• 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.

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

• The Korean Journal of Physiology and Pharmacology
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• v.24 no.6
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• pp.463-472
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• 2020

Direct reprogramming, also known as a trans-differentiation, is a technique to allow mature cells to be converted into other types of cells without inducing a pluripotent stage. It has been suggested as a major strategy to acquire the desired type of cells in cell-based therapies to repair damaged tissues. Studies related to switching the fate of cells through epigenetic modification have been progressing and they can bypass safety issues raised by the virus-based transfection methods. In this study, a protocol was established to directly convert fully differentiated fibroblasts into diverse mesenchymal-lineage cells, such as osteoblasts, adipocytes, chondrocytes, and ectodermal cells, including neurons, by means of DNA demethylation, immediately followed by culturing in various differentiating media. First, 24 h exposure of 5-azacytidine (5-aza-CN), a well-characterized DNA methyl transferase inhibitor, to NIH-3T3 murine fibroblast cells induced the expression of stem-cell markers, that is, increasing cell plasticity. Next, 5-aza-CN treated fibroblasts were cultured in osteogenic, adipogenic, chondrogenic, and neurogenic media with or without bone morphogenetic protein 2 for a designated period. Differentiation of each desired type of cell was verified by quantitative reverse transcriptase-polymerase chain reaction/western blot assays for appropriate marker expression and by various staining methods, such as alkaline phosphatase/alizarin red S/oil red O/alcian blue. These proposed procedures allowed easier acquisition of the desired cells without any transgenic modification, using direct reprogramming technology, and thus may help make it more available in the clinical fields of regenerative medicine.

• ALGAE
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• v.33 no.2
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• pp.157-166
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• 2018

Cryptic species complexes are increasingly recognized in phycological research, obscuring taxonomy and raising questions about factors influencing speciation. A recent exploration of kelp genetic diversity on Haida Gwaii, British Columbia revealed the existence of a new species, Saccharina druehlii, which is cryptic with Saccharina sessilis. This suggests that molecular investigations further north may be required to elucidate the taxonomy and evolutionary history of this lineage. Although, for several decades, S. sessilis was considered a single highly variable species, its taxonomy has been far from straightforward. In particular, Hedophyllum subsessile (Areschoug) Setchell is now recognized as a synonym of S. sessilis in North America, but as a growth form of Saccharina bongardiana in Far East Russia. To resolve this taxonomic confusion, we sequenced mitochondrial (CO1-5P) and nuclear (internal transcribed spacer) markers of S. sessilis populations from the Aleutian Islands, Alaska, USA. Interestingly, none of our sequences matched S. sessilis sensu stricto. Instead, CO1-5P sequences from populations in the central and eastern Aleutians matched exactly S. druehlii with increasing sequence divergence occurring westward. Samples from Attu, the western-most island, composed a genetic group that clearly represents Kjellman's concept of Hafgygia bongardiana f. subsessilis and is distinct enough from S. druehlii and S. sessilis to potentially constitute a distinct species. Therefore, Saccharina subsessilis comb. nov. is proposed for this entity. Our results suggest the existence of a species complex at the crown node of S. sessilis and thus further investigation of Saccharina in Alaskan waters should be conducted to reconstruct the evolutionary history of this fascinating lineage.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.257-257
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• 2022

Late blight, caused by the hemibiotrophic oomycete pathogen Phytophthora infestans, has been the most important disease limiting potato production worldwide. P. infestans undergo major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to divide the 86 South Korea isolates into six clonal lineages: KR_1_A1, KR_2_A2, SIB-1, US-11, SIB-1 like, and KR-2 like. We documented the emergence of a new lineage, termed SIB-1 like, and KR-2 like, and their rapid replacement of other lineages to exceed 35% of the pathogen population across South Korea. Genome analyses of the Korean P. infestans populations revealed extensive genetic polymorphism, particularly in effector genes. Importantly, SIB-1 like isolates carry an intact Avr8 effector gene that triggers resistance in potato carrying the corresponding R immune receptor gene R8 cloned from Solarium demissum. These findings point toward a strategy for deploying genetic resistance to mitigate the impact of the SIB-1 like lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics. Further study is being done on pathogenicity of the SIB-1 like isolates on cultivated potatoes and changes in expression patterns of disease effector genes within the SIB-1 like isolates

• Korean Journal of Plant Taxonomy
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• v.37 no.4
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• pp.323-333
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• 2007

The degree to which parallel evolution utilizes the same genetic mechanisms indicates the degree to which developmental processes constrain or channel phenotypic evolution. A transgenetic strategy was used to elucidate the role of one floral meristem identity gene, LEAFY (LFY), in the evolution of rosette flowering, a plant architecture that has evolved in parallel in several lineages of the mustard family, Brassicaceae. The LFY genes from three rosette flowering species were cloned and introduced into a species with the ancestral architecture, and results indicated that changes at the LFY locus contributed to the evolution of rosette flowering in two of the three lineages, but that in each lineage a different set of genetic partners was involved. Also, LFY was shown to play a role in the evolution of flower size. Transgenetic strategy may be useful in the study of plant morphological evolution and parallelism.

• Journal of Veterinary Science
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• v.24 no.3
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• pp.40.1-40.6
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• 2023

Analysis of the VP1 gene sequence of the foot and mouth disease virus (FMDV) is critical to understanding viral evolution and disease epidemiology. A standard set of primers have been used for the detection and sequence analysis of the VP1 gene of FMDV directly from suspected clinical samples with limited success. The study validated VP1-specific degenerate primer-based reverse transcription polymerase chain reaction (RT-PCR) for the qualitative detection and sequencing of serotype O FMDV lineages circulating in India. The novel degenerate primer-based RT-PCR amplifying the VP1 gene can circumvent the genetic heterogeneity observed in viruses after cell culture adaptation and facilitate precise viral gene sequence analysis from clinical samples.

• 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.

• Parasites, Hosts and Diseases
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• v.53 no.2
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• pp.237-242
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• 2015

Analysis of ancient DNA (aDNA) extracted from Ascaris is very important for understanding the phylogenetic lineage of the parasite species. When aDNAs obtained from a Joseon tomb (SN2-19-1) coprolite in which Ascaris eggs were identified were amplified with primers for cytochrome b (cyt b) and 18S small subunit ribosomal RNA (18S rRNA) gene, the outcome exhibited Ascaris specific amplicon bands. By cloning, sequencing, and analysis of the amplified DNA, we obtained information valuable for comprehending genetic lineage of Ascaris prevalent among pre-modern Joseon peoples.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.2
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• pp.163-170
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• 2013

In order to analyze the genetic diversity and phylogenetic status of the Korean Chikso breed, we determined sequences of mtDNA cytochrome b (cyt b) gene and performed phylogenetic analysis using 239 individuals from 5 Chikso populations. Five non-synonymous mutations of a total of 15 polymorphic sites were identified among 239 cyt b coding sequences. Thirteen haplotypes were defined, and haplotype diversity was 0.4709 ranging from 0.2577 to 0.6114. Thirty-five haplotypes (C1-C35) were classified among 9 Asia and 3 European breeds. C2 was a major haplotype that contained 206 sequences (64.6%) from all breeds used. C3-C13 haplotypes were Chikso-specific haplotypes. C1 and C2 haplotypes contained 80.5% of cyt b sequences of Hanwoo, Yanbian, Zaosheng and JB breeds. In phylogenetic analyses, the Chikso breed was contained into B. taurus lineage and was genetically more closely related to two Chinese breeds than to Korean brown cattle, Hanwoo. These results suggest that Chikso and Hanwoo have a genetic difference based on the mtDNA cyt b gene as well as their coat color, sufficient for classification as a separate breed.