• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.402-402
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• 2005

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.8
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• pp.1085-1089
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• 2006

The objectives of this study were to confirm a location of the calpastatin (CAST) gene in chromosome 2 and to detect associations of genetic variations with economic traits in the porcine CAST gene as a candidate gene for growth and meat quality traits in pigs. Calpastatin is a specific endogenous inhibitor of calpains. The calpain protease system is ubiquitous, and is involved in numerous growth and metabolic processes. Three single nucleotide variations were identified within a 1.6 kb fragment of the porcine CAST gene and these polymorphisms were used for genetic linkage mapping. Linkage and QTL mapping were performed with the National Livestock Research Institute (NLRI) reference families using eight microsatellites and SNP makers in the CAST gene. The porcine CAST gene was mapped adjacent to the markers, SW395 and SW1695 on SSC2 with LOD scores of 15.32 and 8.50, respectively. According to the QTL mapping, a significant association was detected at 82 cM between SW395 and CAST-Hinf I for weight at the age of 30 weeks. In addition, an association study was performed with the $F_2$ animals of NLRI reference families for Hinf I, Msp I and Rsa I polymorphisms in the CAST gene. Two polymorphisms, CAST-Rsa I and CAST-Hinf I, showed significant correlation for growth traits at p<0.01 and p<0.05, respectively.

• Genomics & Informatics
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• v.1 no.2
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• pp.101-107
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• 2003

Loss of heterozygosity (LOH) has been used to detect deleted regions of a specific chromosome in cancer cells. LOH on chromosome 16q has been reported to occur frequently in progressed hepatocellular carcinoma (HCC). Liver tissues from 37 Korean HCC patients were analyzed for LOH by using 25 polymorphic microsatellite markers distributed along 16q. Out of the 37 HCC patients studied, 21 patients (56.8%) showed LOH in various regions of 16q with at least one polymorphic marker. Puring the analysis of these 21 LOH cases, 6 patients showed interstitial LOHs in which the boundary of the LOH region was defined. With two rounds of LOH analysis, five commonly occurring interstitial LOH regions were identified; 16q21-22.1, 16q22.2 - 22.3, 16q22.3, 16q23.2 and 16q23.3 - 24.1. Among the five LOH regions the 16q23.3 - 24.1 region has been reported to be related with chromosome instability. A complete physical map, which covers the 3.2 Mb region of 16q23.3 - 24.1 (D16S402 and D16S486), was constructed to identify novel candidate tumor suppressor genes. We provide the minimally tiling path map consisting of 28 BAC clones. There was one gap between NT_10422.11 and NT_019609.9 of the human genome sequence contig (NCBI sequence build 33, April 29, 2003). This gap can be filled by sequencing the R-1425M20 clone which bridges these sequence contigs.

• Horticultural Science & Technology
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• v.30 no.6
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• pp.751-756
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• 2012

Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA sequences in the specific region of the chromosomes. As well as for the integrated physical mapping, FISH karyotype analysis has to be preceded. Karyotype of Raphanus sativus 'Wonkyo 10039' was analyzed by a dual-color FISH technique; using various repetitive DNA probes, including 5S rDNA, 45S rDNA, and centromere retrotransposon. The length of the somatic metaphase chromosome ranged from 1.35 to $2.06{\mu}m$ with a total length of $15.29{\mu}m$. The chromosome complements comprised of eight pairs of metacentrics and one pair of submetacentric. Bleached DAPI Band analysis revealed a heterochromatin region, covering 28.6% to 50.4% each chromosomes. 5S and 45S rDNA sequences were located on two and three pairs of chromosomes, respectively. The centromere retrotransposon of Brassica (CRB) is a major component in Brassica related species that has been maintained as a common centromere component. CRB signals were detected on the centromere and pericentromeric region of R. sativus 'Wonkyo 10039' and three basic Brassica species (B. rapa, B. nigra, and B. oleracea). These results will provide a valuable background for physical mapping and elucidation of the evolutionary relationship among the Brassica related species.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.145-145
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• 2017

Foxglove aphid, Aulacorthum solani (Kaltenbach), is a Hemipteran insect that infected a wide variety of plants worldwide and caused serious yield losses in crops. The objective of this study was to identify the putative genes to foxglove aphid resistance in wild soybean, PI 366121 (Glycine soja Sieb. and Zucc.). One hundred and forty-one F4:8 recombinant inbred lines developed from a cross between susceptible variety, Williams 82 and foxglove aphid resistance wild soybean, PI 366121 were used. The two type of resistance response, antibiosis and antixenosis resistance were evaluated through choice and no-choice test, graded by the degree of total plant damage and primary infestation leaf damage; a genome-wide molecular linkage map was constructed with 29,898 single-nucleotide polymorphism markers utilizing a Axiom(R) 180K soyaSNP array. Using inclusive composite interval mapping analysis for foxglove aphid resistance, one major candidate QTL on chromosome 7 was identified. The major QTL on chromosome 7 showed both antixenosis and antibiosis resistance responses. The newly identified major QTL was consistent with previously reported QTL, Raso2, which showed around 5 times narrow down interval range with 8 candidate genes. Furthermore, total 1,115 soybean varieties including Glycine soja and Glycine max were exposed to germplasm screening, and 31 varieties, which showed significant antibiosis type foxglove aphid resistance were identified. This result could be useful in breeding for new foxglove aphid resistant soybean cultivars and developing novel insecticides.

• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.470-480
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• 2010

The objectives of this study were to identify QTLs for agronomic traits using introgression lines from a cross between a japonica weedy rice and a Tongil-type rice. A total of 75 introgression lines developed in the Tongil-type rice were characterized. A total of 368 introgressed segments including 285 homozygous and 83 heterozygous loci were detected on 12 chromosomes based on the genotypes of 136 SSR markers. Each of 75 introgression lines contained 0-9 homozygous and 0-8 heterozygous introgressed segments with an average of 5.8 segments per line. A total of 31 quantitative and 2 qualitative loci were identified for 14 agronomic traits and each QTL explained 4.1% to 76.6% of the phenotypic variance. Some QTLs were clustered in a few chromosomal regions. A first cluster was located near RM315 and RM472 on chromosome 1 with QTLs for 1,000 grain weight, culm length, grain width and thickness. Another cluster was detected with four QTLs for 1,000 grain weight, grain length, grain width and grain length/width ratio near the SSR marker RM249 on chromosome 5. Among the 31 QTLs, 9 (28.1%) Hapcheonaengmi3 alleles were beneficial in the Milyang23 background. ILs would be useful to confirm QTLs putatively detected in a primary mapping population for complex traits and serve as a starting point for map-based cloning of the QTLs. Additional backcrosses are being made to purify nearly isogenic lines (NILs) harboring a few favorable Hapcheonaengmi3 alleles in Milyang23 background.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1826-1835
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• 2019

Objective: Testicular growth and development are strongly influenced by androgen. Although both testis weight and plasma testosterone level are inherited traits, the interrelationship between them is not fully established. Males of DDD/Sgn (DDD) mice are known to have extremely heavy testes and very high plasma testosterone level among inbred mouse strains. We dissected the genetic basis of testis weight and analyzed the potential influence of plasma testosterone level in DDD mice. Methods: Quantitative trait loci (QTL) mapping of testis weight was performed with or without considering the influence of plasma testosterone level in reciprocal $F_2$ intercross populations between DDD and C57BL/6J (B6) mice, thereby assessing the influence of testosterone on the effect of testis weight QTL. Candidate genes for testis weight QTL were investigated by next-generation sequencing analysis. Results: Four significant QTL were identified on chromosomes 1, 8, 14, and 17. The DDDderived allele was associated with increased testis weight. The $F_2$ mice were then divided into two groups according to the plasma testosterone level ($F_2$ mice with relatively "low" and "high" testosterone levels), and QTL scans were again performed. Although QTL on chromosome 1 was shared in both $F_2$ mice, QTL on chromosomes 8 and 17 were identified specifically in $F_2$ mice with relatively high testosterone levels. By whole-exome sequencing analysis, we identified one DDD-specific missense mutation Pro29Ser in alpha tubulin acetyltransferase 1 (Atat1). Conclusion: Most of the testis weight QTL expressed stronger phenotypic effect when they were placed on circumstance with high testosterone level. High testosterone influenced the QTL by enhancing the effect of DDD-derived allele and diminishing the effects of B6-derived allele. Since Pro29Ser was not identified in other inbred mouse strains, and since Pro29 in Atat1 has been strongly conserved among mammalian species, Atat1 is a plausible candidate for testis weight QTL on chromosome 17.

• Journal of Animal Science and Technology
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• v.45 no.6
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• pp.939-948
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• 2003

The objective of this study was to identify the quantitative traits loci(QTL) for economically important traits such as growth, carcass and meat quality on pig chromosome 6. A three generation resource population was constructed from cross between Korean native boars and Landrace sows. A total of 240 F$_2$ animals were produced using intercross between 10 boars and 31 sows of F$_1$ animals. Phenotypic data including body weight at 3 weeks, backfat thickness, muscle pH, shear force and crude protein level were collected from F$_2$ animals. Animals including grandparents(F$_0$), parents(F$_1$) and offspring(F$_2$) were genotyped for 29 microsatellite markers and PCR-RFLP marker on chromosome 6. The linkage analysis was performed using CRI-MAP software version 2.4(Green et al., 1990) with FIXED option to obtain the map distances. The total length of SSC6 linkage map estimated in this study was 169.3cM. The average distance between adjacent markers was 6.05cM. For mapping of QTL, we used F$_2$ QTL Analysis Servlet of QTL express, a web-based QTL mapping tool(http://qtl.cap.ed.ac.uk). Five QTLs were detected at 5% chromosome-wide level for body weight of 3 weeks of age, shear force, meat pH at 24 hours after slaughtering, backfat thickness and crude protein level on SSC6.

• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.282-287
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• 2011

Bacterial pustule (BP) is a leaf disease of soybean that is most common in Korea. Inoculation of 8ra, pathogen strain, to resistant and susceptible cultivars for finding the BP resistance gene (rxp) was much tried but the sequence of the exact gene is not found. This research performed in order to confirm the rxp gene near molecular marker by using the resistant and susceptible cultivars. Soybean BP resistance gene which related to region of near molecular marker could select the resistant cultivar. For the near molecular marker of rxp, reference genomics data available at sequenced Phytozome was used for designing molecular markers. The rxp was mapped between Satt372 and Satt486 on chromosome 17. According to previous study, rxp released in find mapping 7.2 Mbp to 7.3 Mbp on chromosome 17. In this study, we developed 3 random markers near from 6.6 Mbp to 7.3 Mbp on chromosome 17 identified to increase the genetic resolution of the rxp gene region using resistant and susceptible cultivars. Particularly, Rxp17-700 marker was mostly coincided resistance and susceptible genotype to rxp. This result suggests that Rxp17-700 marker will be more tightly linked to rxp gene.

• Korean Journal of Plant Resources
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• v.20 no.5
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• pp.446-450
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• 2007

Tiarella polyphylla D. Don(Saxifragaceae) is a perennial herb and distributed in China, Japan, Taiwan and Korea. Especially, it only grows in Ulleung island of Korea. It has been using for asthma, bruise and audition troubles with main components of some Triterpenoids and seven oleanolic Saponins. There is only known its chromosomal number rarely and cytogenetic study was not done. From this study, karyotype analysis and chromosomal localization of 5S and 45S rDNAs using bicolor-FISH(fluorescence in situ hybridization) were carried out. The somatic metaphase chromosome number was 2n=2x=14 and the size of chromosomes ranged $1.66{\sim}3.50{\mu}m$. The chromosome complement consisted of four pairs of submetacentrics(chromosomes 1, 2, 3 and 6), two pairs of subtelocentrics(chromosomes 5 and 7) and one pair of telocentrics(chromosome 4). We also observed NOR(nucleolus organizer region) on the chromosome 4. In bicolor-FISH, one pair of 55 and 45S rDNA sites was detected on the centromeric region of chromosome 3 and short arm of chromosome 4, respectively. Bicolor FISH was very useful tool for the localization and identification of rDNAs on the chromosomes in Tiarella polyphylla.