• Plant Resources
• /
• 제1권2호
• /
• pp.81-91
• /
• 1998

Fifty-nine Korean soybean (Glycine max L. Merr.) landrace accessions were tested for genotype fingerprinting, differentiation and association between morphological traits and SSR profile. Using 8 SSR loci, 59 varieties were divided into 55 groups, and only 4 pairs of varieties were not uniquely identified. The resolving power of SSR for soybean genotyping was much higher than that of the morphological traits that were studied. Identification efficiency also differed among SSR loci. Those loci with higher numbers of alleles distinguished varieties more effectively. Genetic differentiation values of the soybean landraces varied from 0.57 to 0.82 with a mean of 0.68. The number of alleles detected by the 8 loci ranged from 3 to 8. and the effective number of alleles ranged from 2.3 to 5.1. In a study of the association of SSR alleles with morphological traits, some alleles seemed to be related with some specific morphological traits. Comparison of two kinds of dendrograms which were derived from SSR markers and quantitative traits indicated that the dendrograms were not consistent. Considering the correlation between single SSR locus and qualitative traits governed by major genes, the data suggest that alleles of microsatellite loci be more closely related to some traits determined by major genes than those determined by minor genes.

• 한국작물학회:학술대회논문집
• /
• 한국작물학회 2017년도 9th Asian Crop Science Association conference
• /
• pp.103-103
• /
• 2017

Vigorous root growth at the seedling stage in dry direct-seeded conditions is considered as a critical trait because it is involved in seedling emergence, early vegetative vigour, nutrient uptake as well as drought tolerance. In this study, we performed QTL mapping using the recombinant inbred lines obtained from the cross between Tongil-type Dasan and temperate japonica TR22183 (DT-RILs) to identify QTL underlying early root development. TR22183, which was previously reported to have high nitrogen utility and cold tolerance, showed vigorous root growth at the seedling stage in semi-drought conditions. Root length, fresh weight and dry weight of TR22183 were significantly higher than in Dasan. By QTL analysis with genotyping-by-sequencing method, we identified two QTLs for root fresh weight (RFW) in chromosome 7 and root dry weight (RDW) in chromosome 8, explaining phenotypic variances of 13.5% and 10.6%, respectively. These QTLs would be used to develop rice varieties adapted to direct-seeded cultivating system.

• 한국작물학회:학술대회논문집
• /
• 한국작물학회 2017년도 9th Asian Crop Science Association conference
• /
• pp.114-114
• /
• 2017

The aim of this research is to improve Korean lettuce varieties in terms of Fusarium wilt, bolting under hot weather and nutritional function applying genomics approaches. To find related gene/molecular markers, we selected 96 lettuce varieties which are popular in domestic fresh vegetable markets. To construct frame works of the genomic approaches, we exploited GBS(Genotyping by Sequencing) and found total 61,407 SNPs from lettuce whole genomes (MAF>0.02). We observed that Three SNPs array per 100kb of lettuce genome. Average LD decay is expected to expand up to 3.9M(million)bp. Thus, we concluded that about 104 SNPs exist within a LD, which is sufficient to use GWAS(Genome-wide Association Study) to explore the useful gene/molecular markers. In addition, we optimized mass screening method to evaluate disease resistance levels against Fusarium wilt and are testing the bolting sensitivity during summer growing season for those lettuce allele mining set.

• 원예과학기술지
• /
• 제31권2호
• /
• pp.219-223
• /
• 2013

DNA markers can determine the genotype of many species. Single nucleotide polymorphism (SNP) detection is difficult without sequencing but it becomes easier with sdCAPS method. Here an experiment was performed for developing molecular markers using two SNPs, CSatpB-SNP and CSycf1-SNP, of chloroplast in cucumber plants. Properly designed primers with nucleotide sequences for restriction enzymes proved success of PCR and efficacy of digestion by the restriction enzymes. Then these markers were used to study the genotyping of cucumber breeding lines and cultivars obtained from various sources in respect of their chilling stress response. We confirmed that a U.S. cucumber line, 'NC76' known to possess a nuclear factor for the chilling tolerance showed the chloroplast genotypes related to chilling tolerance. However all Korean cucumber cultivars tested in this study showed the chloroplast genotypes related to chilling susceptibility. In conclusion, to develop chilling tolerant cucumber, both maternal and a nuclear factors related to chilling tolerance should be transferred from 'NC76' when 'NC76' is used as a female source and other elite lines as recurrent parents.

• 원예과학기술지
• /
• 제35권2호
• /
• pp.149-164
• /
• 2017

Next generation sequencing (NGS) technologies have led to the rapid accumulation of genome sequences through whole-genome sequencing and re-sequencing of crop species. Genomic resources provide the opportunity for a new revolution in plant breeding by facilitating the dissection of complex traits. Among vegetable crops, reference genomes have been sequenced and assembled for several species in the Solanaceae and Cucurbitaceae families, including tomato, pepper, cucumber, watermelon, and melon. These reference genomes have been leveraged for re-sequencing of diverse germplasm collections to explore genome-wide sequence variations, especially single nucleotide polymorphisms (SNPs). The use of genome-wide SNPs and high-throughput genotyping methods has led to the development of new strategies for dissecting complex quantitative traits, such as genome-wide association study (GWAS). In addition, the use of multi-parent populations, including nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) populations, has helped increase the accuracy of quantitative trait loci (QTL) detection. Consequently, a number of QTL have been discovered for agronomically important traits, such as disease resistance and fruit traits, with high mapping resolution. The molecular markers for these QTL represent a useful resource for enhancing selection efficiency via marker-assisted selection (MAS) in vegetable breeding programs. In this review, we discuss current genomic resources and marker-trait association analysis to facilitate genome-assisted breeding in vegetable species in the Solanaceae and Cucurbitaceae families.

• Journal of Korean Biological Nursing Science
• /
• 제10권2호
• /
• pp.147-153
• /
• 2008

Purpose: Methicillin Resistant Staphylococcus aureus (MRSA) has become a major clinical problem and one of the major nosocomial pathogen worldwide. The aim of the study was to investigate the epidemiological characteristics of genotypes of MRSA isolated in the A-hospital ICU. Methods: In the period between December 2007 and May 2008, MRSA was isolated from ICU patients and its surrounding environment. Polymerase Chain Reaction (PCR) was conducted for the detection of MRSA gene. The incidence of MRSA in the clinical isolates of Staphylococcus aureus was examined by using a multiplex PCR. The spa gene of Staphylococcus aureus encodes protein A and is used for typing of MRSA. We used sequence typing of the spa gene repeat region to study the epidemiology of MRSA at a hospital. Results: Two different genotypes of MRSA were identified with 90 isolated from the patients and its surrounding environments in the ICU. Conclusion: This study may contribute to the development of effective strategies for preventing nosocomial infections. Genotyping may have more general application for the study of MRSA epidemic outbreak in hospital and community infection.

• Asian-Australasian Journal of Animal Sciences
• /
• 제24권2호
• /
• pp.173-180
• /
• 2011

Osteocalcin (OC), a marker of bone turnover, displays patterns in relation to physiological and genetic factors. Here, we present an association study in a population of Chinese Holstein cattle (n = 24) with OC serum concentration as a phenotypic trait. We hypothesised that OC status is associated with phylogeny, vitamin D serum level and single nucleotide polymorphisms (SNPs). Mitochondrial DNA (mtDNA) was used as an unlinked marker to examine phylogeny and linkage to measured phenotypic traits of vitamin D and OC status. Following an association study with OC serum variability as the trait, genotyping of SNPs (n = 27) in OC-related genes was performed. Candidate SNPs were chosen in genes with an emphasis on the vitamin D and vitamin K pathways. Multivariant factor analysis revealed a correlation between vitamin D serum concentration and a SNP in the gene GC (rs43338565), which encodes a vitamin D-binding protein, as well as between a SNP in NFATc1 (rs42038422) and OC concentration. However, univariate analysis revealed that population structure, vitamin D serum levels and SNPs were not significant determinants of OC status in the studied group.

• Asian Pacific Journal of Cancer Prevention
• /
• 제15권15호
• /
• pp.6151-6154
• /
• 2014

A growing body of literature is evidence that identifying subtypes of high-risk human papillomavirus (HR-HPV) has impacted on various steps of cervical cancer prevention.Thus, it is mandatory to determine the background prevalence and distribution of HPV subtypes for designing and implementing area-specific management. The present study was conducted to evaluate prevalence and distribution of HPV subtypes among women aged 30-70 years living in Lampang, an area with a high incidence of cervical cancer, through use of a mobile screening unit. Of 2,000 women recruited in this study, 108 (5.40%, 95%CI: 4.45-6.48) were found to have HR-HPV infection. Risk was significantly correlated with age and number of partners. Singly or in combination, the most common genotype was HPV 52 (17.6%), followed by HPV 16 (14.81%), HPV 58 (13.89%), HPV 33 (11.11%), HPV 51 (11.11%), and HPV 56 (9.26%). HPV 18 was found in only 5.6% of cases. Together, HPV 16/18 were noted in approximately 20.4% of cases. Eighteen(16.67%) women were positive with multiple subtypes of HR-HPV. Co-infection most frequently involved HPV 16 or HPV 58. These findings have obvious implications for vaccine policy.

• Asian Pacific Journal of Cancer Prevention
• /
• 제15권15호
• /
• pp.6333-6337
• /
• 2014

Background: In this case-control study, we aimed to investigate the relationship between the methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and lung cancer. Materials and Methods: Total 200 individuals including 100 patients with lung cancer and 100 controls were analyzed. Genotyping of MTHFR C677T was performed using PCR and RFLP methods. Results: The majority of the patients were men and 90% were smokers. We found that the risk ratio for development of LC was 13-times higher in smokers compared with non-smokers between patient and control groups in our study (OR:13.5, 95%CI:6.27-29.04, p:0.0001). Besides, the risk ratio for development of LC was nine times higher in individuals with cancer history in their family than those without cancer history (OR:9.65, 95%CI: 2.79-33.36; p:0.0001). When genotype distributions and allele frequencies were analyzed in the study groups, no significant difference was apparent (${\chi}^2$:0.53, p=0.76). In addition, no correlation between genotypes of MTHFRC677T polymorphism and histological type of LC was found (${\chi}^2$:0.99, p=0.60). Conclusions: These results suggest that there was no association between the MTHFR C677T polymorphism and lung cancer in the Turkish population.

• Asian Pacific Journal of Cancer Prevention
• /
• 제14권8호
• /
• pp.4595-4598
• /
• 2013

We conducted a comprehensive study to investigate the role of genes involved in transport pathways in response to chemotherapy and clinical outcome of osteosarcoma cases. Genotyping of six SNPs was performed in a 384-well plate format on the Sequenom MassARRAY platform for 208 osteosarcoma patients to reveal any correlations of the six SNPs with response to chemotherapy and clinical outcome. Individuals with the ABCB1 rs1128503 TT and ABCC3 rs4148416 TT genotypes had a higher probability of responding poorly to chemotherapy, indicated by odds ratios (ORs) of 2.46 (95%CI, 1.21-5.74) and 3.78 (95% CI, 1.20-13.85), respectively. Moreover, the ABCB1 rs1128503 TT and ABCC3 rs4148416 TT genotypes were significantly associated with shorter diseasefree survival (DFS) and overall survival (OS). Our study found the two SNPs in two transporter genes and one phase II metabolism enzyme to be associated with response to chemotherapy and overall survival in osteosarcoma patients, suggesting potential prognostic biomarker applications of the two SNPs.