• Journal of Life Science
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• v.21 no.9
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• pp.1329-1335
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• 2011

Korean native goats, which are characterized by black coat color, have existed on the Korean peninsula for a long time. Until now, there has been no comprehensive investigation concerning their genetic diversity, phylogenetic analysis or origin. In this study, we investigated the genetic diversity and verified phylogenetic status of the Korean native goat using the 453-bp fragment of the hypervariable fragment I (HVI) of mitochondrial DNA (mtDNA) D-loop region from 60 individuals among 5 populations. The Korean native goat showed less haplotype diversity when compared with goats from other countries. In addition, 6 haplotypes that had not been previously reported were verified in this study. In phylogenetic analyses with other country's goats, 10 haplotypes from Korean native goats were classified into mtDNA lineage A. Moreover, in a phylogenetic tree for goats which contained mtDNA lineage A, 8 of 10 haplotypes could be included in a subgroup with goats from Vietnam and an area of China. However, none of the remaining haplotypes belonged to a major group of Korean native goats and were located on different independent positions. These results suggest that almost Korean native goats aligned more closely to China and Vietnam breeds in mtDNA lineage A and there was no gene flow from other mtDNA lineages. Our results will contribute to conservation strategies and genetic breeding of Korean native goats.

• Journal of Korean Society of Forest Science
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• v.107 no.4
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• pp.378-384
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• 2018

Chinese jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is an economically important species. It has high nutritional value in fruits, and its medicinal properties have led to extensive use in traditional oriental medicine. In this study, we investigated the genetic characteristics of 270 jujube germplasms collected from the six major jujube fruit production areas in Korea including Boeun and Gyeongsan, in order to understand the current situation on cultivated varieties of domestic jujube and to obtain useful data for selection of superior germplasms and establishing their breeding plans. The results of ISSR marker analysis revealed that the Shannon's information index of the 270 germplasms was 0.107 and the genetic similarity was as high as 0.935 showing the dominance of a specific cultivar or germplasm, and almost 67% (180) of them were identified at the same genotype with 'Bokjo'. The domestic commercial jujube populations could be characterized by very low genetic diversity and thus may be vulnerable to external disturbances. In addition, it seems that most of the jujube fruits in domestic market were largely produced through parthenocarpy.

• Animal Bioscience
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• v.36 no.4
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• pp.570-583
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• 2023

Objective: Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods: Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq. Results: A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A-F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure. Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4-6, 9-10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and mitogen-activated protein kinase (MAPK) proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. Kyoto encyclopedia of genes and genomes pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1- and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through quantitative real-time polymerase chain reaction and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R² = 0.92-0.95, p<0.01). Conclusion: This study provides significant insights into the potential functions of FGFs in chickens, including the regulation of MAPK signaling pathways and the immune response of chickens to HPAIV infections.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.53-53
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• 2015

Agrobacterium tumefaciens-mediated transformation(ATMT) of Flammulina velutipes was used to produce a diverse number of transformants to discover the functions of gene that is vital for its variation color, spore pattern and cellulolytic activity. Futhermore, the transformant pool will be used as a good genetic resource for studying gene functions. Agrobacterium-mediated transformation was conducted in order to generate intentional mutants of F. velutipes strain KACC42777. Then Agrobacterium tumefaciens AGL-1 harboring pBGgHg was transformed into F. velutipes. This method is use to determine the functional gene of F. velutipes. Inverse PCR was used to insert T-DNA into the tagged chromosomal DNA segments and conducting sequence analysis of the F. velutipes. But this experiment had trouble in diverse morphological mutants because of dikaryotic nature of mushroom. It needed to make monokaryotic fruiting varients which introduced genes of compatible mating types. In this study, next generation sequencing data was generated from 28 strains of Flammulina velutipes with different phenotypes using Illumina Hiseq platform. Filtered short reads were initially aligned to the reference genome (KACC42780) to construct a SNP matrix. And then we built a phylogenetic tree based on the validated SNPs. The inferred tree represented that white- and brown- fruitbody forming strains were generally separated although three brown strains, 4103, 4028, and 4195, were grouped with white ones. This topological relationship was consistently reappeared even when we used randomly selected SNPs. Group I containing 4062, 4148, and 4195 strains and group II containing 4188, 4190, and 4194 strains formed early-divergent lineages with robust nodal supports, suggesting that they are independent groups from the members in main clades. To elucidate the distinction between white-fruitbody forming strains isolated from Korea and Japan, phylogenetic analysis was performed using their SNP data with group I members as outgroup. However, no significant genetic variation was noticed in this study. A total of 28 strains of Flammulina velutipes were analyzed to identify the genomic regions responsible for producing white-fruiting body. NGS data was yielded by using Illumina Hiseq platform. Short reads were filtered by quality score and read length were mapped on the reference genome (KACC42780). Between the white- and brown fruitbody forming strains. There is a high possibility that SNPs can be detected among the white strains as homozygous because white phenotype is recessive in F. velutipes. Thus, we constructed SNP matrix within 8 white strains. SNPs discovered between mono3 and mono19, the parental monokaryotic strains of 4210 strain (white), were excluded from the candidate. If the genotypes of SNPs detected between white and brown strains were identical with those in mono3 and mono19 strains, they were included in candidate as a priority. As a result, if more than 5 candidates SNPs were localized in single gene, we regarded as they are possibly related to the white color. In F. velutipes genome, chr01, chr04, chr07,chr11 regions were identified to be associated with white fruitbody forming. White and Brown Fruitbody strains can be used as an identification marker for F. veluipes. We can develop some molecular markers to identify colored strains and discriminate national white varieties against Japanese ones.

• Korean Journal of Poultry Science
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• v.42 no.1
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• pp.15-26
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• 2015

In this study, genotyping was executed by using 27 microsatellite markers for genetic diversity of 469 Korean Native Chickens [20 population, each population is 24 samples but Hanhyup A line is 13 samples). in total 469 samples were collected from National Institute of Animal Science (Korean Native Chicken (NR, NY, NG, NL and NW), Ogye (NO), Leghorn F,K (NF and NK), Black and Brown cormish (NH and NS), Rhode Island Red C, D (NC and ND), Total is 12 populations] and Hanhyup [H line (HH), F line (HF), G line (HG), V line (HV), S line (HS), W line (HW), Y line (HY), A line (HA), total is 8 populations]. [The allele number were observed 5 (ADL0268) to 20 (MCW0127) each markers. Observed heterozygostiy ($H_{obs}$), expected heterozygosity ($H_{exp}$), polymorphism Information Content (PIC) were observed 0.359 to 0.677, 0.668 to 0.881 and 0.646 to 0.869, respectively. Using these markers, the calculated the heterozygote deficit within chicken line ($F_{is}$) value each population from mean 0.117. Phylogenetic tree showing the genetic relationship among 20 population using standard genetic distance calculated from 27 microsatellite markers. genetic distances revealed the closest (0.175) between NC and ND. on the other hand, Farthest genetic distances (0.710) revealed between NF and HV. STRUCTURE analysis and Principal Components Analysis (PCA) showed that results of similar phylogenetic tree. The expected probability of identity values on random individuals (Total population and only Hanhyup line) was estimated at $8.80{\times}10^{-83}$ and $3.87{\times}10^{-117}$, respectively. In conclusion, This study shows the useful data that be utilized as a basic data of Korean Native Chicken breeding and development for commercial chicken industry to meet the consumer's demand.

• Journal of Korean Society of Forest Science
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• v.89 no.5
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• pp.666-676
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• 2000

For the study of morphological variation of Q. variabilis natural population in Korea, 19 populations were selected through the country in considering latitude, longitude, and geographical characters. Thirty trees were randomly selected from each population and 60 mature leaves were sampled from each tree. Four characters (leaf blade length, maximum blade width, petiole length, and vein number) were measured, and their ratios (the ratio of blade length to maximum blade width, the ratio of blade length to petiole length, the ratio of petiole length to vein number, upper 1/3 blade width to maximum blade width, and upper 1/3 blade width to lower 1/3 blade width) were calculated. 1. Analysis of variance for all leaf characters were significantly different among populations and among individuals within population. Contributions of variance among individuals within population in all the characters were higher than those among populations. Therefore, selection of plus trees may be preferable to desirable populations for breeding program of Q. variabilis. 2. Among principal component analysis for leaf characters, primary 2 principal components appeared to be major variables for leaf form of Q. variabilis because of the loading contribution of 80.5%. The first contribution component was petiole length/vein number and petiole length ; the second one was upper 1/3 blade width/maximum blade width, upper blade width/lower 1/3 blade width and vein number, respectively. 3. Latitude was positively correlated with blade length/maximum blade width and blade length/petiole length, but negatively correlated with petiole length/vein number, upper 1/3 blade width/maximum blade width, upper 1/3 blade width/lower 1/3 blade width, petiole length, and vein number. But, for longitude and altitude the former two traits and the later five traits exhibited the negative and positive correlation, respectively. 4. Cluster analysis using complete linkage method for leaf characters showed two groups to Euclidean distance 1.6. They were group I of population 1. 4, 5, and 13 and group II of population 2, 3, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, and 19. However, group II was divided again to Euclidean distance 1.3, that is a group including population 3, 7, 10, 14, 15, and 17(group II-1) and the other group comprising population 2, 6, 8, 9, 11, 12, 16, 18, and 19(group II-2). This cluster could be mainly observed due to difference among population in aspect (group I : NE, group II-1 : SE, and group II-2 : SW).

• Korean Journal of Environmental Agriculture
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• v.35 no.3
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• pp.175-183
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• 2016

BACKGROUND: There's a long rainy season during the Summer in Northeast Asia, including Korea. Heavy rainfall during this season causes harm to tree's root, and damped injury in the pear has been continuously reported. Pear Research Institute is breeding damp resistant rootstocks and investigating their mechanisms to relieve damped damages in the pear.METHODS AND RESULTS: Seedlings of Pyrus betulaefolia and P. calleryana were divided into two groups: control and damped, respectively. Damped group was treated by constant irrigation for 77 days and control group was maintained to keep the soil moisture pressure between 0 and -10 kPa. After the treatment, we analysed trees' growth rate, chlorophyll content, amino acids and total phenolic compounds. As a result, P. betulaefolia was sensitive to damped treatment while P. calleryana did not have significant differences between the control and damped treatment. It was observed that total contents for phenolic compounds were dramatically increased in P. betulaefolia while trees' growth rate, chlorophyll b and general amino acid contents were lowered by damping treatment.CONCLUSION: In some pear cultivars, growth habit is suppressed by damped damage. Pyrus calleryana displayed tolerances to damped damage in growth rate and some organic compound contents compared to P. betulaefolia. So we recommend to exploit P. calleryana as a pear rootstock rather than using P. betulaefolia.

• Horticultural Science & Technology
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• v.34 no.2
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• pp.305-313
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• 2016

Brassica juncea (2n = 4x = 36, AABB genome, 1,068 Mb) is a U's triangle species and an amphidiploid derivative of B. rapa and B. nigra. Fifteen varieties were used to study the ITS (internal transcribed spacer) regions of ribosomal DNA and MITEs (miniature inverted-repeat transposable elements) with a view of developing specific molecular markers. ITSs and MITEs are an excellent resource for developing DNA markers for genomics and evolutionary studies because most of them are stably inherited and present in high copy numbers. The ITS (ITS1 and ITS2) sequence was compared with the consensus sequence of B. rapa and B. nigra. Variation in ITS1 created two separate groups among 15 varieties, with 10 varieties in one group and 5 in the other. Phylogenetic analysis revealed two major clusters for those 10 and 5 varieties. Among the 160 different MITE primers used to evaluate the selected 15 varieties of B. juncea, 70 were related to the Stowaway, 79 to the Tourist, 6 to the hAT, and 5 to the Mutator super-families of MITEs. Of 160 markers examined, 32 were found to be polymorphic when fifteen different varieties of B. juncea were evaluated. The variety 'Blackgat' was different from the other mustard varieties with respect to both phenotype and genotype. The diversity of 47 additional accessions could be verified using eight selected molecular markers derived from MITE family sequences. The polymorphic markers identified in this study can be used for varietal classification, variety protection, and other breeding purposes.

• Journal of Bio-Environment Control
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• v.24 no.3
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• pp.161-166
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• 2015

To determine the adequate levels of light intensity and $CO_2$ concentration for mango grown in greenhouses, quantitative measurements of photosynthetic rates at various leaf positions in the tree are required. The objective of this study was to develop two-variable leaf photosynthetic models of Irwin mango (Mangifera indica L. cv. Irwin) using light intensity and $CO_2$ concentration at different leaf positions. Leaf photosynthetic rates at different positions (top, middle, and bottom) were measured by a leaf photosynthesis analyzer at light intensities (0, 50, 100, 200, 300, 400, 600, and $800{\mu}mol{\cdot}m^{-2}{\cdot}s^{-1}$) with $CO_2$ concentrations (100, 400, 800, 1200, and $1600{\mu}mol{\cdot}mol^{-1}$). The two-variable model consisted of the two leaf photosynthetic models expressed as negative exponential functions for light intensity and $CO_2$ concentrations, respectively. The photosynthetic rates of top leaves were saturated at a light intensity of $400{\mu}mol{\cdot}^{-2}{\cdot}s^{-1}$, while those of middle and bottom leaves saturated at $200{\mu}mol{\cdot}^{-2}{\cdot}s^{-1}$. The leaf photosynthetic rates did not reach the saturation point at a $CO_2$ concentration of $1600imolmol^{-1}$. In validation of the model, the estimated photosynthetic rates at top and bottom leaves showed better agreements with the measured ones than the middle leaves. It is expected that the optimal conditions of light intensity and $CO_2$ concentration can be determined for maximizing photosynthetic rates of Irwin mango grown in greenhouses by using the two-variable model.

• Journal of Korean Society of Forest Science
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• v.99 no.1
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• pp.102-110
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• 2010

This study was performed to find out the inhibitory effect of Rhus Verniciflua extract on lipid peroxidation and inflammatory cytokines during endurance exercise training for 8 weeks in rats. For this study, Sprague-Dawley rats were divided into 4 groups; sedentary (SED), exercise training (TRA), RVS extract ingestion (RVE), and RVS extract ingestion and exercise training (RVE-TRA). TRA and RVE-TRA were trained on treadmill with increasing speed gradually and administered 10 mL/kg/d of Rhus Verniciflua extract orally to RVE and RVE-TRA. In order to analyze antioxidant function, blood SOD (superoxide dismutase), GSH-Px (glutathione peroxidase), and MDA (malondialdehyde) were examined. And, analysis of inflammatory cytokines were examined using IL-6 (interleukin-6), TNF-${\alpha}$ (tumor necrosis factor-alpha), CRP (C-reactive protein), and NO (nitric oxide). SOD in TRA was significantly higher than SED and RVE (p<0.05), and RVE-TRA was highest among the groups (p<0.05). The MDA content of TRA, RVE and RVE-TRA were significantly lower than SED. GSH-Px activity of SED was significantly lower than other groups (p<0.05). IL-6 and TNF-${\alpha}$ content of RVE and RVE-TRA were significantly lower than SED and TRA (p<0.05). CRP concentration of SED was the lowest among groups (p<0.05). Finally, NO concentration of SED and TRA were higher than RVE and RVE-TRA (p<0.05). These results suggested that it is efficient for rats to reduce lipid peroxidation and induce anti-inflammatory by taking RVS extract during exercise training. Afterwards, if studies on the properties of RVS extract can be made with various ways, use of Rhus Verniciflua trees might be made widely which are growing naturally in mountains in Korea.