• International Journal of Industrial Entomology and Biomaterials
• /
• v.28 no.2
• /
• pp.39-50
• /
• 2014

In order to understand the diversity and genetic relationships of silkworm strains preserved in Korea, we genotyped 78 Bombyx mori strains (Bombycidae: Lepidoptera) originating from Japan, using eight polymorphic microsatellite loci. We obtained per-locus allele numbers ranging from 5 to 16 (with an average value of 9.1), per-locus observed heterozygosity ranging from 0.13 to 1.00, and per-locus polymorphic information content ranging from 0.36 to 0.77, indicating that some loci are highly variable. Phylogenetic analysis with the eight concatenated microsatellite loci showed no clustering based on known strain characteristics and origin. Nineteen strain-specific apomorphic alleles, which discriminated 16 of the 78 silkworm strains, were obtained from eight loci. These strain-specific alleles can thus be utilized for routine discrimination of strains from Japan, without any further typing of other loci. Homozygotes were also observed at some loci (27 of 118 genotypes), which can also be used to discriminate several strains by typing a few loci. These results showed that eight microsatellite loci described herein were sufficiently variable to discriminate among the 78 silkworm strains we examined, and may be useful for future investigations of this economically important species.

• Korean Journal of Clinical Oncology
• /
• v.9 no.2
• /
• pp.80-86
• /
• 2013

Purpose: Hypermethylation of human mut L homologue 1 (hMLH1) promoter region is known to cause sporadic microsatellite instability (MSI) colorectal cancers. 5,10-methylenetetrahydrofolate reductase (MTHFR) is the key enzyme in folate metabolism, acting as a methyl donor for DNA methylation. In this study, we investigate whether the polymorphism of MTHFR 677C>T plays a role in the alteration of the promoter-specific hypermethylation, predisposing to MSI colorectal cancers. Methods: Total of 487 sporadic colorectal cancer patients in CHA Bundang Medical Center were collected. MSI was identified when two or more are positive among five microsatellite markers (BAT25, BAT26, D17S250, D5S346, D2S123). The others were classified as microsatellite stable (MSS). Polymorphism of MTHFR 677C>T was genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results: MSI was observed in 65 of 487 patients (12.73%). MSI colorectal cancers showed similar clinicopathological features with previously reported; younger age onset, right-sided preponderance, mucinous and poorly differentiated histology, lower stage, fewer lymph node metastases than MSS tumors (each P<0.05). The frequency of MTHFR 677TT genotype was 17.7% in the MSI group higher than 14.6% in the MSS group (P=0.17). Although not statistically significant, compared to the MTHFR 677CC referent, MTHFR 677 CT+TT genotype was more likely to have MSI than MSS (odds ratio, 1.81; 95% confidence interval, 0.94 to 3.68; P=0.06). Conclusion: This study demonstrated higher frequency of MTHFR 677TT genotype in MSI colorectal cancers. Furthermore, individuals with MTHFR 677CT+TT variant type might potentially develop MSI rather than MSS colorectal cancers.

• Korean Journal of Ichthyology
• /
• v.21 no.4
• /
• pp.221-226
• /
• 2009

Six microsatellite DNA markers were used to investigate the genetic variability between wild populations and cultured stocks of olive flounder Paralichthys olivaceus. The average of observed (Ho) and expected heterozygosity (He) ranged from 0.722 to 0.959, and from 0.735 to 0.937, respectively. There was no distinguishable difference between the wild populations and cultured stocks in terms of the observed and expected heterozygosities. However, number of alleles per locus differed markedly between the two fish groups: 19.7 to 21.8 for the wild populations and 12.0 to 14.7 for the cultured stocks. This result gives important information concerning the production of seedling for the improvement of genetic diversity in this species.

• Journal of agriculture & life science
• /
• v.44 no.6
• /
• pp.91-99
• /
• 2010

We used a multiplex PCR primer set composed of 11 microsatellite (MS) markers and two sexing markers for gender detection. Genomic DNA extracted from hair roots of 3,510 Hanwoo were genotyped. Based on the 11MS markers, no animals had identical genotypes(TGLA227, BM2113, TGLA53, ETF10, SPS115, TGLA122, ETH3, ETH225, BM1824 and INRA23). The expected probability of identity among genotypes of random individuals (PI), the probability of identity among genotypes from random half-sibs ($PI_{half-sibs}$) and among genotypes of random individuals, and the probability of identity among genotypes from random sibs ($PI_{sibs}$) were estimated as $1.31{\times}10^{-23}$, $2.52{\times}10^{-16}$and $1.09{\times}10^{-6}$, respectively using the API-CALC program, version 1.0. We successfully completed the genotype analysis of 3,510 Hanwoo with a 3.93% genotyping failure rate. It was revealed that extracting DNA from the hair root was a time-efficient and cost-effective method to collect specimens for DNA isolation from live animals. This method also minimized stress for the animals during specimen collection. Among the hair roots from the back, belly, upper tail and lower tail, 5~13 hair roots of the lower tail led to the best genotype analysis results. Finally, we established a 96-well-format method of DNA preparation applicable for high- throughput genotype analysis.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
• /
• v.26 no.4
• /
• pp.337-344
• /
• 2000

Germ-line mutations at DNA repair loci confer susceptibility to colon cancer in hereditary non-polypopsis colorectal cancer. Somatic loss of DNA mismatch repair gene has been reported in a large variety of other tumor types. Replication errors(RERs) judged by microsatellite instability(MSI) and its associated mutations have been recognized as an important mechanism in various tumor types. To investigate associations between MSI and oral squamous cell carcinoma, the frequency of MSI using 12 microsatellite markers were analyzed for the series of oral tumors. Of 17 tumors, 8 cases(47%) did not show instability at any of the 12 loci; 5(29%) showed instability at $2{\sim}3$ loci; and 4(24%) showed instability above 4 loci. The 4 cases showing widespread MSI did not differ from those without evidence of instability in terms of age at diagnosis, degree of differentiation, metastasis to lymph node, tumor location or the presence of mutations in the p53 tumor suppressor gene. DCC and D17S 796 were the most frequently detected in MSI analysis. There were no correlation between smoking and MSI frequency, instead, smoking was suggested to increase the mutation rate of p53 and development of oral carcinomas.

• The Korean Journal of Malacology
• /
• v.28 no.3
• /
• pp.269-274
• /
• 2012

The genetic variation of Ark Shell, Scapharca broughtonii black was estimated using six polymorphic microsatellite (MS) loci in 443 individuals collected from five populations in Korea. The mean numbers of alleles per locus in five populations were 10-28. The mean number of alleles per locus in Jinhae Hatchery (JHH) population showed the least value as 15.5, but that in Gangjin (GJ) population showed the most value as 20.3. The mean expected heterozygosity in Saryangdo (SR) population showed the least value as 0.817, but that in Gangjin (GJ) population showed the most value as 0.831. In Jinhae hatchery(JHH) population, the mean expected heterozygosity was 0.822, there was no significant difference from those of wild population. The $F_{ST}$ values in Gangjin (GJ) population showed significant difference from those of the other populations, which revealed Gangjin (GJ) population is genetically different from the other populations. The $F_{ST}$ values among Jinhae Hatchery (JHH) population, Jinhae (JH) population and Saryangdo (SR) population showed lower values than the others, which implies there was a gene flow among these three populations. The $F_{ST}$ value and genetic distance between Jinhae (JH) population and Saryangdo (SR) population showed the least value as 0.0001 and 0.0386, indicating that these two populations were genetically the same.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
• /
• v.37 no.6
• /
• pp.550-555
• /
• 2011

Chromosomal loss of heterozygosity (LOH) is a common mechanism for the inactivation of tumor suppressor genes in human epithelial cancers. LOH patterns can be generated through allelotyping using polymorphic microsatellite markers; however, owing to the limited number of available microsatellite markers and the requirement for large amounts of DNA, only a modest number of microsatellite markers can be screened. Hybridization to single nucleotide polymorphism (SNP) arrays using Affymetarix GeneChip Mapping 10 K 2.0 Array is an efficient method to detect genome-wide cancer LOH. We determined the presence of LOH in oral SCCs using these arrays. DNA was extracted from tissue samples obtained from 10 patients with tongue SCCs who presented at the Hospital of Tokyo Dental College. We examined the presence of LOH in 3 of the 10 patients using these arrays. At the locus that had LOH, we examined the presence of LOH using microsatellite markers. LOH analysis using Affymetarix GeneChip Mapping 10K Array showed LOH in all patients at the 1q31.1. The LOH regions were detected and demarcated by the copy number 1 with the series of three SNP probes. LOH analysis of 1q31.1 using microsatellite markers (D1S1189, D1S2151, D1S2595) showed LOH in all 10 patients (100). Our data may suggest that a putative tumor suppressor gene is located at the 1q31.1 region. Inactivation of such a gene may play a role in tongue tumorigenesis.

• Korean Journal of Ichthyology
• /
• v.20 no.4
• /
• pp.248-254
• /
• 2008

Olive flounder (Paralichthys olivaceus) is one of the most popular farmed fish in Korea. Genetic variability of the fish was investigated by means of microsatellite DNA markers. All of the 8 microsatellite loci were analyzed in this study. For the confirmation of genetic variation during a shift in generation, microsatellite variability was compared within the same hatchery strains but produced in different spawning years. When genetic variability of farmed flounders produced in 2006 and 2007 was compared with that of 2003, a marked reduction of genetic variability was observed in the 2006 and 2007 populations. Mean number of alleles per locus and expected mean heterozygosity decreased from 9.75 and 0.796 (in 2003 population) to 7.78 and 0.785 (in 2006 population), respectively. Moreover, we have observed the distortion of allele frequency. These results show that reduced genetic variability of farmed olive flounder in processed generation has lower numbers of alleles and genetic variability than these of wild fish. Our results suggest that to have a sustainable aquaculture of this species, there is need for scientific broodstock management based on genetic variation and more intensive breeding practices to improve genetic diversity and to avoid detrimental inbreeding effects.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.4
• /
• pp.457-466
• /
• 2015

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan's early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value ($F_{IS}$) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high $F_{ST}$ values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes.

• Plant Resources
• /
• v.7 no.2
• /
• pp.93-103
• /
• 2004

Genetic background and phylogenetic relationships among 20 Korean wheat cultivars were assessed using microsatellites after amplifying with 13 SSR primer pairs. Average allele number per primer pair was 3.36. Genetic similarities for every pair of cultivars ranged from 0.42 to 0.97, with 0.69 of overall average. Korean cultivars were divided into two major groups based on microsatellite DNA polymorphisms. Group I consisted of relatively old cultivars developed until 1970s, and group II contained the recent cultivars developed during 1980s and 1990s. Amongst old elite cultivars/lines, ‘Yukseung 3’, ‘Norin 12’ and ‘Norin 72’ contributed most to the genetic background of cultivars belonging to group I, and ‘Norin 4’, ‘Norin 12’, ‘Norin 43’ and ‘Norin 72’ to group II, respectively. The phylogenetic relationship of Korean wheat cultivars was in accordance with the genealogical data of each cultivar. The genetic background of each cultivar was assessed from the point of breeding and germplasm management such as variety identification and duplicated accessions for assisting in developing a system for the registration of new variety based on the molecular characterization in future.