• Asian-Australasian Journal of Animal Sciences
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• v.19 no.12
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• pp.1685-1690
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• 2006

Kenkatha cattle, a draft purpose breed, which can survive in a harsh environment on low quality forage, was explored genetically exploiting FAO-suggested microsatellite markers. The microsatellite genotypes were derived by means of the polymerase chain reaction (PCR) followed by electrophoretic separation in agarose gels. The PCR amplicons were visualized by silver staining. The allelic as well as genotypic frequencies, heterozygosities and gene diversity were estimated using standard techniques. A total of 125 alleles was distinguished by the 21 microsatellite markers investigated. All the microsatellites were highly polymorphic with mean allelic number of 5.95${\pm}$1.9 (ranging from 3-10 per locus). The observed heterozygosity in the population ranged between 0.250 and 0.826 with a mean of 0.540${\pm}$0.171, signifying considerable genetic variation. Bottleneck was examined assuming all three mutation models which showed that the population has not experienced bottleneck in recent past. The population displayed a heterozygote deficit of 21.4%. The study suggests that the breed needs to be conserved by providing purebred animals in the breeding tract.

• Journal of Plant Biology
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• v.38 no.1
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• pp.39-45
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• 1995

Glycine soja Sieb. et Zucc., a predominantly selfing annual, has been served as a reservoir of germplasm for soybean, G. max (L.) Merr., cultivar improvement. This study describes the levels and distribution of genetic variation within and among 22 Korean populations of G. soja using starch gel electrophoresis. The species maintains very similar levels of genetic variability within populations observed in most other annuals. At the population level, the mean percent of polymorphic loci (P) was 32.6%, mean number of allele per locus (A) was 1.32, and mean expected heterozygosity (He) was 0.112. In addition, total genetic diversity (HT) calculated only for polymorphic loci was 0.347. However, significant differences in allele frequencies among populations were found for all loci (P<0.001 in each case) and, on average, about 70% of the total variation in the species is common to all populations. Indirects estimate of the number of migrants per generation (Nm=0.58, calculated from mean GST) indicates that gene flow is low among Korean populations of the species. In addition, analysis of fixation indices revealed a substantial heterozygote deficiency in most populations and at all loci. This indicates that most populations sampled may have been substructed largely due to inbreeding (predominantly selfing) and restricted gene flow, coupled with founder effect and genetic drift. Considering a high genetic divergence among populations, it is recommended that several Korean populations of the species should be preserved, especially such as populations in the eastern and southeastern Korean peninsula with high variation.

• Journal of Korean Society of Forest Science
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• v.98 no.5
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• pp.531-538
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• 2009

We used enzyme electrophoresis to evaluate genetic diversity in five populations of endemic ash, Fraxinus chiisanensis in Korea. Of 15 putative allozyme loci examined 26.7% were polymorphic and expected heterozygosity for the species was low (0.082). Within the range, population were highly differentiated ($F_{ST}$=0.356) and little genetic variation was explained by geography. The pattern of distribution of variation showed low genetic variation within populations and pronounced divergence among populations, which was consistent with the prediction for the effects of limited gene flow and local genetic erosion. Although the frequencies of male plants were dominant ranging from 79.3% to 89.4%, most mating events seems to be inevitable mating between relatives in small populations based on heterozygote deficiency of this species. Small effective population size and the limited dispersal contributed to the low rates of gene flow within as well as between populations.

• BMB Reports
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• v.51 no.1
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• pp.1-2
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• 2018

Positive selection on a new beneficial mutation generates a characteristic pattern of DNA sequence polymorphism when it reaches an intermediate allele frequency. On genome sequences of African Drosophila melanogaster, we detected such signatures of selection at 37 candidate loci and identified "sweeping haplotypes (SHs)" that are increasing or have increased rapidly in frequency due to hitchhiking. Based on geographic distribution of SH frequencies, we could infer whether selective sweeps occurred starting from de novo beneficial mutants under simple constant selective pressure. Single SHs were identified at more than half of loci. However, at many other loci, we observed multiple independent SHs, implying soft selective sweeps due to a high beneficial mutation rate or parallel evolution across space. Interestingly, SH frequencies were intermediate across multiple populations at about a quarter of the loci despite relatively low migration rates inferred between African populations. This invokes a certain form of frequency-dependent selection such as heterozygote advantage. At one locus, we observed a complex pattern of multiple independent that was compatible with recurrent frequency-dependent positive selection on new variants. In conclusion, genomic patterns of positive selection are very diverse, with equal contributions of hard and soft sweeps and a surprisingly large proportion of frequency-dependent selection in D. melanogaster populations.

• Korean Journal of Plant Taxonomy
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• v.39 no.3
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• pp.125-129
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• 2009

The genetic diversity plays a significant role in determining a species' survival and perseverance. Endangered species often lack genetic variation, which makes them vulnerable to numerous dangers of extinction including selection, genetic drifts and human interference. Knowing an endangered species' genetic background greatly enhances conservation efforts since it reveals why, what and how to conserve that species. Cotoneaster wilsonii is an endangered plant species endemic to Ulleung island, but not enough genetic research has been done on this taxon for its effective conservation plans. In this study, three populations of C. wilsonii in Ulleung island underwent allozyme analysis through starch gel electrophoresis. 10 loci were analyzed and F-statistics was calculated. Overall data indicated that C. wilsonii possessed low genetic diversity with intense inbreeding, heterozygote deficiency and low differentiation among populations. These results implied that C. wilsonii was recently introduced to the Ulleung island from ancestor species, and did not have much time to differentiate. Current status of C. wilsonii habitats is very fragile and vulnerable, with increasing tourism constantly threatening the species' survival. It is very likely that C. wilsonii will become extinct in near future unless organized conservation protects its populations and genetic diversity.

• Journal of Genetic Medicine
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• v.15 no.2
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• pp.110-114
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• 2018

Ataxia-telangiectasia (AT; OMIM 208900) is a rare autosomal recessive inherited progressive neurodegenerative disorder, with onset in early childhood. AT is caused by homozygous or compound heterozygous mutations in ATM (OMIM 607585) on chromosome 11q22. The average prevalence of the disease is estimated at 1 of 100,000 children worldwide. The prevalence of AT in the Republic of Korea is suggested to be extremely low, with only a few cases genetically confirmed thus far. Herein, we report a 5-year-old Korean boy with clinical features such as progressive gait and truncal ataxia, both ankle spasticity, dysarthria, and mild intellectual disability. The patient was identified as a compound heterozygote with two novel genetic variants: a paternally derived c.5288_5289insGA p.(Tyr1763*) nonsense variant and a maternally derived c.8363A>C p.(His2788Pro) missense variant, as revealed by next-generation sequencing and confirmed by Sanger sequencing. Based on claims data from the Health Insurance Review and Assessment Service Republic of Korea, we calculated the prevalence of AT in the Republic of Korea to be about 0.9 per million individuals, which is similar to the worldwide average. Therefore, we suggest that multi-gene panel sequencing including ATM should be considered early diagnosis.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.4
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• pp.2337-2342
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• 2013

Meta-analyses have shown that microRNA polymorphisms have variable effects in different population. Yet, no meta-analysis investigated the association of two common polymorphisms of miRNA, mir-499 rs3746444 polymorphism and mir-149 rs2292832 polymorphism, with cancer risk in the Chinese population. We searched the PubMed, Web of Knowledge, MEDLINE, CNKI databases, as well as Cochrane library, updated on December 31, 2012 for assays regarding cancer risk association with these two common polymorphisms in the present meta-analysis. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were used to explore the strength of associations. The results showed that rs3746444 polymorphism was associated with increased cancer risk (dominant model: GG/AG vs. AA: OR = 1.43, 95% CI: 1.14-1.80; recessive model: GG vs. AG/AA: OR = 1.54, 95% CI: 1.04-2.30; homozygote model: GG vs. AA: OR = 1.69, 95% CI: 1.10-2.60; heterozygote model: AG vs. AA: OR = 1. 35, 95% CI: 1.09-1.67), and rs3746444 was associated with liver cancer in the subgroup of cancer types. For the rs2292832 polymorphism, the results showed no significant risk association in both overall pooled analysis and subgroup of cancer types, smoking status, gender and tea drinking status in the Chinese population. This meta-analysis suggested that the rs3746444 GG genotype is associated with increased cancer risk, especially liver cancer, while the rs2292832 polymorphism showed no association with cancer risk in Chinese.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.9
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• pp.1234-1240
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• 2009

Gene flow, genetic structure and differentiation of Kutchi, Mehsana and Sirohi breeds of goat from North-Western India were evaluated based on 25 microsatellite markers so as to support breed conservation and improvement decisions. The microsatellite genotyping was carried out using an automated DNA sequencer. The gene diversity across the studied loci for the Kutchi breed varied from 0.57 (ILST 065) to 0.93 (OarFCB 304, OMHC 1, ILSTS 058) with an overall mean of 0.79${\pm}$0.02. The corresponding values for Mehsana and Sirohi breeds were 0.16 (ILST 008) to 0.93 (OMHC 1, ILSTS 058) with an average of 0.76${\pm}$0.04, and 0.50 (ILSTS 029) to 0.94 (ILSTS 058) with an average of 0.78${\pm}$0.02, respectively. The Mehsana breed had lowest gene diversity among the 3 breeds studied. All the populations showed an overall significant heterozygote deficit ($F_{is}$). The Fis values were 0.26, 0.14 and 0.36 for Kutchi, Mehsana and Sirohi goat breeds, respectively. Kutchi and Mehsana were more differentiated (16%) followed by Mehsana and Sirohi (13%).The measures of standard genetic distance between pairs of breeds indicated that the lowest genetic distance was between Kutchi and Sirohi breeds (0.73) and the largest genetic distance was between Mehsana and Kutchi (1.0) followed by Sirohi and Mehsana (0.75) breeds. Mehsana and Kutchi are distinct breeds and this was revealed by the estimated genetic distance between them. All measures of genetic variation revealed substantial genetic variation in each of the populations studied, thereby showing good scope for their further improvement.

• Journal of Gastric Cancer
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• v.20 no.2
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• pp.127-138
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• 2020

Purpose: Mucin 1 (MUC1) was identified as a gastric cancer (GC) susceptibility gene by genome-wide association studies in Asians and candidate gene studies in Europeans. This study aimed to investigate the association between the MUC1 rs4072037 polymorphism and GC in terms of the Lauren classification and long-term clinical outcomes. Materials and Methods: A total of 803 patients with GC and 816 unrelated healthy controls were enrolled in the study. The association between the MUC1 rs4072037 variant and GC histological types and clinical outcomes, including tumor recurrence and prognosis was investigated. Results: The major A allele of rs4072037 was associated with increased GC risk (P<0.05). In subtype analysis, the association was most significant for diffuse-type GC (P<0.05) and in a dominant model (P<0.05), whereas there was no association with intestinal-type GC (P>0.05). Cox proportional hazards analysis revealed the heterozygote AG rs4072037 allele as an independent risk factor influencing tumor recurrence and disease-related death in diffusetype GC (P<0.05). but not in intestinal-type GC (P>0.05). Conclusions: The exonic single nucleotide polymorphism rs4072037 in MUC1 was associated with diffuse-type GC and was an independent risk factor influencing tumor recurrence and disease-related death in diffuse-type GC.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5451-5454
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• 2012

Objective: The objective of this study was to evaluate the association of MDR1 gene polymorphisms with susceptibility to hepatocellular carcinoma (HCC). Methods: A total of 689 HCC patients and 680 cancer-free subjects were enrolled. Human MDR1 gene polymorphisms were investigated by created restriction site-polymerase chain reaction (CRS-PCR) and DNA sequencing methods. Multiple logistic regression models were applied to estimate the association between MDR1 gene polymorphisms and susceptibility to HCC. Results: We detected a novel c.4125A>C polymorphism and our findings suggested that this variant was significantly associated with susceptibility to HCC. A significantly increased susceptibility to HCC was noted in the homozygote comparison (CC versus AA: OR=1.621, 95% CI 1.143-2.300, ${\chi}^2$=7.4095, P=0.0065), recessive model (CC versus AC+AA: OR=1.625, 95% CI 1.167-2.264, ${\chi}^2$=8.3544, P=0.0039) and allele contrast (C versus A: OR=1.185, 95% CI 1.011-1.389, ${\chi}^2$=4.4046, P=0.0358). However, no significant increase was observed in the heterozygote comparison (AC versus AA: OR=0.995, 95% CI 0.794-1.248, ${\chi}^2$=0.0017, P=0.9672) and dominant model (CC+AC versus AA: OR=1.106, 95% CI 0.894-1.369, ${\chi}^2$=0.8560, P=0.3549). Conclusions: These findings suggest that the c.4125A>C polymorphism of the MDR1 gene might contribute to susceptibility to HCC in the Chinese population. Further work will be necessary to clarify the relationship between the c.4125A>C polymorphism and susceptibility to HCC on larger populations of diverse ethnicity.