• Plant Biotechnology Reports
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• v.4 no.1
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• pp.61-73
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• 2010

Quantitative trait loci (QTL) associated with six physical traits of cooked rice and seven chemical properties of rice grain were identified using a recombinant inbred (RI) population of rice evaluated over 3 years at the National Honam Agricultural Research Institute in Korea. The RI population consisted of 164 lines derived from a cross between Milyang23 and Gihobyeo, and the genetic map consisted of 414 molecular markers. A total of 49 QTL were identified for the 13 physico-chemical properties using composite interval mapping. Of these, 13 QTL were identified for 2 or more years, while 36 were detected in only 1 year. Five QTL were identified over all 3 years and will be useful for marker-assisted improvement of rice grain quality in Korea. The two QTL with the highest LOD scores, adhesiveness1.2 and potassium content7.1, provide a valuable starting point for positional cloning of genes underlying these QTL.

• Journal of Aquaculture
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• v.16 no.1
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• pp.8-14
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• 2003

To generate expressed sequence tags for genomics research involving genetic linkage analysis, to examine gene expression profiles in muscles of channel catfish in a non-normalized muscle cDNA library, to compare gene expression in young and mature channel catfish muscles using the EST reagents and gene filters to demonstrate the feasibility of functional genomics research in small laboratories. 102 randomly picked cDNA clones were analyzed from the catfish muscle cDNA library. Of the sequences generated, 90.2% of ESTs was identified as known genes by identity comparisons. These 92 clones of known gene products represent transcriptional products of 24 genes. The 10 clones of unknown gene products represent 8 genes. The major transcripts (70.1% of the analyzed ESTs) in the catfish muscle are from many major genes involved in muscle contraction, relaxation, energy metabolism and calcium binding such as alpha actin, creatine kinase, parvalbumin, myosin, troponins, and tropomyosins. Gene expression of the unique ESTs was comparatively studied in the young and adult catfish muscles. Significant differences were observed for aldolase, myostatin, myosin light chain, parvalbumin, and an unknown gene. While myosin light chain and an unknown gene (CM 192) are down-regulated in the mature fish muscle, the aldolase, myostatin, and parvalbumin are significantly up-regulated in the mature fish muscle. Although the physiological significance of the changes in expression levels needs to be further addressed, this research demonstrates the feasibility and power of functional genomics in channel catfish. Channel catfish muscle gene expression profiles provide a valuable molecular muscle physiology blueprint for functional comparative genomics.

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.3 no.1
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• pp.52-57
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• 2003

In this paper, we propose a Fuzzy Classifier System(FCS) to find a set of fuzzy rules which can carry out the edge detection. The classifier system of Holland can evaluate the usefulness of rules represented by classifiers with repeated learning. FCS makes the classifier system be able to carry out the mapping from continuous inputs to outputs. It is the FCS that applies the method of machine learning to the concept of fuzzy logic. It is that the antecedent and consequent of classifier is same as a fuzzy rule. In this paper, the FCS is the Michigan style. A single fuzzy if-then rule is coded as an individual. The average gray levels which each group of neighbor pixels has are represented into fuzzy set. Then a pixel is decided whether it is edge pixel or not using fuzzy if-then rules. Depending on the average of gray levels, a number of fuzzy rules can be activated, and each rules makes the output. These outputs are aggregated and defuzzified to take new gray value of the pixel. To evaluate this edge detection, we will compare the new gray level of a pixel with gray level obtained by the other edge detection method such as Sobel edge detection. This comparison provides a reinforcement signal for FCS which is reinforcement learning. Also the FCS employs the Genetic Algorithms to make new rules and modify rules when performance of the system needs to be improved.

• Korean Journal of Medicinal Crop Science
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• v.18 no.3
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• pp.186-190
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• 2010

The chromosome number was identified and fluorescence in situ hybridization(FISH) mapping of 5S and 45S rDNAs were conducted for C. minima and C. lanceolata in the genus Codonopsis from Jeju island. In this study, we have confirmed that the somatic metaphase chromosome number determined as 2n=2x=16 was the same as the findings from the previous studies. While the conventional staining method makes it rather difficult to distinguish satellite chromosomes due to high degree of variability, FISH analysis produced the exact number and location of 5S and 45S rDNAs. Both species in the genus Codonopsis have a pair of 5S rDNA and their gene loci were observed on chromosome 3. Although two pairs of 45S rDNAs (one on chromosome 1 and the other on chromosome 8) were identified in both species, the 45S rDNA signals on chromosome 8 in C. minima were significantly weaker than those on chromosome 1. In addition, the 45S rDNA signals on chromosome 1 in C. lanceolata showed that the chromosome is non-homologus. In this study, we have determined cytogenetic characteristics of C. minima and C. lanceolata according to their gene replication patterns.

• The Plant Pathology Journal
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• v.37 no.1
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• pp.1-23
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• 2021

Resistance to diseases caused by turnip mosaic virus (TuMV) in crop species of the family Brassicaceae has been studied extensively, especially in members of the genus Brassica. The variation in response observed on resistant and susceptible plants inoculated with different isolates of TuMV is due to a combination of the variation in the plant resistome and the variation in the virus genome. Here, we review the breadth of this variation, both at the level of variation in TuMV sequences, with one eye towards the phylogeny and evolution of the virus, and another eye towards the nature of the various responses observed in susceptible vs. different types of resistance responses. The analyses of the viral genomes allowed comparisons of pathotyped viruses on particular indicator hosts to produce clusters of host types, while the inclusion of phylogeny data and geographic location allowed the formation of the host/geographic cluster groups, the derivation of both of which are presented here. Various studies on resistance determination in particular brassica crops sometimes led to further genetic studies, in many cases to include the mapping of genes, and in some cases to the actual identification of the genes. In addition to summarizing the results from such studies done in brassica crops, as well as in radish and Arabidopsis (the latter as a potential source of candidate genes for brassica and radish), we also summarize work done using nonconventional approaches to obtaining resistance to TuMV.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.188-188
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• 2022

Our previous study identified a resistance locus to Phytophthora sojae (isolate 2457) in an interval of 3.8-4.7 Mbp on chromosome 3 via genetic mapping using a 'Daepung'×'Daewon' recombinant inbred population. Since differential gene expression between Daepung (susceptible) and Daewon (resistant) after inoculation of P. sojae is unknown, RNA sequencing was carried out to compare transcriptomic changes between the two genotypes following inoculation with P. sojae isolate 2457. The two varieties were inoculated using hypocotyl inoculation at the VC stage and stem tissue of 1 cm above and below of the inoculated site were sampled at 0, 6, 12 hours after inoculation (hai), respectively. Differentially expressed genes (DEGs) under same cultivar in different time point and Daepung vs. Daewon in same time point were investigated. In comparison of Daepung vs. Daewon at 12 hai, a total of 3,513 DEGs were identified, including two nucleotide-binding site-leucine rich repeat (NBS-LRR) genes (Glyma.03g034800 and Glyma.03g034900) that are located in the previously reported resistance locus on chromosome 3. In addition, 14,966 DEGs were detected between 0 vs. 6 hai, containing one of candidate genes (Glyma.03g035300). This gene was upregulated by up to 4-fold in Daewon and Daepung. Additional results will be further discussed in the presentation. This study will provide valuable information for soybean crop improvement.

• Journal of Korean Society of Forest Science
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• v.112 no.1
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• pp.40-56
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• 2023

Tree species within the Populus genus grow rapidly and have an excellent capacity to absorb carbon, conferring substantial ability to effective purify the environment. Poplar breeding can be achieved rapidly and efficiently if a genetic linkage map is constructed and quantitative trait loci (QTLs) are identified. Here, a high-density genetic linkage map was constructed for the control pollinated progeny using the genotyping-by-sequencing (GBS) technique, which is a next-generation sequencing method. A search was also performed for the genes associated with quantitative traits located in the genetic linkage map by examining the variables of height and diameter at root collar, and resilience to insect damage. The height and diameter at root collar were measured directly, while the ability to recover from insect damage was scored in a 4-year-old breeding population of aspen hybrids (Odae19 × Bonghyeon4 F1) established in the research forest of Seoul National University. After DNA extraction, paternity was confirmed using five microsatellite markers, and only the individuals for which paternity was confirmed were used for the analysis. The DNA was cut using restriction enzymes and the obtained DNA fragments were prepared using a GBS library and sequenced. The analyzed results were sorted using Populus trichocarpa as a reference genome. Overall, 58,040 aligned single-nucleotide polymorphism (SNP) markers were identified, 17,755 of which were used for mapping genetic linkages. The genetic linkage map was divided into 19 linkage groups, with a total length of 2,129.54 cM. The analysis failed to identify any growth-related QTLs, but a gene assumed to be related to recovery from insect damage was identified on linkage group (chromosome) 4 through genome-wide association study.

• Genomics & Informatics
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• v.6 no.1
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• pp.18-28
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium (LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centre d'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes (frequency $\geq$ 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

• Clinical and Experimental Reproductive Medicine
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• v.23 no.3
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• pp.367-377
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• 1996

Genes on the long arm of Y chromosome, particularly interval 6, are believed to playa critical role in human spermatogenesis. The objective of this study was to validate a sequenced-tagged site(STS)-mapping strategy for the detection of Yq microdeletion and to use this method to determine the proportion of men with Yq microdeletions in idiopathic, obstructive, nonobstructive azoospermia, severe OATS and in normal males. We analyzed three STS markers mapped to interval 6 within long arm of the Y chromosome from 106 nonobstructive, 30 obstructive azoospermia, 15 severe OATS patients, and normal 42 males in Korean men. By PCR, we tested leukocyte DNA, for the presences of STS markers(DAZ, sY129 and sY134) and SRY gene as internal control. And PCR results were confirmed by Southern hybridization, and were investigated by SSCP analysis for DAZ gene mutation. None of 42 normal males and 30 obstructive azoospermia had microdeletions, Of the 15 severe OATS typed with DAZ, sY129 and sY134, 3(20.0%) patients failed to amplify 1 or more STS markers, and of the 106 nonobstructive azoospermia typed with DAZ, sY129 and sY134, 12(11.3%) patients failed to amplify 1 or more STS markers. From these results, high prevalence(12.4%) of Yq deletion(DAZ, sY129, sY134) in men with nonobstructive idopathic azoospermia and severe OATS were observed in Korean infertility patients. To avoid the infertile offspring by assisted reproductive technique using ICSI or ROSI, genetic diagnosis will be needed in IVF-ET program.

• Korean Journal of Breeding Science
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• v.43 no.1
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• pp.81-91
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• 2011

Rice wild relatives have been recognized as reservoirs of genetic reinforcements to improve cultivating rice against biotic and abiotic stresses. A wild relative, Oryza. minuta(BBCC; Acc. 101141), was hybridized with a Korean Japonica cultivar, 'Hwaseong'(AA), followed by ovule culture and several times of back crossings to overcome high level of sterility. During evaluation of the introgression lines, breeding line exhibited resistance to bacterial blight with reasonable agronomic performances, and nominated as an elite breeding line, the 'Suweon497'. A mapping population, to dissect genetic basis of the resistance, was constructed by using $F_2$ progenies of the 'Suweon497' ${\times}$ 'Milyang23'. Association analysis between SSR marker genotypes and pathogenisity levels of each $F_2$ progeny revealed the end terminal region of rice chromosome 11 as the nesting place for the wild rice derived bacterial blight resistance gene, where at least four other genes, Xa3, Xa4, Xa26 and Xa31, have been reported.