• Proceedings of the Ginseng society Conference
• /
• 1993.09a
• /
• pp.138-142
• /
• 1993

Korean ginseng has been widely used as medicine from ancient times in Asia. Current breeding efforts in Korea include the individual plant selection and the subsequent pure - line isolation, and considerable number of lines with desirable traits have thus been isolated. However, there were rare data on genetic maker and its analysis for selection of superior varieties. For taxonomic characterization and development of genetic markers for ginseng breeding, molecular biological methods including the RFLP and RAPD methods were applied. Cytoplasmic DNA of ginseng was analyzed for RFLP analysis. However. there is no different pattern among the chloroplast DNA or mitochondrial DNA of variants. In the case of RAPD analysis, the band patterns using 4 of 10 RAPD primers show the distinctive polymorphism among 9 ginseng variants, and lines, and Similarity Index(SI) on polymorphism was calculated for the extent and nature of these variabilities in ginseng. The sequences of 4 selected primers were TGCCGAGCTG, AATCGGGCTG. GAAACGGGTG, and GTGACGTAGG. By SI based on the polymorphic band patterns, Chungkyung - Chong and Hwangskoog - Chong, and JakyungChong 81783 and Jinjakyung of Russia showed the most close SI. The data of KG10l coincided with the fact that it was released from Hwangskoog - Chong. and Jakyung - Chong 81783 and Jinjakyung of Russia showed the most close SI. The data of KG101 coincided with the fact that it was released from Hwangskoog - Chong by breeding process. The data of Jakyung strains indicated the significant variation among the strains. From these results, RAPD analysis method could be succesively applied to the classification and genetic analysis for breeding of Korean ginseng.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.342-342
• /
• 2017

Rice seeds are a home to endophytic bacterial communities which serve as a source of the plant's endophytes. As rice undergo physiological and adaptive modifications through cross breeding in the process of attaining salinity tolerance, this may also lead to changes in the endophytic bacterial community especially those residing in the seeds. This study explores the community structure of seed bacterial endophytes as influenced by rice parental lineage, genotype and physiological adaptation to salinity stress. Endophytic bacterial diversity was studied through culture dependent technique, cloning and Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. Results revealed considerably diverse communities of bacterial endophytes in the interior of rice seeds. The richness of ribotypes ranges from 5-14 T-RFs corresponding to major groups of bacterial endophytes in the seeds. Endophytic bacterial diversity of the salt-sensitive IR29 is significantly more diverse compared to those of salt-tolerant cultivars. Proteobacteria followed by Actinobacteria and Firmicutes dominated the overall endophytic bacterial communities of the indica rice seeds based on 16S rDNA analysis of clones and isolates. Community profiles show common ribotypes found in all cultivars of the indica subspecies representing potential core microbiota belonging to Curtobacterium, Flavobacterium, Enterobacter, Xanthomonas, Herbaspirillum, Microbacterium and Stenotrophomonas. Multivariate analysis showed that the bacterial endophytic community and diversity of rice seeds are mainly influenced by their host's genotype, physiological adaptation to salt stress and parental lineage.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.244-244
• /
• 2017

Soil salinity due to accumulation of salts particularly sodium chloride affects agricultural lands and their vegetation. Generally, rice is a moderately sensitive plant with some cultivars with varying tolerance to salinity. Though there are physiological differences between salt-sensitive and salt-tolerant rice cultivars, both are still affected especially during high salinity and prolonged exposure. This also ultimately affects their indigenous bacterial endophytes particularly those that inhabit the rice seed endosphere. This study investigates the dynamic structure of seed bacterial endophytes of salt-sensitive and tolerant rice cultivars grown in different levels of soil salinity. Endophytic bacterial diversity was studied Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. Results revealed a very interesting pattern of diversity and shifts in community structure of bacterial endophytes in the rice seeds. There is a general decrease in diversity for the salt-sensitive rice cultivar, IR29 as soil salinity increases. For the salt-tolerant cultivars, IC32 and IC37, diversity interestingly increased at moderate salinity then decreased at high soil salinity. The patterns of community structure is also strikingly different for the salt-sensitive and salt-tolerant rice cultivars. IR29 has a more even distribution of abundance, but under soil salinity, the community shifted where Curtobacterium, Pantoea, Flavobacterium and Microbacterium become the more dominant bacterial communities. For IC32 and IC37, the dominant bacterial groups under normal stress conditions were also the dominant bacterial groups during salt stress conditions. Their seed bacterial community is dominated by endophytes belonging to Microbacterium, Flavobacterium, Pantoea, Kosakonia and Enterobacter. Stenotrophomonas and Xanthomonas have not changed in terms of abundance under different salinity stress level in the salt-sensitive and salt-tolerant rice cultivars. This study showed that soil salinity greatly influenced the seed bacterial communities of rice seeds irrespective of their physiological tolerance to salinity.

• Asian-Australasian Journal of Animal Sciences
• /
• v.25 no.11
• /
• pp.1515-1520
• /
• 2012

Insulin-like growth factor binding protein-3 (IGFBP-3) gene is important for regulation of growth and development in mammals. The present investigation was carried out to study DNA polymorphism by PCR-RFLP of IGFBP-3 gene and its effect on fibre traits of Chinese Inner Mongolian cashmere goats. The fibre traits data investigated were cashmere fibre diameter, combed cashmere weight, cashmere fibre length and guard hair length. Four hundred and forty-four animals were used to detect polymorphisms in the hircine IGFBP-3 gene. A 316-bp fragment of the IGFBP-3 gene in exon 2 was amplified and digested with HaeIII restriction enzyme. Three patterns of restriction fragments were observed in the populations. The frequency of AA, AB and BB genotypes was 0.58, 0.33 and 0.09 respectively. The allelic frequency of the A and B allele was 0.75 and 0.25 respectively. Nucleotide sequencing revealed a C>G transition in the exon 2 region of the IGFBP-3 gene resulting in R158G change which caused the polymorphism. Least squares analysis revealed a significant effect of genotypes on cashmere weight (p<0.0001), cashmere fibre length (p<0.001) and hair length (p<0.05) of the animals. The effect of genotypes on cashmere fibre diameter was not statistically significant (p>0.05). The animals of AB and BB genotypes showed higher cashmere weight, cashmere fibre length and hair length than the animals possessing AA genotype. These results suggested that polymorphisms in the hircine IGFBP-3 gene might be a potential molecular marker for cashmere weight in cashmere goats.

• Asian-Australasian Journal of Animal Sciences
• /
• v.27 no.10
• /
• pp.1487-1492
• /
• 2014

This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp). Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.20
• /
• pp.8963-8967
• /
• 2014

Background: Colon cancer is one of the most common cancers worldwide. Apoptosis is a necessary physiological process for cell elimination which is very important both cellular homeostasis and cell proliferation and differantiation. Dysregulation can lead to uncontrolled cell growth and tumor development. Survivin, a member of the IAP family, plays a key role in promotion of cell proliferation as well as inhibition of apoptosis in cancer cells. The aim of this study was to investigate whether specific genetic polymorphisms of survivin could be associated with colon cancer development and progression in a Turkish population. Our study is the first to our knowledge to investigate the relationship between colon cancer risk and survivin gene polymorphisms. Materials and Methods: The relation between colon cancer and survivin -31 G/C (rs9904341), -241 C/T (rs17878467) and -625 C/G (rs8073069) polymorphism in promotor site of survivin gene associated with apoptosis was investigated using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: Individuals with -31C allele and CC genotype were found to have a higher risk of developing colon cancer (OR=13.4, p=0.01). The -241 CT genotype considerably increased the risk of colon cancer (OR=12.0, p=0.0001). However, there was no significant varaition of the survivin -625 C/G polymorphism among colon cancer patients and controls in our study. Conclusions: This study provides the first evidence that survivin -31 G/C and -241 C/T SNP significantly contribute to the risk of colon cancer in the Turkish population.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.8
• /
• pp.3507-3511
• /
• 2014

Background: The prostaglandin-endoperoxide synthase 2 [PTGS2, commonly known as cyclooxygenase-2 (COX-2)] is an enzyme induced by proinflammatory stimuli that is often overexpressed in malignant tissue and involved in the synthesis of prostaglandins and thromboxanes, regulators of processes such as inflammation, cell proliferation, and angiogenesis, all relevant for cancer development. We investigated whether a functional genetic polymorphism, rs5277, in COX-2 may have a risk-modifying effect on sporadic colorectal cancer in an Iranian population. Materials and Methods: We conducted a case-control study on 167 patients with colorectal cancer and 197 cancer-free controls in Taleghani Hospital in Tehran, Iran, between 2007 and 2011. Peripheral blood samples of both groups were processed for DNA extraction and genotyping of the COX-2 gene polymorphism (rs5277) using PCR-RFLP. RFLP results were confirmed by direct sequencing. Logistic regression analysis was performed to calculate the adjusted odds ratio (OR) and 95% confidence interval (95% CI). Results: There was no significant difference in the distribution of COX-2 gene rs5277 polymorphism genotype and the allelic form, among CRC patients compared with the healthy control group (p: 0.867). Conclusions: Our results suggest that rs5277 polymorphism in COX2 could not be a good prognostic indicator for patients with CRC.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.13
• /
• pp.5443-5447
• /
• 2014

The cholangiocarcinoma (CCA) is a relatively rare cancer worldwide but it is highly prevalent in Thailand where the liver fluke, Opisthorchis viverrini is endemic. There are reports that interleukin 6 (IL-6) may play an important role in the pathogenesis of opisthorchiasis associated CCA. Functionally, IL-6 can act on target cells through its receptor, IL-6R, and IL-6R polymorphisms may affect the functional activity of IL-6 leading to susceptibility to cholangiocarcinogenesis. Therefore, we assessed the association of the 48892 A/C (Asp358Ala) polymorphism in exon 9 of the IL-6R gene in 79 CCA cases compared to 80 healthy controls using the PCR-RFLP technique. The results showed significant differences between CCA cases and controls in overall genotype (p=0.001) and allele frequencies (p=0.0002). Chi-square for trend test revealed a significant association between genotype and CCA susceptibility (p=0.0002). The odds ratios (ORs) for genotype were 0.283 (95% CI=0.131-0.605, AC vs. AA; p=0.0003) and 0.206 (95% CI=0.196-1.245, CC vs. AA; p=0.0416), the OR for alleles was 0.347 (95% CI=0.187-0.633, allele C vs. allele A; p=0.0002) and that for the carrier C variant was 0.272 (95% CI=0.130-0.564; p=0.0001). This study demonstrated a close association between an IL-6R polymorphism, specifically higher A allele, and cholangiocarcinoma.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.sup3
• /
• pp.71-75
• /
• 2016

Pancreatic cancer is a leading cause of fatality worldwide. Several population studies have been conducted on genetic diagnosis of pancreatic cancer but the results from epidemiologic studies are very limited. CYP17A gene has a role in disease formation but its influence on pancreatic cancer is unclear. A polymorphism in the 5'UTR promoter region of CYP17A1-34T/C (A1/A2) has been associated with multiple cancers. The aim of the current study was to assess associations of this polymorphism and socio-demographic risk factors with pancreatic cancer. A total of 255 and 320 controls were enrolled in the study, and were genetically analyzed through PCR-RFLP. Statistical analysis was conducted with observed genotype frequencies and odds ratios (ORs) and 95% CIs were estimated using unconditional logistic regression. The impact of socio-demographic factors was accessed through Kaplen-Meir analysis. According to our results, the A2/A2 genotype was significantly associated with pancreatic cancer (OR=2.1, 95%CI = 1.3-3.5). Gender female (OR=2.6, 95%CI=1.8-3.7), age group 80s/80+ years (OR=2.2, 95% CI=1.2-4), smoking both former (OR=4.6, 95% CIs=2.5-8.8) and current (OR=3.6, 95% CI=2-6.7), and family history (OR=7.1; 95%CI = 4.6-11.4) were also found associated with increased risk. Current study suggests that along with established risk factors for pancreatic cancer CYP17A1-34T/C may play a role. However, on the basis of small sample size the argument cannot be fully endorsed and larger scale studies are recommended.

• Asian-Australasian Journal of Animal Sciences
• /
• v.21 no.1
• /
• pp.25-28
• /
• 2008

In order to distinguish Korean cattle (Hanwoo) beef from the imported beef from Australia in Korean markets, DNA markers based on PCR-RFLP from mitochondrial genes and SRY gene were applied. A total of 2,826 beef samples comprising 1,495 Hanwoo and 1,331 foreign cattle breeds were obtained in Korea. An 801 bp fragment of the SRY gene on the bovine Y chromosome, a 343 bp fragment of ND4 gene and a 528 bp fragment of ND5 gene in the bovine mtDNA were amplified by PCR and digested with three restriction enzymes, MseI, HpyCH4III and Tsp509I, respectively. The results showed that Bos taurus (T) type was the majority in Hanwoo by combining three markers (99.5%). However, 78.2% of Bos indicus (I) type was observed in the imported beef samples. These results indicated that three markers used in this study will be used as valuable markers for discriminating imported beef against Hanwoo.