic relatedness between and or among the cultivated subpopulations and the wild based on PUL genomic region.