• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.96-96
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• 2017

Rice is a staple food for nearly half of the world's population, with more than 10,000 rice varieties providing almost one-quarter of the global per capita dietary energy supply. Grain size, panicle size and branch number, grain number in a panicle are directly associated with rice productivity. Recently several genes which increase grain yield were identified through map-based cloning. Gn1a, Cytokinin oxidase, is a major grain number QTL and regulates grain number per panicle. Dep1 increases panicle branching and reduced rachis length. SCM2 (APO1) was identified by a QTL for culm strength and increased spikelet number. OsSPL16 (GW8) controls grain size and shape and then increases 1000-weight of seed. In here, to identify genotype of genes related to yield in 400 of rice germplasms possessed in National Institute of Crop Science, we had first chosen 4 of well-known genes related to yield; Gn1a, Dep1, SCM2, and OsSPL16. Among these germplasms, 195, 382, 165, and 353 of germplasms harbored the dominant type of Gn1a, Dep1, SCM2, and OsSPL16, respectively. We grouped these germplasms into a total of 10 groups using genotypes of Gn1a, Dep1, SCM2 and OsSPL16. Most rice germplasms belong to group 1, harbored Gn1a, dep1, gw8 and APO1, and group 10, harbored gn1a, Dep1, GW8 and apo1. Hanareum2 is the highest productive cultivar in Korea but do not have dominant type OsSPL16, so belong to group 1. On the other hand, in the case of Unkwang, belongs to group 10, which has dominant type of OsSPL16 but do not have the remaining genes. We can grasp the differences in rice germplasms through the Profiling of genes related to these grain yield, which will be useful for cross-breeding to integrate grain yield genes. We are continuously observing the genotype and phenotype of rice that possesses grain yield genes.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2489-2493
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• 2015

Background: Loss of heterozygosity (LOH) on chromosomal regions is crucial in tumor progression and this study aimed to identify genome-wide LOH in pancreatic cancer. Materials and Methods: Single-nucleotide polymorphism (SNP) profiling data GSE32682 of human pancreatic samples snap-frozen during surgery were downloaded from Gene Expression Omnibus database. Genotype console software was used to perform data processing. Candidate genes with LOH were screened based on the genotype calls, SNP loci of LOH and dbSNP database. Gene annotation was performed to identify the functions of candidate genes using NCBI (the National Center for Biotechnology Information) database, followed by Gene Ontology, INTERPRO, PFAM and SMART annotation and UCSC Genome Browser track to the unannotated genes using DAVID (the Database for Annotation, Visualization and Integration Discovery). Results: The candidate genes with LOH identified in this study were MCU, MICU1 and OIT3 on chromosome 10. MCU was found to encode a calcium transporter and MICU1 could encode an essential regulator of mitochondrial $Ca^{2+}$ uptake. OIT3 possibly correlated with calcium binding revealed by the annotation analyses and was regulated by a large number of transcription factors including STAT, SOX9, CREB, NF-kB, PPARG and p53. Conclusions: Global genomic analysis of SNPs identified MICU1, MCU and OIT3 with LOH on chromosome 10, implying involvement of these genes in progression of pancreatic cancer.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.9
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• pp.5037-5041
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• 2013

Accumulated evidence has indicated that Ephrin A1 (EFNA1) is associated with angiogenesis and tumorigenesis in various types of malignancies, including colorectal cancer (CRC). In the current study, we performed an online search using the public microarray database to investigate whether EFNA1 expression might be altered in CRC tissues. We then conducted a case-control study including 306 subjects (102 cases and 204 well-matched controls) in Xiaoshan County to assess any association between genetic polymorphisms in EFNA1 and CRC susceptibility. Searches in the Oncomine expression profiling database revealed EFNA1 to be overexpressed in CRC tissue compared with adjacent normal tissue. The rs12904 G-A variant located in the 3' untranslated region (UTR) of EFNA1 was observed to be associated with CRC susceptibility. Compared with the AA homozygous genotype, those carrying GA genotype had a decreased risk of developing CRC (odds ratio (OR)=0.469, 95% confidence interval (CI): 0.225-0.977, and P=0.043). The association was stronger among smokers and tea drinkers, however, no statistical evidence of interaction between rs12904 polymorphism and smoking or tea drinking on CRC risk was found. Our results suggest that EFNA1 is involved in colorectal tumorigenesis, and rs12904 A>G polymorphism in the 3' UTR of EFNA1 is associated with CRC susceptibility. Larger studies and further mechanistic investigations are warranted to confirm our findings.

• Korean Journal of Agricultural Science
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• v.47 no.1
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• pp.105-117
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• 2020

Abiotic stress is one of the most serious problems in plant productivity because it dramatically delays plant growth and development. One of the abiotic stresses, soil salinity, has an adverse effect on plant growth, particularly in areas where irrigation is necessary like semiarid Asia and Africa. Among several physiological parameters, anthocyanin accumulation is a valuable indicator of the condition of the plant, and it tends to increase under salt stress conditions because of its protective role in such an environment. Consequently, it may be important to search for well adapted genotypes for upcoming climate changes. Anthocyanins are known to have important roles in defense against biotic and abiotic stresses, providing important functions for protecting plant cells from reactive oxygen species. In this study, we investigated the anthocyanin accumulation between two Korean sorghum genotypes, Sodamchal and Nampungchal. The two genotypes were subjected to a regulated salinity condition, and the anthocyanin contents were evaluated in both. In Nampungchal, the anthocyanin content increased with 150 mM NaCl treatment during the time course of the experiment. However, the anthocyanin content of Sodamchal decreased in the same condition. The measured values of the anthocyanin content should be useful to identify the intensity of the salt tolerance in Sorghum bicolor L. Furthermore, we studied gene expression profiling of salt stress related genes with qRT-PCR. These results suggest that Nampungchal is a more tolerant genotype to salt stress compared to Sodamchal. This information should be useful for breeding salt-resistant cultivars in sorghum.