• Korean Journal of Plant Taxonomy
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• v.49 no.2
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• pp.118-126
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• 2019

The taxonomic rank of the tiny-leaved terrestrial orchid Cephalanthera subaphylla Miyabe & $Kud{\hat{o}}$ has been somewhat controversial, as it has been treated as a species or as an infraspecific taxon, under C. erecta (Thunb.) Blume [C. erecta var. subaphylla (Miyabe & $Kud{\hat{o}}$) Ohwi and C. erecta f. subaphylla (Miyabe & $Kud{\hat{o}}$) M. Hiro]. Allozyme markers, traditionally employed for delimiting species boundaries, are used here to gain information for determining the taxonomic status of C. subaphylla. To do this, we sampled three populations of five taxa (a total of 15 populations) of Cephalanthera native to the Korean Peninsula [C. erecta, C. falcata (Thunb.) Blume, C. longibracteata Blume, C. longifolia (L.) Fritsch, and C. subaphylla]. Among 20 putative loci resolved, three were monomorphic (Dia-2, Pgi-1, and Tpi-1) across the five species. Apart from C. longibracteata, there was no allozyme variation within the remaining four species. Of the 51 alleles harbored by these 17 polymorphic loci, each of the 27 alleles at 14 loci was unique to a single species. Accordingly, we found low average values of Nei's genetic identities (I) between ten species pairs (from I = 0.250 for C. erecta versus C. longifolia to I = 0.603 for C. falcata vs. C. longibracteata), with C. subaphylla being genetically clearly differentiated from the other species (from I = 0.349 for C. subaphylla vs. C. longifolia to 0.400 for C. subaphylla vs. C. falcata). These results clearly indicate that C. subaphylla is not genetically related to any of the other taxa of Cephalanthera that are native to the Korean Peninsula, including C. erecta. In a principal coordinate analysis (PCoA), C. subaphylla was positioned distant not only from C. falcata, C. longibracteata, and C. longifolia, but also from C. erecta. Finally, K = 5 was the best clustering scheme using a Bayesian approach, with five clusters precisely corresponding to the five taxa. Thus, our allozyme results strongly suggest that C. subaphylla merits the rank of species.

• Journal of Korean Medicine for Obesity Research
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• v.18 no.2
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• pp.106-114
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• 2018

Objectives: We investigated about the microbial properties and changes in the efficacy of the Codonopsis lanceolata (CL) by natural fermentation. Methods: CL was fermented for four weeks in a well-ventilated place with 2.5% salt. pH, total sugar, total polyphenol, and total flavonoid were measured to determine fermentation characteristics according to fermentation period and salt treatment. Polymerase chain reaction denaturing gradient gel electrophoresis and random amplification of polymorphic DNA-polymerase chain reaction were carried out for microbial analysis during fermentation. In addition, HepG2 cell was cultured to check the lipid accumulation through oil red O staining and the glucose uptake was analyzed by measuring the 2-NBDG at C2C12 cell. Results: The pH level and the total sugar decreased with the CL fermentation. Total polyphenol and flavonoid increased after CL fermentation. It was confirmed that Leuconostoc mesenteroides were maintained continuously during fermentation. In the salt treatment CL, there was a sharp increase in Rahnella aquatilis. Lactobacillus plantarum matrix was observed in fermented CL. In addition, Lactococcus lactis, Weissella koreensis, R. aquatilis, L. plantarum, Leu. mesenteroides have been added to the salt treatment. Glucose uptake were significantly increased after fermentation with salt for four weeks. Lipid accumulation in the HepG2 cells was observed that there was difference (P<0.01) between free fatty acid group (100%) and decreased 4 weeks after fermentation (90.38%) at $800{\mu}g/mL$. Conclusions: Total polyphenol and flavonoid were increased after CL fermentation. Especially, percentage of the glucose uptake and lipid accumulation inhibition increased in CL fermentation with salt. It is expected that fermentation of salt treated CL will be more effective in diabetes and fatty liver.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.7
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• pp.913-921
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• 2019

Objective: The objectives of this study were to compare identified informative regions through two genome-wide association study (GWAS) approaches and determine the accuracy and bias of the direct genomic value (DGV) for milk production traits in Korean Holstein cattle, using two genomic prediction approaches: single-step genomic best linear unbiased prediction (ss-GBLUP) and Bayesian Bayes-B. Methods: Records on production traits such as adjusted 305-day milk (MY305), fat (FY305), and protein (PY305) yields were collected from 265,271 first parity cows. After quality control, 50,765 single-nucleotide polymorphic genotypes were available for analysis. In GWAS for ss-GBLUP (ssGWAS) and Bayes-B (BayesGWAS), the proportion of genetic variance for each 1-Mb genomic window was calculated and used to identify informative genomic regions. Accuracy of the DGV was estimated by a five-fold cross-validation with random clustering. As a measure of accuracy for DGV, we also assessed the correlation between DGV and deregressed-estimated breeding value (DEBV). The bias of DGV for each method was obtained by determining regression coefficients. Results: A total of nine and five significant windows (1 Mb) were identified for MY305 using ssGWAS and BayesGWAS, respectively. Using ssGWAS and BayesGWAS, we also detected multiple significant regions for FY305 (12 and 7) and PY305 (14 and 2), respectively. Both single-step DGV and Bayes DGV also showed somewhat moderate accuracy ranges for MY305 (0.32 to 0.34), FY305 (0.37 to 0.39), and PY305 (0.35 to 0.36) traits, respectively. The mean biases of DGVs determined using the single-step and Bayesian methods were $1.50{\pm}0.21$ and $1.18{\pm}0.26$ for MY305, $1.75{\pm}0.33$ and $1.14{\pm}0.20$ for FY305, and $1.59{\pm}0.20$ and $1.14{\pm}0.15$ for PY305, respectively. Conclusion: From the bias perspective, we believe that genomic selection based on the application of Bayesian approaches would be more suitable than application of ss-GBLUP in Korean Holstein populations.

• Laboraroty Animal Research
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• v.34 no.4
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• pp.176-184
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• 2018

In this study, we observed chronological changes in the immunoreactivity and expression level of myelin basic protein (MBP), one of the most abundant proteins in the central nervous system, in the hippocampus of Zucker diabetic fatty (ZDF) rats and their control littermates (Zucker lean control; ZLC). In the ZLC group, body weight steadily increased with age; the body weight of the ZDF group, however, peaked at 30 weeks of age, and subsequently decreased. Based on the changes of body weight, animals were divided into the following six groups: early (12-week), middle (30-week), and chronic (52-week) diabetic groups and their controls. MBP immunoreactivity was found in the alveus, strata pyramidale, and lacunosum-moleculare of the CA1 region, strata pyramidale and radiatum of the CA3 region, and subgranular zone, polymorphic layer, and molecular layer of the dentate gyrus. MBP immunoreactivity was lowest in the hippocampus of 12-week-old rats in the ZLC group, and highest in 12-week-old rats in the ZDF group. Diabetes increased MBP levels in the 12-week-old group, while MBP immunoreactivity decreased in the 30-week-old group. In the 52-week-old ZLC and ZDF groups, MBP immunoreactivity was detected in the hippocampus, similar to the 30-week-old ZDF group. Western blot results corroborated with immunohistochemical results. These results suggested that changes in the immunoreactivity and expression of MBP in the hippocampus might be a compensatory response to aging, while the sustained levels of MBP in diabetic animals could be attributed to a loss of compensatory responses in oligodendrocytes.

• Journal of Life Science
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• v.31 no.1
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• pp.52-58
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• 2021

Pseudomonas syringae pv. actinidiae, which causes bacterial canker in kiwifruit, is divided into five biovars (1, 2, 3, 5, 6) on the basis of genetic characteristics and toxin productivity. Among them, biovar 3 is responsible for the current global outbreak, and has been isolated in Korea since 2011. Biovar 3 strains isolated from Korea are subdivided into six genetically different lineages (subgroup I, IV, V, VI, VII, and VIII) based on random amplified polymorphic DNA (RAPD) analysis. In this work, the subgroup-specific sequence characterized amplified region (SCAR) primers were developed from sequenced differential RAPD bands. Distribution of the subgroups of the biovar 3 strains collected in Korea from 2011-2017 were examined using these subgroup-specific primer sets. Among the 54 strains tested, 35 strains (64.8%) belonged to subgroup V, 9 strains (16.7%) belonged to subgroup IV, 4 strains (7.4%) belonged to subgroup VI, 3 strains (5.6%) belonged to subgroup VII, 2 strains (3.7%) belonged to subgroup VIII, and 1 (1.9%) strain belonged to subgroup I. Strains belonging to subgroups IV, V, and VI were shown to be related to strains isolated from China, New Zealand, and Chile, respectively. The study revealed that the biovar 3 strains in Korea are genetically diverse and are estimated to have been introduced through pollen sourced from foreign countries.

• Animal Bioscience
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• v.34 no.7
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• pp.1105-1115
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• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

• Journal of Mushroom
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• v.19 no.1
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• pp.76-80
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• 2021

To develop a method for the differentiation of Pleurotus ostratus cultivars, the multiplex-simple sequence repeat (SSR) primer set based on the SSRs obtained from whole genomic DNA sequence analysis was designed with two polymerase chain reaction (PCR) primer sets. These SSR primer sets were employed to distinguish 10 cultivars and strains. Twenty polymorphic markers were selected based on the genotyping results. PCR with each primer produced 1-4 distinct bands ranging in size from 150 to 350 bp, which was within the expected range. However, since a sole SSR marker was unable to detect polymorphisms in every cultivar, multiplex PCRs with composite PCR primer sets were employed. The multiplex primer, "166+115," completely discriminated 12 cultivars and strains with 40 loci, which were 12 more than the simple arithmetic addition of each locus of the primers 115 and 166. These results might be useful to provide an efficient method for the differentiation of P. ostreatus cultivars with separate PCRs for the quality control of spawn and protection of breeders' rights.

• Journal of Life Science
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• v.31 no.6
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• pp.537-542
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• 2021

Schisandra nigra Max., a dioecious plant native to Jeju Island in Korea, is cultivated on a small scale for fruit production. As fruit-producing female individuals are generally considered to be more valuable than male, early identification of plant sex at the seedling stage is important. In this study, a sequence-characterized amplified region (SCAR) marker associated with a female-specific region in the genome of S. nigra was investigated. Of 120 randomly amplified polymorphic DNA (RAPD) primers, one primer (OPB-03) consistently amplified a 749 bp band in female plants. The female-specific PCR product was isolated and cloned, and the nucleotide sequences were then determined. Southern hybridization performed using the female-specific fragment as a probe produced positive signals only in genomic DNA from the female plants. This result revealed that the 749 bp segment of DNA was present in the genome of female plants but absent in the genome of male plants. A SCAR primer pair was designed based on the RAPD marker to amplify a 436 bp fragment in the genomic DNA of female plants. This primer pair amplified the expected size of DNA fragment in female plants and four monoecious individuals collected from a natural population. The SCAR marker identified in this study can be used to distinguish female-flowering individuals at the seedling stage.

• Animal Bioscience
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• v.35 no.2
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• pp.281-289
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• 2022

Objective: The aim of this study was to characterize the exopolysaccharides (EPS)-producing lactic acid bacteria from Taiwanese ropy fermented milk (TRFM) for developing a clean label low-fat fermented milk. Methods: Potential isolates from TRFM were selected based on the Gram staining test and observation of turbid suspension in the culture broth. Random amplified polymorphic DNA-polymerase chain reaction, 16S rRNA gene sequencing, and API CHL 50 test were used for strain identification. After evaluation of EPS concentration, target strains were introduced to low-fat milk fermentation for 24 h. Fermentation characters were checked: pH value, acidity, viable count, syneresis, and viscosity. Sensory evaluation of fermented products was carried out by 30 volunteers, while the storage test was performed for 21 days at 4℃. Results: Two EPS-producing strains (APL15 and APL16) were isolated from TRFM and identified as Lactococcus (Lc.) lactis subsp. cremoris. Their EPS concentrations in glucose and lactose media were higher than other published strains of Lc. lactis subsp. cremoris. Low-fat fermented milk separately prepared with APL15 and APL16 reached pH 4.3 and acidity 0.8% with a viable count of 9 log colony-forming units/mL. The physical properties of both products were superior to the control yogurt, showing significant improvements in syneresis and viscosity (p<0.05). Our low-fat products had appropriate sensory scores in appearance and texture according to sensory evaluation. Although decreasing viable cells of strains during the 21-day storage test, low-fat fermented milk made by APL15 exhibited stable physicochemical properties, including pH value, acidity, syneresis and sufficient viable cells throughout the storage period. Conclusion: This study demonstrated that Lc. lactis subsp. cremoris APL15 isolated from TRFM had good fermentation abilities to produce low-fat fermented milk. These data indicate that EPS-producing lactic acid bacteria have great potential to act as natural food stabilizers for low-fat fermented milk.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.42 no.6
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• pp.790-799
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• 1997

Aegilops genus is known to include the donor species of the Band D genome of the bread wheat(ABD). An effort to establish a better strategy for phylogenetic relationships about Aegilops polyploids by AFLPs(Amplified Fragment Length Polymorphisms) was conducted using the 19 Aegilops sPP. and T. aestivum. The 207 polymorphic bands from the amplified products on the 6% acrylamide denaturing sequencing gels were obtained with the 7 AFLP primer combinations, and used to account for the genetic similarities and cluster analysis using NTSYS program. According to the genome analysis, the $M^h$-genome of Ae. heldreichii was estimated as an intermediate genome between the M-genome of Ae. comosa and N-genome of Ae. uniaristata and supposed to be incorporated in the establishing process of UM-genome as a possible diploid donor. And Ae. ventricosa(DN) was more close to Ae. umbellulata(U) than Ae. squarrosa(D). The close relationship between Ae. squarrosa and T. aestivum was perceived as a diploid donor of D-genome. As for the polyploid species, hexaploid Ae. triaristata was more closely related to Ae. columnaris rather than tetraploid Ae. triaristata. The clustered groups were, basically same to the previous Gihara's sections based on phenotypes and pairing analysis of interspecific hybrids. AFLP was evaluated as an efficient and powerful method in the genome evaluation of closely related species.