• Asian-Australasian Journal of Animal Sciences
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• v.16 no.4
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• pp.473-480
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• 2003

In order to control the genetic background noise in QTL mapping, cofactor markers were incorporated in single marker analysis (SMACO) and interval mapping (CIM). A simulation was performed to see how effective the cofactors were by the number of QTL, the number and the type of markers, and the marker spacing. The results of QTL mapping for the simulated data showed that the use of cofactors was slightly effective when detecting a single QTL. On the other hand, a considerable improvement was observed when dealing with more than one QTL. Genetic background noise was efficiently absorbed with linked markers rather than unlinked markers. Furthermore, the efficiency was different in QTL mapping depending on the type of linked markers. Well-chosen markers in both SMACO and CIM made the range of linkage position for a significant QTL narrow and the estimates of QTL effects accurate. Generally, 3 to 5 cofactors offered accurate results. Over-fitting was a problem with many regressor variables when the heritability was small. Various marker spacing from 4 to 20 cM did not change greatly the detection of multiple QTLs, but they were less efficient when the marker spacing exceeded 30 cM. Likelihood ratio increased with a large heritability, and the threshold heritability for QTL detection was between 0.30 and 0.05.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.282-282
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• 2022

Arsenic (As) is a toxic heavy metal that affects the major rice-growing regions of the world and can cause cancer in humans. Rice paddy fields in South Asia are mostly dependent on arsenic-contaminated water sources due to which rice takes up the arsenic from the soil through roots and accumulates it in plant different parts. Here, we present a quantitative trait locus (QTL) mapping study to find out candidate genes conferring As toxicity tolerance in rice (Oryza sativa L.) at the seedling stage. Three weeks old, 120 double haploid CNDH lines derived from a cross between the Indica variety Cheongcheong and the Japonica variety Nagdong and their parental lines were used by treating with 25 μM As. After 2 weeks ofAs stress, 5 traits such as; shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), and chlorophyll contents (CHC) were measured. A linkage map of 12 rice chromosomes was constructed from genotypic data DH lines using 778 SSR markers. The linkage map covered a total genetic distance of 2121.7 cM of the rice genome with an average interval of 10.6 cM between markers. A total of seventeen QTLs (LOD>2) were mapped on chromosomes 1, 2, 3, 6, 7, 8, 9, 11, and 12 using composite interval mapping with trait-increasing alleles coming from both parents. Five QTLs for SL, Two QTLs for RL, Five QTLs for SHL, Three QTLs for RFW, and Two QTLs for CHC were detected. The QTLs related to CHC were selected for forther study.

• Genomics & Informatics
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• v.6 no.1
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• pp.8-13
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• 2008

High-density lipoprotein (HDL) whose primary role is to transport cholesterol from peripheral tissues to the liver, is associated with the incidence of coronary heart disease. We analyzed HDL cholesterol levels in a genetically isolated population of extended Mongolian families. A total of 1002 individuals (54.5% women) from 95 families were enrolled. After genotyping by use of 1000 microsatellite markers, we performed a genome-wide linkage search with variance component analysis. The estimated heritability of HDL cholesterol was 0.45, revealing that HDL cholesterol was under significant genetic influence. We found peak evidence of linkage (LOD score=1.88) for HDL cholesterol level on chromosome 6 (nearest marker D6S1660) and potential evidences for linkage on chromosomes 1, 12 and 19 with the LOD scores of 1.32, 1.44 and 1.14, respectively. These results should pave the way for the discovery of the relevant genes by fine mapping and association analysis.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.5
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• pp.423-428
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• 2004

Soybean seeds contain high amounts of isoflavones that display biological effects and isoflavone content of soybean seed can vary by year, environment, and genotype. Objective of this study was to identify quantitative trait loci that underlie isoflavone content in soybean seeds. The study involved 85 $F_2$ populations derived from Korean soybean cultivar 'Kwangkyo' and wild type soybean 'IT182305' for QTL analysis associated with isoflavone content. Isoflavone content of seeds was determined by HPLC. The genetic map of 33 linkage groups with 207 markers was constructed. The linkage map spanned 2,607.5 cM across all 33 linkage groups. The average linkage distance between pair of markers among all linkage groups was 12.6 cM in Kosambi map units. Isoflavone content in $F_2$ generations varied in a fashion that suggested a continuous, polygenic inheritance. Eleven markers (4 RAPD, 3 SSR, 4 AFLP) were significantly associated with isoflavone content. Only two markers, Satt419 and CTCGAG3 had F-tests that were significant at P<0.01 in $F_2$ generation for isoflavone content. Interval mapping using the $F_2$ data revealed only two putative QTLs for isoflavone content. The peak QTL region on linkage group 3, which was near OPAG03c, explained $14\%$ variation for isoflavone content. The peak QTL region on linkage group 5, which was located near OPN14 accounted for $35.3\%$ variation for isoflavone content. Using both Map-Maker-QTL $(LOD{\geq}2.0)$ and single-factor analysis $(P{\leq}0.05)$, one marker, CTCGAG3 in linkage group 3 was associated with QTLs for isoflavone content. This information would then be used in identification of QTLs for isoflavone content with precision

• Proceedings of the Korean Statistical Society Conference
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• 2003.05a
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• pp.305-311
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• 2003

K-Means 모델을 이용하여 한우 유전자 6번의 BM4311의 중요 DNA marker을 찾기위해 여러 가지로 시도해 왔다. 이번 논문에선 QTL(Quantitative Trait Loci)과 data mining modeling를 이용하여 BM4311에서 중요 DNA marker를 찾아 보도록 하겠다.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.11
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• pp.1505-1510
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• 2001

A method for mapping quantitative trait loci (QTL) was introduced incorporating the information of mixed progeny from complex pedigrees. The method consisted of two steps based on single marker analysis. The first step was to examine the marker-trait association with a mixed model considering common environmental effect and reversed QTL-marker linkage phase. The second step was to estimate QTL effects by a weighted least square analysis. A simulation study indicated that the method incorporating mixed progeny from multiple generations improved the accuracy of QTL detection. The influence of within-genotype variance and recombination rate on QTL analysis was further examined. Detecting a QTL with a large within-genotype variance was more difficult than with a small within-genotype variance. Most of the significant marker-QTL association was detectable when the recombination rate was less than 15%.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 1986.12a
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• pp.512.2-512
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• 1986

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 causing the altered deoxycytidine-cytidine deaminase, cdd, 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 as trp-lys-dnaE-cdd-aroD. The cdd gene was linked 72% with the aroD and 20% with the lys.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.428-428
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• 2005

• Molecules and Cells
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• v.25 no.2
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• pp.196-204
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• 2008

Despite increasing awareness of the importance of WRKY genes in plant defense signaling, the locations of these genes in the Capsicum genome have not been established. To develop WRKY-based markers, primer sequences were deduced from the conserved sequences of the DNA binding motif within the WRKY domains of tomato and pepper genes. These primers were derived from upstream and downstream parts of the conserved sequences of the three WRKY groups. Six primer combinations of each WRKY group were tested for polymorphisms between the mapping parents, C. annuum 'CM334' and C. annuum 'Chilsung-cho'. DNA fragments amplified by primer pairs deduced from WRKY Group II genes revealed high levels of polymorphism. Using 32 primer pairs to amplify upstream and downstream parts of the WRKY domain of WRKY group II genes, 60 polymorphic bands were detected. Polymorphisms were not detected with primer pairs from downstream parts of WRKY group II genes. Half of these primers were subjected to $F_2$ genotyping to construct a linkage map. Thirty of 41 markers were located evenly spaced on 20 of the 28 linkage groups, without clustering. This linkage map also consisted of 199 AFLP and 26 SSR markers. This WRKY-based marker system is a rapid and simple method for generating sequence-specific markers for plant gene families.

• Journal of Animal Science and Technology
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• v.46 no.4
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• pp.525-536
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• 2004

The objective of this study was to identify the quantitative traits loci(QTL) for meat quality traits in pigs. Three-generation resource population was constructed from a cross between Korean native boars and Landrace sows. The resource population including founders, $F_1$ and $F_2$ was genotyped for 23 microsatellite markers on chromosome 7. The sex average total length of linkage map on chromosome 7 was estimated 154.6 cM. Meat quality traits including meat pH, meat color, drip loss, shear force, heating loss, crude fat, crude protein, crude ash and water content in muscle were collected from $F_2$ animals. For the QTL mapping, we used $F_2$ QTL Analysis Servlet of QTL express for web-based QTL mapping tools(http://qtl.cap.ed.ac.uk/). The QTLs for CIE-a and CIE-b on SSC7 were significantly detected at 1% and 5% chromosome-wide level, respectively.