• Pediatric Infection and Vaccine
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• v.13 no.2
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• pp.106-114
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• 2006

Purpose : Studying the serotypes and emm genotype of group A streptococci(GAS) hold a key role in the investigation of epidemiology, pathogenesis, and resistance to antibiotics. We planed to find out the possible differences in serotypes and genotypes between the invasive and the non-invasive GAS infection. Methods : We obtained 39 isolates from the patients hospitalized in 2004 with the diagnosis of invasive GAS infectious diseases in the Severance Hospital, Yonsei University. We sent the isolates to the WHO Collaboratory Center in University of Minnesota and analyzed T serotypes and emm genotypes. These results were compared with non-invasive GAS infections in our hospital. Results : Compared this data with the results of 2003 to 2004, T2/28, T3, T5/27/44, T9 and NT were more prevalent. The NT showed statistically significant difference(P=0.019). The emm 3, emm 9, emm 18, emm 44 and emm provision type STG485 were more frequent genotypes compared with the study in 2003~2004, relatively. The emm provision type STG485 had statistically significant difference(P=0.000). The incidence of T12 plus T4, known as erythromycin(EM) resistant serotypes, was as low as 17.9% in this study, compared with those of non-invasive strains. Conclusion : The incidence of EM-resistant strains is supposed not to be higher in invasive GAS infection. We could find out possible higher incidence of rheumatogenic strains in the invasive GAS infections. It seems to be important to have an effort on studying of serotyping and genotyping for the monitoring of strains and to know the epidemiologic characteristics.

• Journal of Animal Science and Technology
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• v.53 no.2
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• pp.89-97
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• 2011

In this study, the efficiency of microsatellite (MS) markers for pork quality was examined and further, their suitability to domestic pork industry also was verified, by measuring meat quality parameters of Berkshire breeds. A total of 323 pigs of Berkshire breeds were slaughtered and subjected to meat quality evaluation. In addition, the genomic DNAs from blood samples of slaughtered pigs were used for genotyping analysis of 50 MS markers. The results revealed that Berkshire breeds have excellent meat quality, compared with the popular domestic breeds such as Duroc, Yorkshire, and Landrace. Noticeably, the Berkshire breeds exhibited a significant post-mortem pH24hr ($5.88{\pm}0.01$) and fat content ($2.878{\pm}0.06$). Through the linkage analysis between MS markers, 14 MS markers showed significant association with meat quality traits (p<0.05). Maximum significant differences of 0.55 pH24hr value and 2.04% fat content were observed between the highest and lowest allele populations. If these 14 MS markers are applied to the pork quality diagnosis kit, the synergistic effect can be expected in meat quality parameters such as meat color, fat content, pH 24 hr, cooking loss, drip loss and water-holding capacity.

• Journal of Life Science
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• v.20 no.6
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• pp.825-830
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• 2010

Two diallelic markers at candidate gene loci, the prolactin receptor 3 (PRLR3) gene and the retinol-binding protein 4 (RBP4) gene were evaluated for their association with growth and litter size traits in Berkshire. Genetic evaluation was conducted for 5,919 pigs with pedigree information, which included 3,480 growth performance records and 775 litter size records of 224 sows. From the same herd, genotyping was carried out on 144 and 156 animals for PRLR3 and RBP4, respectively. After assigning a genotype to subjects in which both parents had a homozygous genotype, numbers of genotyped animals increased to 474 and 338, for the PRLR3 gene and RBP4 gene, respectively. The genotype effects of two markers were estimated with breeding values of the genotyped animals. The additive effects of total number of piglets born and number of piglets born alive in the PRLR3 locus were -0.28 and -0.13, respectively. The dominance effect of the RBP4 locus on average daily gain was -10.58 g. However, the polymorphism of the RBP4 locus in total number of piglets born and number of piglets born alive has shown -0.34 and -0.33 of the additive genetic effects. In view of the results, MAS (marker-assisted selection) favoring B alleles of RBP4 and PRLR3 loci could potentially accelerate the rate of the genetic improvement in the litter size traits.

• Sleep Medicine and Psychophysiology
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• v.20 no.2
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• pp.63-68
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• 2013

Objectives: Several evidence has been suggested that the circadian gene variants contribute to the pathogenesis of seasonal affective disorder. In this study, we aimed to investigate the polymorphism in RORA (Retinoid-related orphan receptor A) gene in relation to seasonal variations among healthy young adults in Seoul, Korea. Methods: A total of 507 young healthy adult subjects were recruited by advertisement. Seasonal variations were assessed by the Seasonality Pattern Assessment Questionnaire (SPAQ). Single-nucleotide polymorphism in the RORA rs11071547 gene was genotyped by PCR in 507 individuals. Considering summer type as confounding factor, we conducted analysis 478 subjects except 29 subjects of summer type. The Chi-square test was conducted to compare differences between groups of seasonals and non-seasonals. Association between genotypes and Global Seasonality Score (GSS) were tested using ANCOVA (Analysis of covariance). Results: In this sample, the prevalence of SAD was 12.1% (winter type 9.3%, summer type 2.8%). There is no significant difference in genotyping distribution of RORA rs11071547 between groups of seasonals and non-seasonals. Global seasonality score (GSS) and scores of all subscales except body weight and appetite were not significantly different between the group with C allele homozygote and the group with T allele homozygote and heterozygote (p-value 0.138). Scores of body weight and appetite were significantly higher in group with C allele homozygotes. Conclusion: These results suggest that RORA gene polymorphism play a role in seasonal variations in appetite and body weight and is associated with susceptibility to seasonal affective disorder in some degree in the population studied.

• Journal of Life Science
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• v.22 no.3
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• pp.366-372
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• 2012

This study was conducted to estimate the extent of linkage disequilibrium (LD) and effective population size using whole genomic single nucleotide polymorphisms (SNP) genotyped by DNA chip in Hanwoo. Using the blood samples of 35 young bulls born from 2005 to 2008 and their progenies (N=253) in a Hanwoo nucleus population collected from Hanwoo Improvement Center, 51,582 SNPs were genotyped using Bovine SNP50 chips. A total of 40,851 SNPs were used in this study after elimination of SNPs with a missing genotyping rate of over 10 percent and monomorphic SNPs (10,730 SNPs). The total autosomal genome length, measured as the sum of the longest syntenic pairs of SNPs by chromosome, was 2,541.6 Mb (Mega base pairs). The average distances of all adjacent pairs by each BTA ranged from 0.55 to 0.74 cM. Decay of LD showed an exponential trend with physical distance. The means of LD ($r^2$) among syntenic SNP pairs were 0.136 at a range of 0-0.1 Mb in physical distance and 0.06 at a range of 0.1-0.2 Mb. When these results were used for Luo's formula, about 2,000 phenotypic records were found to be required to achieve power > 0.9 to detect 5% QTL in the population of Hanwoo. As a result of estimating effective population size by generation in Hanwoo, the estimated effective population size for the current status was 84 heads and the estimate of effective population size for 50 generations of ancestors was 1,150 heads. The average decreasing rates of effective population size by generation were 9.0% at about five generations and 17.3% at the current generation. The main cause of the rapid decrease in effective population size was considered to be the intensive use of a few prominent sires since the application of artificial insemination technology in Korea. To increase and/or sustain the effective population size, the selection of various proven bulls and mating systems that consider genetic diversity are needed.

• Journal of agriculture & life science
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• v.46 no.5
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• pp.73-82
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• 2012

Allele information from the analysis of the 13 microsatellite (MS) markers, were classified into the $F_0$, $F_1$ and $F_2$ generations, and probabilities of the same individual emergency in each generation was calculated. As a result, the 13 MS markers showed an estimate of $3.84{\times}10^{-23}$ on the premise of the randomly mated group of $F_2$, which implies that the same individuals may emerge by the use of 37 kinds of SNP markers. In this study, the experimental pigs were intercross between only 2 breeds (Korean native pig and Landrace). In addition, the success rate of paternity tests was analyzed on the whole group, by the use of the 13 MS markers and 37 SNP markers. As regards the exclusionary power of the second parent ($PE_{pu}$), MS markers and SNP markers showed 0.97897 and 0.99149, respectively. In relation to the parent exclusion power of both parent (PE), MS markers and SNP markers showed 0.99916 and 0.99949, respectively. In the case of the estimate to identify parental candidates that had the highest probability ($PNE_{pp}$), the two showed 1.00000 all. The Korean pig industry tends to mass produce hogs with limited numbers of alleles in limited parents. Such being the case, there is a need to organize a marker, for which it is imperative to find markers with high efficiency and high economic feasibility of the characteristics of DNA markers, sample size, the accuracy and expenses of genotyping cost, the manageability of data and the compatibility among analysis systems.

• Journal of Korean Society of Forest Science
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• v.112 no.2
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• pp.157-172
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• 2023

Controlled pollination (CP) is an important method in tree breeding programs because CP quickly generates desirable genotypes and rapidly maximizes genetic gains. However, few studies have evaluated the efficiency and success rate of CP in the breeding program of Pinus densiflora. To evaluate CP and the management of control pollinated progenies, we used 159 individuals in CB2 × KW40 or KW40 × CB2 populations that were established in 2015. After genotyping microsatellite loci, we estimated whether the number of primers was sufficient or not. Then, we performed pedigree analysis. The result showed that the number of primers was sufficient. By pedigree analysis, we found out that 60 of 159 individuals had been generated by the mating between CB2 and KW40. In the maternity analysis, there was evidence to indicate the possibility of management problems. Therefore, we excluded 54 individuals and repeated the pedigree analysis. In the second analysis, 47 of 105 individuals were generated by the mating between CB2 and KW40. To increase the efficiency of CP in tree breeding programs, several precautions are required. It is necessary to identify the exact clone names of the mother and father trees. In addition, CP processes should be performed properly, including deciding on the schedule of CP and the isolation of female strobili or flowers. Finally, the monitoring of hybrid progenies management after mating is important. Molecular markers should be used to identify the clone names of the mother and father trees and for monitoring post hoc management. This study provides a reference for tree breeding programs for the future control pollination of pine species.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.68 no.3
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• pp.134-146
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• 2023

Phytophthora root rot (PRR) is a major soybean disease caused by an oomycete, Phytophthora sojae. PRR can be severe in poorly drained fields or wet soils. The disease management primarily relies on resistance genes called Rps (resistance to P. sojae). This study aimed to identify resistance loci associated with resistance to P. sojae isolate 40468 in Daepung × CheonAl recombinant inbred line (RIL) population. CheonAl is resistant to the isolate, while Daepung is generally susceptible. We genotyped the parents and RIL population via high-throughput single nucleotide polymorphism genotyping and constructed a set of genetic maps. The presence or absence of resistance to P. sojae was evaluated via hypocotyl inoculation technique, and phenotypic distribution fit to a ratio of 1:1 (R:S) (χ² = 0.57, p = 0.75), indicating single gene mediated inheritance. Single-marker association and the linkage analysis identified a highly significant genomic region of 55.9~56.4 megabase pairs on chromosome 18 that explained ~98% of phenotypic variance. Many previous studies have reported several Rps genes in this region, and also it contains nine genes that are annotated to code leucine-rich repeat or serine/threonine kinase within the approximate 500 kilobase pairs interval based on the reference genome database. CheonAl is the first domestic soybean genotype characterized for resistance against P. sojae isolate 40468. Therefore, CheonAl could be a valuable genetic source for breeding resistance to P. sojae.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.23
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• pp.10061-10066
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• 2015

Background: The aetiological relationship between human papillomavirus (HPV) infection and cervical cancer (CC) is widely accepted. Our goal was to determine the prevalence of HPV types in Mexican women attending at the Mexican Institute for Social Security from different areas of Mexico. Materials and Methods: DNAs from 2,956 cervical samples were subjected to HPV genotyping: 1,020 samples with normal cytology, 931 with low-grade squamous intraepithelial lesions (LGSIL), 481 with high grade HGSIL and 524 CC. Results: Overall HPV prevalence was 67.1%. A total of 40 HPV types were found; HPV16 was detected in 39.4% of the HPV-positive samples followed by HPV18 at 7.5%, HPV31 at 7.1%, HPV59 at 4.9%, and HPV58 at 3.2%. HPV16 presented the highest prevalence both in women with altered or normal cytology and HPV 18 presented a minor prevalence as reported worldwide. The prevalence ratio (PR) was calculated for the HPV types. The analysis of PR showed that HPV16 presents the highest association with CC, HPV 31, -33, -45, -52 and -58 also demonstrating a high association. Conclusions: The most prevalent HPV types in cervical cancer samples were -16, -18, -31, but it is important to note that we obtained a minor prevalence of HPV18 as reported worldwide, and that HPV58 and -52 also were genotypes with an important prevalence in CC samples. Determination of HPV genotypes is very important in order to evaluate the impact of vaccine introduction and future cervical cancer prevention strategies.