• 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.

• Journal of Genetic Medicine
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• v.11 no.2
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• pp.49-55
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• 2014

Genetic ultrasonography refers to the evaluation of risk of chromosomal abnormalities via various soft sonographic markers. Although the maternal serum test is the primary screening method for chromosomal abnormalities, genetic ultrasonography is also widely used and can help increase detection rates. To date, many soft markers, including choroid plexus cysts, echogenic intracardiac foci, mild ventriculomegaly, nuchal fold thickening, echogenic bowel, mild pyelectasis, short femur and humerus length, and absent or hypoplastic nasal bone, have been reported. An aberrant right subclavian artery was the most novel soft marker introduced. Because these soft markers involve diverse relative risks of chromosomal abnormalities, it is difficult to apply them to clinical practice. To optimize the efficacy of genetic ultrasonography, it is important to understand the precise relative risks of chromosomal abnormalities innumerous soft markers and integrate these risks with each other and the results of maternal serum screening.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.48 no.6
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• pp.419-423
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• 2003

Bacterial blight caused by Xantomonas oryzae pv. oryzae is one of the most serious diseases of rice especially in southern area of Korea. Three races, $\textrm{K}_1$, $\textrm{K}_2$ and $\textrm{K}_3$, are the most dominant species. lo improve rice breeding efficiency using marker assisted selection, some RFLP markers were surveyed for polymorphism between resistant and susceptible to $\textrm{K}_1$ and $\textrm{K}_3$. And, 127 doubled-haploid (DH) lines derived from Milyang121/HRl1650-1-4-2 and 131 DH lines derived from Milyang123/HR10624-AC5 were evaluated to bacterial blight ($\textrm{K}_1$ and $\textrm{K}_3$). Milyang121 and HR10624-AC5 have Xa-1, resistant to $\textrm{K}_1$ race, and Milyang123 has Xa-3, resistant to $\textrm{K}_1$ and $\textrm{K}_3$ race. Three markers, RZ590, RZ536 and RG303, showing polymorphism between parents and resistance gene, Xa-1 and Xa-3, were analysed in the two combinations of DH lines. The segregation pattern of resistant DH population of Milyang123/HR10624-AC5 to susceptible showed 3:1 and 1:1 in $\textrm{K}_1$ and $\textrm{K}_3$ race. In three RFLP markers, RZ590 was linked to Xa-1 on chromosome 4, and RZ536 and RG303 were linked to Xa-3 on chromosome 11. The map distance between Xa-1 and RZ590 was 3.1cM on chromosome 4, and Xa-3 and RZ536/RG303 were 7.6/16.0cM on chromosome 11, respectively. The results of RFLP mapping will be useful for the selection and pyramiding of bacterial blight resistant genes.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.76-81
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• 2016

We performed a molecular marker-based analysis of quantitative trait loci for traits that determine the quality of appearance of grains using 120 doubled haploid lines developed by anther culture from the F1 cross between 'Cheongcheong' (Oryza sativa L. ssp. Indica) and 'Nagdong' (Oryza sativa L. ssp. Japonica). We therefore calculated the alkali digestion value (ADV), used to indirectly measure gelatinization temperature, to evaluate the quality of cooked rice in 2013 and 2014. The ADV score of frequency distribution was higher milled rice than brown rice. In total, nine different quantitative trait loci (QTLs) were found on 5 chromosomes in 2013 and 2014. Also, chromosome 5, 8 were detected over two years. We conclude that selected molecular markers from this QTL analysis could be exploited in future rice quality. In conclusion, we investigated ADV of brown and milled rice in CNDH population. This study found nine QTLs related to the ADV of brown and milled rice. The detected one marker can be used to select lines with desirable eating-quality traits because ADV is closely associated with the eating quality of cooked rice. Therefore, it will be useful to collect resources and distinguishable in many varieties for rice breeding program.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.50 no.6
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• pp.453-456
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• 2005

This study was carried out to select DNA markers closely linked to brown planthopper (BPH) resistance gene originated from a rice cultivar 'Cheongcheong­byeo'. For the mapping of resistant gene to BPH, a doubled-haploid (DH) population was developed by anther culture of $F_1$ plants from a cross 'Cheongcheong­byeo/Nagdongbyeo'. In BPH bioassay and marker screen­ing for the DH population, the segregation of resistant and susceptible plants to BPH fitted to a 1:1 ratio. A total of 310 RAPDs of 520 markers showed polymorphism in parental survey using 'Cheongcheongbyeo' and 'Nag­dongbyeo'. In the analysis of relationship between BPH resistance and marker pattern for 40 DH lines, the OPE16 produced a specific dominant fragment, 700 bp, which was closely linked with BPH resistance gene of 'Cheong­cheongbyeo'. Based on the linkage analysis using 7 markers, BPH resistance of 'Cheongcheongbyeo' was mapped on chromosome 12, which was closely linked with $OPE16_{700}$ at a distance of 4.6 cM.

• Proceedings of the Korea Society of Poultry Science Conference
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• 2004.11a
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• pp.13-15
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• 2004

Telomeres are the end of chromosomes and consist of a tandem repeat sequence of (TTAGGG)n and associated proteins. Telomeres are essential for chromosome stability and are related with cell senescence and apoptosis. This study was carried out to analyze the amount of telomeric DNA of chicken lymphocytes, which is to considered as bio-marker. The amount of telomeric DNA of lymphocytes in Korean Native Chicken and White Leghorn was analyzed by quantitative-fluorescence in situ hybridization (Q-FISH) technique using the chicken telomeric DNA probe. Telomere quantifies were compared among breeds, ages and sex, and the relationship between the amount of telomeres and their productive trait was also analyzed. Comparing the amount of telomeric DNA on lymphocytes during growing period, the amount of telomeres was gradually decreased as growing older. The telomere quantity was also significantly different in breeds and sex. Estimating correlation coefficient, the amount of telomeres was positively correlated to sexual maturity and body weight but negatively correlated to hen day egg production and egg weight. These results implicate the telomere quantity is considered as an individual bio-marker.

• Korean Journal of Breeding Science
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• v.50 no.4
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• pp.387-395
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• 2018

This study was conducted to identify DNA markers related to resistance to herbicide containing mesotrione in Tongil type rice. Two Tongil type elite lines; Milyang154 and Suweon382, showed resistance to mesotrione, whereas the others were susceptible at 20 days after mesotrione application, and severe growth inhibition was observed in the remaining 13 lines. As a result of analysis of mesotrione resistance using 190 $F_2$ populations derived from a cross of Hanareum2 (susceptible) and Milyang154 (resistant), the mesotrione resistance locus was shown to be a single dominant gene with a 3:1 segregation ratio ($X^2=1.19$, P=0.31). To identify a DNA marker closely linked to the mesotrione resistance gene, bulked segregant analysis (BSA) was adopted. The DNA marker RM3501 was identified on chromosome 2 with a recombinant value of 0.53 to the mesotrione resistance gene. Mst1(t) was located between SSR (simple sequence repeat) markers RM3501 and RM324 with a physical map distance of 10.2 Mb-11.4 Mb on chromosome 2. The band pattern of agarose gel electrophoresis of the SSR marker RM3501 showed the same segregation pattern with respect to mesotrione treatment in 20 Tongil type varieties and a $BC_2F_2$ segregation population derived from a cross between Unkwang (resistant) and Hanareum2 (susceptible). Thus, the RM3501 DNA marker could be used in breeding programs for Marker Assisted Selection in mesotrione resistant rice breeding.

• Journal of Plant Biotechnology
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• v.45 no.3
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• pp.242-249
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• 2018

This study was conducted to develop an SNP set that can be useful for marker-assisted breeding (MAB) in watermelon (Citrullus. lanatus L) using Genotyping-by-sequencing (GBS) analysis of 20 commercial elite watermelon inbreds. The result of GBS showed that 77% of approximately 1.1 billion raw reads were mapped on the watermelon genome with an average mapping region of about 4,000 Kb, which indicated genome coverage of 2.3%. After the filtering process, a total of 2,670 SNPs with an average depth of 31.57 and the PIC (Polymorphic Information Content) value of 0.1~0.38 for 20 elite inbreds were obtained. Among those SNPs, 55 SNPs (5 SNPs per chromosome that are equally distributed on each chromosome) were selected. For the understanding genetic relationship of 20 elite inbreds, PCA (Principal Component Analysis) was carried out with 55 SNPs, which resulted in the classification of inbreds into 4 groups based on PC1 (52%) and PC2 (11%), thus causing differentiation between the inbreds. A similar classification pattern for PCA was observed from hierarchical clustering analysis. The SNP set developed in this study has the potential for application to cultivar identification, F1 seed purity test, and marker-assisted backcross (MABC) not only for 20 elite inbreds but also for diverse resources for watermelon breeding.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.92-92
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• 2017

Bakanae disease is one of the most serious and oldest problems of rice production, which was first described in 1828 in Japan. This disease has also been identified in Asia, Africa, North America, and Italy. Germinating rice seeds in seed boxes for mechanical transplantation has caused many problems associated with diseases, including bakanae disease. Bakanae disease has become a serious problem in the breeding of hybrid rice, which involves the increased use of raising plants in seed beds. The indica rice variety Shingwang was selected as resistant donor to bakanae disease. One hundred sixty nine NILs, YR28297 ($BC_6F_4$) generated by five backcrosses of Shingwang with the genetic background of susceptible japonica variety, Ilpum were used for QTL analysis. Rice bakanae disease pathogen, CF283, was mainly used in this study and inoculation and evaluation of bakanae disease was performed with the method of the large-scale screening method developed by Kim et al. (2014). SSR markers evenly distributed in the entire rice chromosomes were selected from the Gramene database (http://www.gramene.org), and the polymorphic markers were used for frame mapping of a $BC_5F_5$ resistant line. Here, we developed 168 near-isogenic rice lines (NILs, $BC_6F_4$) to locate a QTL for resistance against bakanae disease. The lines were derived from a cross between Shingwang, a highly resistant variety (indica), and Ilpum, a highly susceptible variety (japonica). The 24 markers representing the Shingwang allele in a bakanae disease-resistant NIL, YR24982-9-1 (parental line of the $BC_6F_4$ NILs), were located on chromosome 1, 2, 7, 8, 10, 11, and 12. Single marker analysis using an SSR marker, RM9, showed that a major QTL was located on chromosome 1. The QTL explained 65 % of the total phenotype variation in $BC_6F_4$ NILs. The major QTL designated qBK1 was mapped in 91 kb region between InDel15 and InDel21. The identification of qBK1 and the closely linked SSR marker, InDel18, could be useful for improving rice bakanae disease resistance in marker-assisted breeding.

• Genomics & Informatics
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• v.7 no.3
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• pp.152-158
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• 2009

Although the genetic basis for bone mineral density (BMD) has been studied by many groups so far, genes responsible for this complex trait has not been completely revealed. In order to localize quantitative trait loci (QTLs) for BMD variation in Asian population, the study was designed using a group of Mongolian population, a genetically closed population with a homogeneous lifestyle. BMD was measured at the left and right wrists and ankles using DEXA in 1,082 participants from 142 families. Genotyping of 13 polymorphic microsatellite markers on chromosome 13 (average spacing 8-9 cM) and two-point and multipoint linkage analysis were performed. In two-point linkage analysis, we identified two markers, D13S175 (6.03 cM) and D13S265 (68.73 cM) that had LOD scores greater than 1 for left ankle (LOD=2.09, LOD=1.49, respectively). We also found a marker D13S175 (6.03 cM) with a high LOD for left wrist (LOD=1.49) and the markers D13S265 (68.73 cM) and D13S217 (17.21 cM) for the right wrist (LOD= 1.82, LOD= 1.62, respectively). Among these significant marker regions, only two regions at 17 cM (13p11) and 65 cM (13q21) for the right wrist overlapped with major QTLs reported in following multipoint linkage analysis (LOD= 1.7549, LOD=1.4462, respectively). This study provides the possible evidence of the presence of QTLs affecting right wrist BMD in Mongolian populations on 13p11 and 13q21. Modest evidence was also found for genes affecting left ankle and left wrist BMD on 13p13.