• Toxicological Research
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• v.24 no.1
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• pp.69-78
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• 2008

Mutant mouse which show dwarfism has been developed by N-ethyl-N-nitrosourea (ENU) mutagenesis using BALB/c mice. The mutant mouse was inherited as autosomal recessive trait and named Small Body Size (SBS) mouse. The phenotype of SBS mouse was not apparent at birth, but it was possible to distinguish mutant phenotype from normal mice 1 week after birth. In this study, we examined body weight changes and bone mineral density (BMD), and we also carried out genetic linkage analysis to map the causative gene(s) of SBS mouse. Body weight changes were observed from birth to 14 weeks of age in both affected (n = 30) and normal mice (n = 24). BMD was examined in each five SBS and normal mice between 3 and 6 weeks of age, respectively. For the linkage analysis, we produced backcross progeny [(SBS${\times}$C57BL/6J) $F_1{\times}$ SBS] $N_2$ mice (n = 142), and seventy-four microsatellite markers were used for primary linkage analysis. Body weight of affected mice was consistently lower than that of the normal mice, and was 43.7% less than that of normal mice at 3 weeks of age (P < 0.001). As compared with normal mice at 3 and 6 weeks of age, BMD of the SBS mice was significantly low. The results showed 15.5% and 14.1 % lower in total body BMD, 15.3% and 8.7% lower in forearm BMD, and 29.7% and 20.1% lower in femur BMD, respectively. The causative gene was mapped on chromosome 10. The map order and the distance between markers were D10Mit248 - 2.1 cM - D10Mit51 - 4.2 cM - sbs - 0.7 cM - D10Mit283 - 1.4cM - D10Mit106 - 11.2cM - D10Mit170.

• Journal of Plant Biotechnology
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• v.44 no.4
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• pp.349-355
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• 2017

The amino acid composition of rice is a major concern of rice breeders because amino acids are among the most important nutrient components in rice. In this study, a genetic map was constructed with a population of 134 recombinant inbred lines (RILs) from a cross between Dasanbyeo (Tongil-type indica) and TR22183 (temperate japonica), as a means to detect the main and epistatic effect quantitative trait loci (QTLs) for the amino acid content (AAC). Using a linkage map which covered a total of 1458 cM based on 239 molecular marker loci, a total of six main-effect QTLs (M-QTLs) was identified for the content of six amino acids that were mapped onto chromosome 3. For all the M-QTLs, the TR22183 allele increased the trait values. The QTL cluster (flanked by id3015453 and id3016090) on chromosome 3 was associated with the content of five amino acids. The phenotypic variation, explained by the individual QTLs located in this cluster, ranged from 10.2 to 12.4%. In addition, 26 epistatic QTLs (Ep-QTLs) were detected and the 25 loci involved in this interaction were distributed on all nine chromosomes. Both the M-QTLs and Ep-QTLs detected in this study will be useful in breeding programs which target the development of rice with improved amino acid composition.

• Journal of Crop Science and Biotechnology
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• v.11 no.3
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• pp.163-170
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• 2008

The detection, characterization and use of quantitative traits loci, QTL, have significant potential to improve the efficiency of selective breeding of species. Therefore, a population with 59 advanced backcross lines($BC_2F_5$), derived from a cross between IR64 and Tarome molaei, were studied in Tonekabon Rice Research Station of Iran in order to map QTLs for panicle length, number of grain per panicle, and panicle grain sterility in rice. The parental screening wtih 235 SSR markers in agarose and polyacrylamide gels revealed 114 markers with clear polymorphic bands. To search for QTLs associated with panicle length, number of grain per panicle, and panicle grain sterility, we constructed a genetic linkage map using 114 microsatellite markers. Positive and negative transgressive segregations were observed in $BC_2F_5$ lines for all traits. Using multiple interval mapping(MIM), a total of 20 putative QTLs were detected, of which eight were for panicle length, three for number of grains, and nine for panicle grain sterility. The maximum number of QTLs were mapped on chromosomes 1 and 2 with eight QTLs. These QTL markers could possible be utilized for marker-assisted selection.

• Horticultural Science & Technology
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• v.31 no.4
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• pp.473-482
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• 2013

Molecular markers, as an efficient selection tool, have been and is being used for practical breeding program in chili pepper (Capsicum annuum L.). Recently, a lot of researches on inheritance and genetic analysis for quantitative traits including capsaicinoids, carotenoids, and sugar content in pepper are being performed worldwide. It has been also reported that QTL mapping is a necessary tool to develop molecular markers associated with the quantitative traits. In this study, we suggested a new method to construct a pepper genetic map using SNP (HRM) markers generated from NGS resequencing of female and male parents. Plant materials were C. annuum 'NB1' (female parent), C. chinense 'Jolokia' (male parent), and their $F_2$ population consisting of 94 progenies. Sequences of 4.6 Gbp and 6.2 Gbp were obtained from NGS resequencing of 'NB1' and 'Jolokia', respectively. Totally, 4.29 million SNPs between 'NB1' and 'Jolokia' were detected and the 1.76 million SNPs were clearly identified. Among them, total 145 SNP (HRM) primer pairs covering pepper genetic map were selected, and the 116 SNP (HRM) markers of them were located on this map. Total distance of the map, which consisted of 12 linkage groups and matched with basic chromosome numbers of pepper, was 1,167.9 cM. According to the mapping result, we concluded that our mapping method was suitable to construct a pepper genetic map fast and accurately. In addition, the genetic map could be directly used for QTL analysis of traits different between both parents.

• International Journal of Industrial Entomology and Biomaterials
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• v.19 no.1
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• pp.143-154
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• 2009

Single nucleotide polymorphisms (SNPs) are the most frequent form of variation in the genome of any organism. Owing to their greater abundance, they are considered useful for identifying cultivars, construction of higher density linkage maps, and detection of genes (QTLs) associated with complex agronomic traits and diseases. Although, SNPs have been used recently for constructing a high density genetic map in silkworm and a set of 118 SNPs have been identified in tasar silkworms, not much progress has been made in sericulture to utilize the vast potential of SNPs. Thus, this review mainly focuses on some of the important methods of SNP discovery, validation and genotyping. Emphasis has also been given to the possible uses of SNP genotyping in the improvement of silkworms and their host plants.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.236-244
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• 2003

Summary: The analysis of human genetic variation is one of the key issues far the understanding of the different drug response among individuals and many programs are developed for this purpose. However, current publicly available programs have so many limitations such as time complexity problem for the analysis of large amount of alleles or SNPs, difficult manipulation for installation, data import, and usage, and low-quality visual output. Here we present workbench for SNP anlaysis, SNPAnalyzer. SNPAnalyzer consists of 3 main modules: 1)Hardy-Weinberg Equilibrium ,2) Haplotype Estimation, and 3) Linkage Disequilibrium. Each module has several different widely-used algorithms for the extensive analysis and can handle large amount of alleles and SNPs with simple format. Analysis results are displayed in user-friendly formats such as table, graph and map. SNPAnalyzer is developed using C and C$^{++}$ and users can easily access through web-interftce. Availability: SNPAnalyzer can be freely implemented at http://www.istech.info/istech/board/login_form.jsp

• Microbiology and Biotechnology Letters
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• v.16 no.6
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• pp.536-539
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• 1988

A mutant of Bacillus subtilis with a defective cdd gene encoding deoxycytidine-cytidine deaminase (EC 3.5.4.5) has been characterized genetically. The genetic lesion, cdd, causing the altered deoxycytidine-cytidine deaminase was mapped at 225 min on the linkage map of B. subtilis by AR9 transduction, Transductional analysis of the cdd region established the gene order in clockwise as trp-lys-cdd-aroD. The cdd gene was linked 72% with the aroD and 20% with the lys.

• Journal of Plant Biotechnology
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• v.46 no.2
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• pp.71-78
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• 2019

The objective of this study was to use 'Danta PR', NGS (Next Generation Sequencing) technology for genome resequencing to develop polymorphic makers between Chinese oriental melon, 'Hyangseo 1' and Korean oriental melon. From the resequencing data that covered about 81 times of the genome size, 104,357 of SSR motifs and Indel, and 1,092,436 of SNPs were identified. 299 SSR and 307 Indel markers were chosen to cover each chromosome with 25 markers. These markers were subsequently used to identify genotypes of 'Danta PR' BC1 (F1 x 'Danta PR') population and a genetic linkage map was constructed. SSR, Indel, and SNPs identified in this study would be useful as a breeding tool to develop new oriental melon varieties.

• Journal of Crop Science and Biotechnology
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• v.11 no.2
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• pp.151-156
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• 2008

The objective of this study is to identify main-effect QTLs, epistatic QTLs, and the interactions between QTL and the environment associated with grain appearances of brown rice. A genetic linkage map was created with 172 DNA markers spanning 12 rice chromosomes based on 120 DH lines, which derived from a cross between 'Samgang'(Tongil) and 'Nagdong'(Japonica). One thousandgrain weight, length, width, length-to-width ratio, and thickness were evaluated regarding the DH population. Twenty independent QTLs and fourteen epistatic QTLs were identified in using CIM by two programs, known as WinQTLcart2.5 and QTLMAPPER. The QTLs of qgw9.1 in an interval of RM434-RM242 on chromosome 9 and qgw11.1 at a peak marker of RM287 on chromosome 11 for one thousand-grain weight, qgwi2.2 for grain width at a peak marker of RM450, qlw2.1 for length-to-width ratio flanked by RM492 and RM324, and qgt2.1 for thickness flanked by 2009 and RM492 on chromosome 2 were detected over two years, which can be considered as stable QTLs. The epistatic effect might be an important component for genetic basis of one thousand-grain weight and width. The main-effect QTLs of grain width and length to width ratio were easily influenced by environments.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.2
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• pp.165-171
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• 2009

The objective of this study was to characterize the main-effect QTLs, epistatic QTLs and QTL-by-environment interactions (QE), which are involved in the control of protein content. A population of 120 doubled haploid (DH) lines derived from a cross between 'Samgang' and 'Nagdong', was planted and determined for protein content over three years. Based on the population and a genetic linkage map of 172 markers, QTL analysis was conducted by WinQTLcart 2.5 and QTLMAPPER. Three main-effect QTLs affecting protein content of brown rice were detected from 2004 to 2006 on chromosomes 1 and 11. The qPC11.2 was repeatedly detected across two years. Seven pairs of epistatic loci were identified on eight chromosomes for protein content and collectively explained 39.15% of phenotype variation. These results suggest that epistatic effects might be an even more important component of the genetic basis for protein content and that the segregation of the DH lines for protein content could be largely explained by a few main-effect QTLs and many epistatic loci.