• Journal of Yeungnam Medical Science
• /
• v.12 no.2
• /
• pp.366-385
• /
• 1995

Epidemiological studies are important in both the prevention and treatment of mycobacterial infections. This study was initiated to establish the pulsed-field gel electrophoresis (PFGE) method, which are not yet extensively studied. The most apprpriate restriction endonucleases included DraI, AsnI, and XbaI. The optimal PFGE condition was different according to the enzymes used. Two stage PFGE was performed, in case of DraI first stage was performed with 10 seconds of initial pulse and 15 seconds of final pulse, while the second stage was performed with 60 seconds of initial pulse and 70 seconds of final pulse. The electrophoresis time for DraI-PFGE was 14 hours for each stage. Electrophoresis was performed for 22 hours, in case of XbaI, with 3 seconds of initial pulse and 12 seconds of final pulse. Electrophoresis was performed for 22 hours, in case of AsnI, with 5 seconds of initial pulse and 25 seconds of final pulse. In all cases the voltage of the electrophoresis was maintained constantly at 200 voltage. Standard mycobacterial strains, which included Mycobacterium bovis BCG, M. tuberculosis, and M. fortuitum, could not be differentiated by PFGE analysis. PFGE analysis was performed to differentiate 9 clinically isolated M. fortuitum strains using AsnI. All M. fortuitum strains showed different genotypes except 2 strains. Cluster analysis divided M. fortuitum strains into 2 large groups. PFGE analysis was performed to further differentiate M. fortuitum isolates using XbaI. The undifferentiated 2 M. fortuitum strains showed different PFGE patterns with Xba I. Cluster analysis of the XbaI-PFGE patterns showed more complex grouping than AsnI-PFGE patterns, which showed that XbaI-PFGE analysis was better than AsnI-PFGE in M. fortuitum genotyping. The top dissimilarity values of AsnI-PFGE and XbaI-PFGE were 0.74 and 0.75, respectively. This value was higher than that of arbitrarily primed polymerase chain reaction (AP-PCR) analysis and lower than that of restriction fragment length polymorphism (RFLP) analysis. This suggested that PFGE can be used as a supportive or alternative genotyping method to RFLP analysis.

• Korean Journal of Ichthyology
• /
• v.18 no.4
• /
• pp.300-310
• /
• 2006

Genomic DNA isolated from three geographical gizzard-shad (Konosirus punctatus) populations in Seocheon (SC), Busan (BS) and Gochang (GC) collected in the West Sea and the southern sea, respectively, off the Korean Peninsula, were PCR-amplified repeatedly. Eight selected decamer and 20-mer primers generated a total of 713 loci in the SC population, 791 in the BS population, and 732 in the GC population, with a DNA fragment size ranging from 100 bp to 2,800 bp. We identified 50 unique loci for the SC population, 70 unique loci for the BS population and 130 for the GC population: 120 shared loci for the three populations. There were 108 specific loci (15.1%) for the SC population, 74 (9.4%) for the BS population, and 67 (9.2%) for the GC population. Eight primers also generated 48 polymorphic loci (6.7%) for the SC population, 26 (3.3%) for the BS population, and 16 (2.2%) for the GC population. The similarity matrix ranged from 0.756 to 0.936 for the SC population, from 0.800 to 0.938 for the BS population, and from 0.731 to 0.959 for the GC population. The dendrogram obtained by the eight primers indicates three genetic clusters: cluster 1 (SEOCHEON 01~SEOCHEON 10), cluster 2 (BUSAN 11~BUSAN 20 and GOCHANG 23~GOCHANG 24), and cluster 3 (GOCHANG 21, 22, 25, 26, 27, 28, 29 and 30). As stated above, some individuals of the GC population appear to belong in BS population. When seeing this result, it was thought with the fact that some individuals of 2 populations seem to come and go partially. Thus, RAPD-PCR analysis revealed a significant genetic distance between the three geographical gizzard-shad populations. Using various decamer and 20-mer primers, RAPD-PCR may be applied to identify specific/polymorphic markers that are particular to a species and geographic population, and to define genetic diversity, polymorphisms, and similarities among geographical gizzard-shad populations.

• Korean Journal of Ichthyology
• /
• v.17 no.3
• /
• pp.173-186
• /
• 2005

Genomic DNA was isolated from two geographic populations of largehead hairtail (Trichiurus lepturus) in Korea and the Atlantic Ocean. The eight arbitrarily selected primers were found to generate common, polymorphic, and specific fragments. The complexity of the banding patterns varied dramatically between primers from the two locations. The size of the DNA fragments also varied widely, from 150 bp (base pairs) to 3,000 bp. Here, 947 fragments were identified in the largehead hairtail population from Korea, and 642 in the largehead hairtail population from the Atlantic Ocean: 148 specific fragments (15.6%) in the Korean population, and 61 (9.5%) in the Atlantic population. In the Korean population, 638 common fragments with an average of 79.8 per primer were observed.; 429 common fragments, with an average of 53.6 per primer, were identified in the Atlantic population. The number of polymorphic fragments in the largehead hairtail population from Korea and the Atlantic Ocean was 76 and 27, respectively. Based on the average bandsharing values of all samples, the similarity matrix ranged from 0.784 to 0.922 in the Korean population, and from 0.833 to 0.990 in the Atlantic population. The bandsharing value of individuals within the Atlantic population was much higher than in the Korean population. The dendrogram obtained by the eight primers indicated two genetic clusters: cluster 1 (KOREAN 01~KOREAN 11), and cluster 2 (ATLANTIC 12~ATLANTIC 22). Individual KOREAN no. 10 from Korea was genetically most closely related to KOREAN no. 11 in the Korean population (genetic distance = 0.038). Ultimately, individual KOREAN no. 01 of the Korean population was most distantly related to ATLANTIC no. 16 of the Atlantic population (genetic distance = 0.708).

• Korean Journal of Agricultural Science
• /
• v.29 no.2
• /
• pp.43-52
• /
• 2002

This study was performed to provide the basic data for preservation and improvement of genetic resources according to finding genetic construction obtained from analysis of genetic characteristics of $\beta$-casein gene in Korean Native goat and Saanen using the PCR-RFLP. This study confirmed the amplified products of 481bp fragments obtained from the amplification of $\beta$-casein loci by PCR. The $\beta$-casein AB genotype showed 481, 284 and 197bp, and $\beta$-casein BB genotype showed 284 and 197bp fragments in Korean Native goat and Saanen. The frequencies of $\beta$-casein genotype in Korean Native goat were 6.25 and 93.75% for AA and AB and the frequencies of $\beta$-casein genotype in Saanen were 57.14 and 42.86% for AA and AB types. The frequencies of $\beta$-casein A and B alleles were 0.031 and 0.969 in Korean Native goat and the frequencies of $\beta$-casein A and B alleles are 0.286 and 0.714 in Saanen, respectively. The nucleotide sequence of $\beta$-casein gene of Korean Native goat was 97.71% higher homology with 11 nucleotide sequences difference of that of goat reported in GeneBank (M90556). Therefore, this study of molecular genetic characteristics by the analysis of genetic polymorphism and sequencing for $\beta$-casein gene should be used as basic and applying data for preservation and improvement of genetic resources in Korean Native goat breeding.

• Development and Reproduction
• /
• v.10 no.4
• /
• pp.227-238
• /
• 2006

Genomic DNAs(gDNAs) were isolated from the venus clam(Gomphina aequilatera) from Samcheok(venus clam from Samcheok; VCS) and Wonsan(venus clam from Wonsan; VCW) located in the East Sea of the Korean Peninsula. The amplified products were generated by agarose gel electrophoresis(AGE) with oligonucleotides primer, detected by staining with ethidium bromide and viewed by ultraviolet ray. The seven arbitrarily selected primers BION-21, BION-23, BION-25, BION-27, BION-29, BION-31 and BION-33 generated the shared loci, polymorphic, and specific loci, with the molecular sizes ranging from 150 bp to 2,400 bp. In this study, 147 polymorphic loci(147/954 loci, 15.41%) in VCS population and 274(274/996 loci, 27.51%) in VCW population were generated with seven primers. These results suggest the genetic variation in VCW population is higher than in VCS population. Especially, the 700 bp bands generated by the primer BION-21 were identified commonly in two Gomphina populations, which identified populations and/or species. This specific primer was found to be useful in the identification of individuals and/or population, resulting from the different DNA polymorphism among individuals/species/population. Two Gomphina populations between the individual SAMCHEOK no. 03 and WONSAN no. 22 showed the longest genetic distance(0.696) in comparison with other individuals used. The complete linkage cluster analysis indicating three genetic groupings and dendrogram revealed close relationships among individual identities within two geographical populations of venus clam(G. aequilatera) from the Samcheok and Wonsan. The intra-species classification and clustering analyses inferred from molecular markers supported the traditional taxonomy of the species based on morphological characters such as shell size, shape and color. Accordingly, as mentioned above, RAPD analysis showed that VCS population was more or less separated from VCW population.

• ANNALS OF ANIMAL RESOURCE SCIENCES
• /
• v.29 no.4
• /
• pp.150-157
• /
• 2018

The Zygote arrest 1 (ZAR1) gene is known to affect early embryonic development in various vertebrates. In this study, we performed the association analysis to check whether there is any significant relationship between semen kinematic characteristics and the ZAR1 gene. To determine semen kinematic characteristics, we measured motility (MOT), straight-line velocity (VSL), curvilinear velocity (VCL), average path velocity (VAP), linearity (LIN), straightness (STR), amplitude of lateral head displacement (ALH), and beat cross frequency (BCF) of spermatozoa in boars. In order to detect single nucleotide polymorphisms (SNPs), we extracted genomic DNA from multiple Duroc boars, and then subsequently used them in sequencing reactions. As a result, three SNPs were detected in the intronic region of ZAR1 gene (g.2435T>C in intron 2, g.2605G>A and g.4633A>C in intron 3 ). SNPs g.2435T>C and g.2605G>A were significantly associated with MOT (p<0.01) and VSL (p<0.05), and g.4633A

• Clinical and Experimental Reproductive Medicine
• /
• v.35 no.2
• /
• pp.99-110
• /
• 2008

Objectives: Preimplantation genetic diagnosis (PGD) has become an assisted reproductive technique for couples carrying genetic conditions that may affect their offspring. Osteogenesis imperfecta (OI) is an autosomal dominant disorder of connective tissue characterized by bone fragility and low bone mass. At least 95% of cases are caused by dominant mutations in the COL1A1 or COL1A2. In this study, we report on our experience clinical outcomes with 5 PGD cycles for OI in two couples. Methods: Before clinical PGD, we assessed the amplification rate and allele drop-out (ADO) rate of alkaline lysis and nested PCR protocol using heterozygous patient's single lymphocytes in the pre-clinical diagnostic tests for OI. We performed 5 cycles of PGD for OI by nested PCR for the causative mutation loci, COL1A1 c.2452G>A and c.3226G>A, in case 1 and case 2, respectively. The PCR products were analyzed by agarose gel electrophoresis, restriction fragment length polymorphism (RFLP) analysis with HaeIII restriction enzyme in the case 1 and direct DNA sequencing. Results: We confirmed the causative mutation loci, COL1A1 c.2452G>A in case 1 and c.3226G>A in case 2. In the pre-clinical tests, the amplification rate was 94.2% and ADO rate was 22.5% in case 1, while 98.1% and 1.9% in case 2, respectively. In case 1, a total of 34 embryos were analyzed and 31 embryos (91.2%) were successfully diagnosed in 3 PGD cycles. Eight out of 19 embryos diagnosed as unaffected embryos were transferred in all 3 cycles, and in the third cycle, pregnancy was achieved and a healthy baby was delivered without any complications in July, 2005. In case 2, all 19 embryos (100.0%) were successfully diagnosed and 4 out of 11 unaffected embryos were transferred in 2 cycles. Pregnancy was achieved in the second cycle and the healthy baby was delivered in March, 2008. The causative locus was confirmed as a normal by amniocentesis and postnatal diagnosis. Conclusions: To our knowledge, these two cases are the first successful PGD for OI in Korea. Our experience provides a further demonstration that PGD is a reliable and effective clinical techniques and a useful option for many couples with a high risk of transmitting a genetic disease.

• Korean Journal of Agricultural Science
• /
• v.36 no.2
• /
• pp.167-177
• /
• 2009

This study was conducted to characterize the DGAT1 gene in Korean Holstein dairy cattle population and examine the relationship of DGAT1 polymorphisms with milk yield and milk fat yield for the genetic improvement of Korean Holstein dairy cattle. Results indicated that the 411 bp PCR products were successfully amplified by DGAT1 specific primers. Sequence analysis indicated that the DGTA1 Q allele had AUG (Lysine, K) nucleotide sequences in 216-218 bp and q allele had GCG (Alanine, A) sequences in the same position. Nucleotide sequence homology between the DGAT1 sequences generated in this study showed 100% homology with bovine DGAT1 sequences in the NCBI database. The genotype frequencies of DGAT1 QQ, Qq, and qq were 16.43, 36.43, and 47.14%, respectively, in Korean Holstein dairy cattle population. The observed Q and q allele frequencies were 0.35 and 0.65, respectively. Statistically significant (P<0.05) results were identified for milk yield and milk fat yield for the DGAT1 genotypes. The Qq genotype Holsteins have significantly higher milk yield and milk fat yield than those of the QQ and qq genotype Holsteins(P<0.05).

• Korean Journal of Poultry Science
• /
• v.45 no.3
• /
• pp.229-236
• /
• 2018

The aim of this study was to evaluate the genetic diversity and relationships of Ogye populations in Korea. A total of 243 genomic DNA samples from 6 Ogye population (Yeonsan Ogye; YSO, Animal Genetic Resources Research Center Ogye; ARO, Chungbuk Ogye; CBO, Chungnam Ogye; CNO, Gyeongbuk Ogye; GBO, Seoul National University Ogye; SUO) and 3 introduced chicken breeds (Rhode Island Red; RIR, White Leghorn; LG, Cornish; CN) were used. Sizes of 25 microsatellite markers were decided using GeneMapper Software(v 5.0) after analyzing ABI 3130XL. A total of 153 alleles were observed and the range was 2 to 10 per each locus. The mean of expected and observed heterozygosity and PIC (Polymorphism Information Content) value was 0.53, 0.50, 0.46 respectively. The lowest genetic distance (0.073) was observed between YSO and SUO, and the highest distance (0.937) between the RIR and CBO. The results of clustering analysis suggested 3 clusters (${\Delta}K=7.96$). Excluding GBO population, 5 Ogye populations (YSO, ARO, CBO, CNO, SUO) were grouped in same cluster with high genetic uniformity (0.990, 0.979, 0.989, 0.994, 0.985 respectively). But GBO population was grouped in cluster 1 with low genetic uniformity (0.340). The results of this study can be use to basic data for the genetic evaluation and management of Ogye populations in Korea.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.51 no.spc1
• /
• pp.185-192
• /
• 2006

This experiment was conducted to assess genetic diversity of waxy corn inbred lines and to identify SSR markers related to major characteristics affected kernel quality for improving waxy corn $F_1$ hybrid with good quality. Diversity of 64 waxy com inbred lines was evaluated using 30 microsatellite markers. The 30 microsatellite markers representing 30 loci in the maize genome detected polymorphisms among the 64 inbred lines and revealed 225 alleles with a mean of 7.5 alleles per primer. The polymorphism Information content (PIC) value ranged from 0.14 to 0.87, with an average of 0.69. Based on Nei's genetic distances, the 64 inbred lines were classified into 9 groups by the cluster analysis. The group I included 26 inbred lines (41%), other groups included 3 to 9 inbred lines. One-way analysis of variance was conducted to identify significant relationship between individual markers and major characteristics that affect kernel quality. The analysis showed that umc1019 was related to amylopectin and crude protein content, me 1020 to amylopectin content and peak viscosity, and bnlg1537 to 100-kernel weight, kernel length, and kernel width.