• Korean Journal of Environmental Biology
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• v.36 no.4
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• pp.463-470
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• 2018

Restoration ecology is the practical study of renewing and restoring a spoilt, degraded, or devastated ecosystems in the environment. Because the Korean industry has been drastically developed for the past few decades, the Korean ecosystem requires restoration using regional seed. In this study, we identified the variation of phylogenic relationship of Miscanthus sinensis or Phragmites australis by locations in Korea. Chloroplast DNA atpF-H and psbA-trnH interspace region were used as a molecular marker to resolve the phylogenic relationship in 10 different locations. We performed the molecular phylogenetic analysis with 10 chloroplast DNAs from each location using Kimura 2-parameter. The analysis of Miscanthus showed that all atpF-H genes were exact matches except for Ose san. In contrast to Mischanthus, the atpF-H genes from Phragmites were observed to have more variation. A total of 7 locations revealed the variation in chloroplast gene. According to the phylogenic tree in Phragmites, 2 of 10 samples in 6 locations and 3 of 10 in 1 location showed variation with 0.160-0.181 genetic distance. According to the genetic distance of the Miscanthus sinensis, there were no mutations in all regions except the Hongsung. These results support regional differences and show the necessity for seed collection by region. In the case of Phragmites australis, genetic variation occurred in all regions.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.10
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• pp.1351-1358
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• 2009

Parentage tests using polymorphic DNA marker are commonly performed to avoid incorrect recording of the parental information of livestock animals, and single-nucleotide polymorphisms (SNPs) are becoming the method of choice. In Japanese Black cattle, parentage tests based on the exclusion method using microsatellite markers are currently conducted; however, an alternative SNP system aimed at parentage tests has recently been developed. In the present study, two types of simulations were conducted using the pedigree data of two subpopulations in the breed (subpopulations of Hyogo and Shimane prefectures) in order to examine the effect of actual genetic and breeding structures. The first simulation (simulation 1) investigated the usefulness of SNPs for excluding a close relative of the true sire; the second one (simulation 2) investigated the accuracy of sire identification tests for multiple full-sib putative sires by a combined method of exclusion and paternity assignment based on the LOD score. The success rates of excluding a single fullsib and sire of the true sires were, respectively, 0.9915 and 0.9852 in Hyogo and 0.9848 and 0.9852 in Shimane, when 50 SNPs with minor allele frequency (MAF: q) of 0.25${\leq}$q${\leq}$0.35 were used in simulation 1. The success rates of sire identification tests based solely on the exclusion method were relatively low in simulation 2. However, assuming that 50 SNPs with MAF of 0.25${\leq}$q${\leq}$0.35 or 0.45${\leq}$q${\leq}$0.5 were available, the total success rates including achievements due to paternity assignment were, respectively, 0.9430 and 0.9681 in Hyogo and 0.8999 and 0.9399 for Shimane, even when each true sire was assumed to compete with 50 full-sibs.

• Journal of Embryo Transfer
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• v.23 no.3
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• pp.197-201
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• 2008

In order to provide information of genetic variants for Haptoglobin (Hp) gene, which may be related to weight traits in pig, a total of 235 animals from National Institute of Animal Science (NIAS) were screened with 3 primers. The primer sequences were selected using the porcine cDNA sequences based on NM_214000, and the exon boundaries were estimated. Genetic variants were observed using direct sequencing analysis, and there were 9 SNPs detected at nucleotide positions 503 (A/G), 509 (A/G), 709 (C/T), 734 (C/A), 742 (G/A), 769 (A/G), 840 (C/T), 876 (C/T) and 882 (C/A). All the SNPs were located in coding regions, and mutations caused amino acid changes at nucleotide positions 503, 509, 734, 742 and 769. Allele frequencies of SNPs were estimated for all segments. The SNPs at nucleotide position 509 (p<0.0001) and 734 (p<0.05) were significantly associated with average daily gain, but no significance was observed with other SNPs. From the results, the identified SNPs may be a useful candidate marker for the porcine weight gain traits.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.5
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• pp.643-649
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• 2018

Objective: POU class 1 homeobox 1 (POU1F1) mediates growth hormone expression and activity by altering transcription, eventually resulting in growth rate variations. Therefore, we aimed to identify chicken POU1F1 polymorphisms and evaluate the association between single nucleotide polymorphisms (SNPs) and growth-related traits, and logistic growth curve parameter traits (${\alpha}$, ${\beta}$, and ${\gamma}$). Methods: Three SNPs (M_1 to M_3) were used to genotype 585 $F_1$ and 88 $F_0$ birds from five Korean native chicken lines using a polymerase chain reaction-restriction fragment length polymorphism method. Results: Single marker analyses and traits association analyses showed that M_2 was significantly associated with body weight at two weeks, weight gain from hatch to 2 weeks, and weight gain from 16 to 18 weeks (p<0.05). M_3 was significantly associated with weight gain from 14 to 16 weeks and from 16 to 18 weeks, and asymptotic body weight (${\alpha}$) (p<0.05). No traits were associated with M_1. The POU1F1 haplogroups were significantly associated with weight gain from 14 to 16 weeks (p = 0.020). Linkage disequilibrium test and Haploview analysis shown one main haploblock between M_2 and M_3 SNP. Conclusion: Thus, POU1F1 significantly affects the growth of Korean native chickens and their growth curve traits.

• Journal of Embryo Transfer
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• v.31 no.3
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• pp.287-291
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• 2016

For evaluating the boar semen quality, sperm motility (MOT) is an important parameter because the movement of spermatozoa indicates active metabolism, membrane integrity and fertilizing capacity. Estrogen receptors 2(ESR2) is involved in estrogen related apoptosis in cell cycle spermatogenesis, but their functions have not been confirmed in pig until now. Therefore, this study was conducted to analyze their association with sperm motility and kinematic characteristics. DNA samples from 105 Duroc pigs with records of semen motility and kinematic characteristics [Total motile spermatozoa (MOT), Curvilinear velocity(VCL), Straight-line velocity(VSL), the ratio between VSL and VCL(LIN), Amplitude of Lateral Head displacement(ALH)] were analyzed. A SNP in coding region of ESR2 g.35547A > G in exon 5 was associated with MOT (p < 0.05) in Duroc population. Therefore, we suggest that the porcine ESR2 gene may be used as a molecular marker for Duroc boar semen quality, although its functional effects were not defined yet. These results might shed new light on the roles of ESR2 in spermatogenesis as candidate gene for boar fertility, but still the lack of association across populations should be considered.

• Korean Journal of Agricultural Science
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• v.44 no.4
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• pp.549-557
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• 2017

As exchanges between countries become more active, new threats such as drugs, illegal imports of food and medicines, and terrorism are present all over the world. From this, increased border security that protects people's safety is becoming a new issue. The activities of special purpose dogs that detect these threats in advance are becoming very important. One of the obstacles in securing superior individuals is musculoskeletal disorders which interfere with the work of special purpose dogs. In order to search for genes associated with these genetic disorders, we conducted genomic analysis using linkage disequilibrium information and investigated genetic characteristics to know heterozygosity and inbreeding status in the population. In this study, two breeds (Malinois, Shepherd) of army dogs and three breeds (Malinois, Shepherd, Retriever) from public databases were used for comparison. The 170K SNP marker panel was used for this study. In the principal component analysis, it was confirmed that clusters were formed for each breed. The number of effective populations differed for each cultivar, but this was due to the difference in numbers of individuals for each breed used for the analysis. The results of heterozygosity decay analysis showed that heterozygous alleles decreased with each generation. In the army dog group, if the population number is maintained properly, the frequency of allele genotype will not decrease significantly.

• Food Science of Animal Resources
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• v.38 no.4
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• pp.711-717
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• 2018

Myogenic factor 5 (MYF5) plays an important role in regulating skeletal muscle fiber characteristics, consequently affecting meat production and quality. We identified a novel p.A41P mutation in exon1 of the porcine MYF5 gene by direct sequencing. The mutation was predicted to be destabilizing in protein structure based on the resultant amino acid substitution. We estimated the significant substitution effect of p.A41P on the energy stabilization of Myf5 protein structure. Then, we demonstrated that the mutation in Yorkshire population significantly affected muscle fiber type I composition (p<0.05), loin-eye area of lean meat content (p<0.05) and filter-fluid uptake of meat quality (p<0.01). Furthermore, dominant effects significantly influenced total muscle fiber number (p<0.05). This study suggests that the novel p.A41P mutation in porcine MYF5 may be a valuable genetic marker to affect the muscle fiber characteristics and consequently improve meat production quality and quantity.

• BMB Reports
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• v.40 no.4
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• pp.577-587
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• 2007

Single-copy chloroplast loci are used widely to infer phylogenetic relationship at different taxonomic levels among various groups of plants. To test the utility of chloroplast loci and to provide additional data applicable to hybrid evolution in Musa, we sequenced two introns, rpl16 and ndhA, and two intergenic spacers, psaA-ycf3 and petA-psbJ-psbL-psbF and combined these data. Using these four regions, Musa acuminata Cola(A)- and M. balbisiana Colla (B)-containing genomes were clearly distinguished. Some triploid interspecific hybrids contain A-type chloroplasts (the AAB/ABB) while others contain B-type chloroplasts (the BBA/BBB). The chloroplasts of all cultivars in 'Namwa' (BBA) group came from the same wild maternal origin, but the specific parents are still unrevealed. Though, average sequence divergences in each region were little (less than 2%), we propose that petA-psbJ intergenic spacer could be developed for diversity assessment within each genome. This segment contains three single nucleotide polymorphisms (SNPs) and two indels which could distinguish diversity within A genome whereas this same region also contains one SNP and an indel which could categorize B genome. However, an inverted repeat region which could form hairpin structure was detected in this spacer and thus was omitted from the analyses due to their incongruence to other regions. Until thoroughly identified in other members of Musaceae and Zingiberales clade, utility of this inverted repeat as phylogenetic marker in these taxa are cautioned.

• Journal of Physiology & Pathology in Korean Medicine
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• v.22 no.4
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• pp.993-999
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• 2008

Ischemic brain injury such as cerebral infarction is characterized by acute local inflammatory response mediated by cytokines. The mechanism of cytokines involved in cerebral infarction progression are uncompletely revealed yet. We investigated to find out the relationship between single nucleotide polymorphism (SNP) of interleukin 4 receptor(IL4R) and Oriental Medicine therapy efficacy in patients with cerebral infarction for 2 weeks. Oriental Korean Medicine therapies (herbal medicine and acupuncture) were applied daily and motor functions of patients were assessed using the modified cerebral vascular accident (MCVA) scores. Genotyping for IL4R polymorphism was done by pyrosequencing analysis. In IL4R genotypes and the frequency of alleles, there was no significant difference between cerebral infarction patients (n=124) and controls group (n=175). And there was also no significant difference among good and bad responders in cerebral infarction patients. In this study the IL4R genotype might not be the risk factor or a good predictive genetic marker for good and bad responders in cerebral infarction patients in Korean. Further studies including different cytokine genes will be necessary for the exact genetic markers.

• The Plant Pathology Journal
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• v.25 no.4
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• pp.408-416
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• 2009

A molecular survey was conducted to identify the presence of the bacterial blight resistance genes (Xa1, Xa4, xa5, xa13 and Xa21) in 86 accessions of aromatic rice obtained from germplasm. The results revealed that the resistance gene Xa4 (32.5%), Xa21 (17%), and xa5 (16%) were widely observed in tested rice germplasm. Among tested rice germplasm, 49 accessions showed the presence of more than one of five R genes, and 37 accessions possessed none of the R gene. TALLi and 05-IRRi-M-46 showed the presence of Xa4, xa5, xa13 and Xa21. Rice race $415{\times}Ir352$ exhibited positive amplicon for the Xa1, Xa4, xa5 and Xa21. Hyangmibyeo1hos, Ir841-85-1-1-2 and Jasmine85 showed the positive amplicon for the Xa1, Xa4 and xa5 genes. Yekywin Yinkya Hmwe and Khao Dawk Mali105 showed the presence of Xa1, Xa4 and Xa21 gene. Masino Basmati showed the presence of xa5, xa13, Xa21 genes. Xa1 and Xa21 genes were noticed in Mihayngbyeo, Tarana Deshi, Mayataung and AZUCENA. Hyangmibyeo2ho, Basmati 6311 and Basmati405 possessed only two R genes such as Xa4 and xa5, and xa5 and xa13, respectively. The evaluation results of bacterial blight resistance genes in aromatic rice germplasm will help in breeding of multi disease resistant varieties.