• Journal of Plant Biotechnology
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• v.48 no.1
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• pp.34-43
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• 2021

Targeted genome editing using the CRISPR/Cas9 system is a ground-breaking technology that is being widely used to produce plants with useful traits. However, for woody plants, only a few successful attempts have been reported. These successes have used Agrobacterium-mediated transformation, which has been reported to be very efficient at producing genetically modified trees. Nonetheless, there are unresolved problems with plasmid sequences that remain in the plant genome. In this study, we demonstrated a DNA-free genome editing technique in which purified CRISPR/Cas9 ribonucleoproteins (RNPs) are delivered directly to the protoplasts of a hybrid poplar (Populus alba × Populus glandulosa). We designed three single-guide RNAs (sgRNAs) to target the stress-associated protein 1 gene (PagSAP1) in the hybrid poplar. Deep sequencing results showed that pre-assembled RNPs had a more efficient target mutagenesis insertion and deletion (indel) frequency than did non-assembled RNPs. Moreover, the RNP of sgRNA3 had a significantly higher editing efficacy than those of sgRNA1 and sgRNA2. Our results suggest that the CRISPR/Cas9 ribonucleoprotein-mediated transfection approach is useful for the production of transgene-free genome-edited tree plants.

• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.217-225
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• 2021

The family Platycephalidae is a taxonomic group of economically important demersal flathead fishes that predominantly occupy tropical or temperate estuaries and coastal environments of the Indo-Pacific oceans and the Mediterranean Sea. In this study, we for the first time analyzed the complete mitochondrial genome (mitogenome) of the flathead Platycephalus cultellatus Richardson, 1846 from Vietnam by Next Generation Sequencing method. Its mitogenome was 16,641 bp in total length, comprising 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The gene composition and order of the mitogenome were identical to those of typical vertebrates. The phylogenetic trees were reconstructed based on the concatenated nucleotide sequence matrix of 13 PCGs and the partial sequence of a DNA barcoding marker, cox1 in order to determine its molecular phylogenetic position among the order Scorpaeniformes. The phylogenetic result revealed that P. cultellatus formed a monophyletic group with species belonging to the same family and consistently clustered with one nominal species, P. indicus, and two Platycephalus sp. specimens. Besides, the cox1 tree confirmed the taxonomic validity of our specimen by forming a monophyletic clade with its conspecific specimens. The mitogenome of P. cultellatus analyzed in this study will contribute valuable information for further study on taxonomy and phylogeny of flatheads.

• Research in Plant Disease
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• v.28 no.4
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• pp.231-236
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• 2022

Oxypetalum coeruleum, commonly known as Tweedia, is a perennial herbaceous plant of the Apocynaceae family native to southern Brazil and Uruguay. Tweedia plants are grown as one of the most popular ornamental flowers for floral arrangement in Korea. In May 2021, several tweedia plants in a single greenhouse in Gimje, Jeollabuk-do were found to show virus-like symptoms including necrotic rings, vein-clearing, chlorotic mottle, and mosaic on the leaves, and necrosis on the stems. Here, we have identified tomato spotted wilt virus (TSWV) in symptomatic tweedia leaves by applying high-throughput RNA sequencing. In the result, a single infection by TSWV was verified without mixed infections of different virus species. To confirm the presence of TSWV, a reverse transcription polymerase chain reaction was performed with a specific primer set to the N gene of TSWV. The complete genomic sequence of L, M, and S segments of TSWV 'Oxy' isolate were determined and deposited in GenBank under accession numbers LC671525, LC671638, and LC671639, respectively. In the phylogenetic tree analysis by maximum likelihood method, 'Oxy' isolate showed a high relationship with TSWV 'Gumi' isolate from Gerbera jamesonii in Gyeongsangbuk-do, Korea; for all three RNA segments. To our knowledge, this is the first report of TSWV infection of O. coeruleum in Korea.

• Animal Bioscience
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• v.35 no.9
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• pp.1340-1350
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• 2022

Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃_π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

• Journal of Korean Society of Forest Science
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• v.42 no.1
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• pp.74-82
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• 1979

Pinus densiflora S. et Z. which has the widest distribution and highest stock at present in Korea and has used as materials for fuel, house construction, furniture and many other purposes for several hundred years, is considered as one of major species of economic importance, although there are a few epidemic insect injuries and silvicultural difficulties in regeneration. However, since disorderly cutting has been conducted for long time, the valuable local stands have disappeared. Therefore immediate attempts should be taken on the gene conservation and genetic studies including heritabilities and genetic gains of desirable characters. One hundred and twently five plus trees have so far been selected from the nationwide area and kept for the purpose of seed orchard establishment and other theoretical studies. In this study, the wind pollinated seeds of grafted stocks of 13 plus trees in clone bank located in Suweon and the seeds of 4 Japanese plus trees were collected and their progenies were used for heritability study. As indicated in figure 1, thirteen plus trees are from the middle part of Korea and two experimental plantations were laid out in ]972 (1-1 stock) by the randomized block design with five replications, consisting of 10 trees line plots of each family in each replication. Tree height, root collar diameter and branch diameter at 1cm apart from the main stem were measured. The results are summarized as follows 1. The rank of height growth of each plus tree progenies by age was greatly changed under age 3 and it was affected more in poor site than good site. 2. The heritabilities of height growth were estimated to be 7.2% at age 3, negative sign at age 4, 9.4% at age 5, 13.0% at age 6, 8.1% at age 7 and abrupt increase of 63.8% at age 8. The heritabilities were generally increased with increase of age. 3. The heritabilities of root collar diameter and branch diameter (average of the three biggest branches) was 3.2% and 11.8% at age 8 respectively. 4. The genetic gain was largest at age 8 and it was 46.6% when a selection intensity, 1/500 was taken. It, therefore, seems to be reasonable that selection should not be made under age 7.

• Journal of Plant Biotechnology
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• v.32 no.3
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• pp.167-173
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• 2005

Three different cDNAS for cinnamate 4-hydroxylase (C4H) which are involved in the second step of the general phenylpropanoid pathway were isolated and designated as pc4h1 (1,755 bp), pc4h2 (1,655 bp), and pc4h3 (1,316 bp), respectively. The nucleotide sequence analysis revealed that both pc4h1 and pc4h2 clones encode polypeptides of 505 amino acids frame but pc4h3 clone was truncated at the 5'-end of coding region. The alignment of the deduced amino acid sequences showed that PC4H1 and PC4H2 are highly homologous (95.8% identical) with each other and contain three conserved domains which are typical in cytochrome P450 monooxygenase: proline-rich region, threonine-containing binding pocket for the oxygen molecule, and heme binding region. In addition, result of the phylogenic tree analysis revealed that both pepper C4Hs belong to Class 1. pc4h2 transcription was strongly induced in wounded fruit (400%) and root (200%) relative to its very low basal level but not in leaf or stem tissue. In case of pc4h1, the basal level of transcription was higher than pc4h2 but induction by wounding was lower in fruit and root while leaf and stem tissues did not respond to wounding. The basal level of pc4h3 transcripts was not, if any, detectable and response to wounding was not observed.

• Journal of Life Science
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• v.20 no.6
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• pp.907-913
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• 2010

Human enteroviruses (HEV) are considered one of the major infectious causes of central nervous system infections such as aseptic encephalomeningitis in pediatrics. This study was focused on providing information related to genetic characteristics and diversities of HEV which prevailed between 2007 and 2009 in Busan, Korea. A total of 2,743 specimens were collected from children and screened for isolation of HEV by cell culture and RT-PCR. Among the specimins, 240 isolates were grouped into 21 different HEV serotypes using VP1 RT-PCR. The major etiological agents were CV-A6 and CV-B2 in 2007, E-6 and E-30 in 2008 and CV-B1 in 2009. The occurrence of HEV infections was the most frequent in the summer (May to August, 188 cases, 78.3%). Most of the isolates were identified from specimens from children under 10 years old, with the highest occurrence in the 2 to 4 year old range (15.2%). However, there were no significant differences between male and female children for the isolates. For analyzing genetic characterization, VP1 gene was amplified by RT-PCR and sequenced. The phylogenetic tree was established by Clustal W method using DNASTAR software. Using the sequence analysis of the VP1 region, it was classified into 2 groups; HEV-A and HEV-B. The HEV-A group contained 6 serotypes and sequences of 31 isolates were compared within each serotype. The HEV-B group contained 10 serotypes and the sequences of 41 isolates were compared within each serotype. Homology analysis of the VP1 region showed that the identity scores of HEV-A and B isolates were different. In conclusion, genetic divergences were observed among the isolates from children between 2007 and 2009 in Busan.

• Korean Journal of Plant Taxonomy
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• v.52 no.1
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• pp.54-63
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• 2022

Prunus subg. Cerasus is the most planted street and landscaping tree in South Korea, but it is difficult to identify species according to their macro-morphologies, leading to problems when attempting properly to manage species quantities. The purpose of this study is to understand the current status of plant types and species compositions in Bundang Central Park in Bundang-gu of Seongnam City and to discuss the necessity of the management of landscaping tree planting. In April of 2021, during the cherry blossom season, a total of 5,866 planted cherry trees were investigated within an area of 6 km² of Bundang-gu in Seongnam City. As a result, 5,744 trees were sorted into eleven taxa, but the remaining 122 trees were not determined due to their complex morphologies. Prunus ×yedoensis Matsum. accounted for the highest proportion (52.1%), followed by P. serrulata Lindl. var. pubescens Nakai and P. jamasakura Siebold ex Koidz. P. ×nudiflora (Koehne) Koidz., a plant native to Jejudo Island, was not found in this survey. In order to help identify cherry trees based on micro-morphologies, an identification key was presented for the eleven taxa planted as major landscaping trees. It is known that cherry trees frequently form interspecific hybrids in nature. In order to prevent a loss of the genetic originality of native species due to hybridization and gene introgression from foreign cherry trees, it is necessary to manage planting species near the habitats of native taxa and track their origins.

• Korean Journal of Poultry Science
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• v.50 no.4
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• pp.231-240
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• 2023

Infectious bursal disease (IBD) is an acute, highly contagious, and immunosuppressive disease in young chickens, and causes considerable economic losses to the poultry industry. More than 30 years ago, an antigenic variant IBDV (avIBDV) was reported in chicken farms in the United States. Recently, a novel avIBDV exhibited clear differences in molecular characteristics compared with previous variant strains. This study investigated the molecular characteristics of recently isolated avIBDV strains in Korea. Strains of avIBDV were confirmed by reverse transcription PCR (RT-PCR) and were propagated in 10-day-old specific-pathogen-free (SPF) embryonated chicken eggs through chorioallantoic membrane (CAM) inoculation. Multiple sequence alignment and phylogenetic analyses of hypervariable regions VP2 gene revealed that the strains originated from two different avIBDV lineages (G2a and G2d). In our results, we confirmed the co-existence and prevalence of avIBDV genogroup G2a and G2d in chicken farms. It is necessary to study the protective efficacy of current vaccines against avIBDVs.

• Journal of Life Science
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• v.18 no.10
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• pp.1442-1446
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• 2008

Seven populations of 586 Hanwoo have been characterized by using 10 microsatellite DNA markers. Size of microsatellite markers decided using GeneMapper Software (v.4.0) after analyze in kinds of ABI machine of name of 3130. Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. Genetic distancesbetween populations were obtained using Ne's DA distance method. Expected heterozygosity between each population was estimated very analogously. Genetic distances (0.0413) between Kangwan (KW) and Gyonggi (GG), Jeonpuk (JP) were nearest than distances between other populations by 0.021. Genetic distances between Gyonggi (GG) and Kyongpuk (KP) showed far distance than other populations by 0.032. In the UPGMA tree that is made based on DA distance matrix. Each individuals were not ramified to different group and were spread evenly in phylogenetic dendrogram about all Hanwoo of each regional area populations. But Hanwoo proven population was ramified to different group.