• Journal of the Korean Institute of Intelligent Systems
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• v.21 no.5
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• pp.575-580
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• 2011

With the increasing expectation on personalized medicine, it is getting importance to analyze medical information in molecular biology perspective. Gene expression data are one of representative ones to show the microscopic phenomena of biological activities. In gene expression data analysis, one of major concerns is to identify markers which can be used to predict disease occurrence, progression or recurrence in the molecular level. Existing markers candidate identification methods mainly depend on statistical hypothesis test methods. This paper proposes a search method based decision tree induction to identify candidate markers which consist of multiple genes. The propose method discretizes numeric expression level into three categorical values and allows candidate markers' genes to be expressed by their negation as well as categorical values. It is desirable to have some number of genes to be included in markers. Hence the method is devised to try to find candidate markers with restricted number of genes.

• Korean Journal of Breeding Science
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• v.50 no.4
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• pp.434-441
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• 2018

High-density genetic linkage mapping is critical for undertaking marker-assisted selection and confirming quantitative trait loci, as well as helping to build pseudomolecules of genomes. We constructed a genetic map using 94 $F_1$ populations generated from the interspecific cross between Korean cultivar "Wonwhang" (Pyrus pyrifolia, NCBI BioSample SAMN05196235) and European cultivar "Bartlett" (Pyrus communis). We designed a total of 24,267 SSR markers based on the genome sequences of "Wonwhang" for this. To select the markers that are linked to the traits important in pear breeding programs, SSR-containing genomic sequences were subjected to nucleotide sequence homology searches, which resulted in 510 SSR markers with high similarity to genes encoding proteins with putative functions such as transcription factors, resistance proteins, flowering time, and regulatory genes. Of these, 70 markers showed polymorphisms in parents and segregating populations and were used to construct a genetic linkage map, together with the unpublished 579 SNPs obtained from genotyping by sequencing analysis. The genetic linkage map covered 3,784.2 cM and the average distance between adjacent markers was 5.8 cM. Seventy SSR markers were distributed across 17 chromosomes with more than one locus.

• Journal of Life Science
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• v.25 no.7
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• pp.839-848
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• 2015

A molecular marker is a molecule contained within a sample taken from an organism or other matter. The development of molecular techniques for genetic analysis has led to a great contribution to our knowledge of plant genetics and our understanding of the structure and behavior of various genomes in plants. Recently, functional molecular markers have been developed to detect the presence of major genes from the analysis of pedigreed data in absence of molecular information. DNA markers have developed into many systems based on different polymorphism-detecting techniques or methods such as RFLP, AFLP, RAPD, SSR, SNP, etc. A new class of very useful DNA markers called genic molecular markers utilizing the ever-increasing archives of gene sequence information being accumulated under the EST sequencing projects on a large number of plant species. Functional markers are derived from polymorphic sequences, and are more likely to be involved in phenotypic trait variation. Based on this conceptual framework, the marker systems discussed below are all (gene)-targeted markers, which have the potential to become functional. These markers being part of the cDNA/EST-sequences, are expected to represent the functional component of the genome i.e., gene(s), in contrast to all other random DNA based markers that are developed/generated from the anonymous genomic DNA sequences/domains irrespective of their genic content/information. Especially I sited Poczai et al’ reviews, advances in plant gene-targeted and functional markers. Their reviews may be some useful information to study molecular markers in plants.

• Journal of Life Science
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• v.25 no.9
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• pp.1059-1071
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• 2015

Watermelon and melon are economically important Cucurbitaceae crops. Recently, the development of molecular markers based on the construction of genetic linkage maps and detection of DNA sequence variants through next generation sequencing are essential as molecular breeding strategies for crop improvement that uses marker-assisted selection and backcrossing. In this paper, we intended to provide useful information for molecular breeding of watermelon and melon by analyzing the current status of international and domestic research efforts on genomics and molecular markers. Due to diverse genetic maps constructed and the reference genome sequencing completed in the past, DNA markers that are useful for selecting important traits including yield, fruit quality, and disease resistances have been reported and publicly available. To date, more than 16 genetic maps and loci and linked markers for more than 40 traits have reported for each watermelon and melon. Furthermore, the functional genes that are responsible for those traits are being continuously discovered by high-density genetic map and map-based cloning. In addition, whole genome resequencing of various germplasm is under progress based on the reference genome. Not only by the efforts for developing novel molecular markers, but application of public marker information currently available will greatly facilitate breeding process through genomics-assisted breeding.

• Proceedings of the Korean Society of Computer Information Conference
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• 2022.07a
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• pp.61-62
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• 2022

알츠하이머성 치매는 현존하는 치료법이 없어 경도인지장애 단계에서의 예방이 중요하다. 지금까지의 알츠하이머 연구는 대부분이 뇌영상 마커와 뇌척수액 마커에 집중되어 있었으며, 경도 인지 장애 단계에서의 탐색은 더욱 적었다. 이러한 점에서 혈액 유전자 발현을 이용한 경도 인지장애 단계 예측은 인지 능력에 따른 관련 유전자 식별과 접근 가능한 진단 및 치료 바이오 마커 탐색에 기여할 수 있다. 그러나 유전자 발현 데이터의 경우 환자 수에 비해 높은 차원을 가지기 때문에 과적합을 막고 질병 관련 유전자를 식별하기 위해서는 데이터에서의 의미 있는 차원만을 뽑아내는 차원 축소가 선행되야 한다. 본 연구는 유전자 발현데이터에서의 인지장애 분류를 위해 차원 축소기법과 신경망을 적용하여 인지 장애 정도를 예측하였다. 그 결과, Lasso 이용 차원축소와 신경망을 이용하여 97%의 정확도로 정상과 조기 경도 인지장애, 후기 경도 인지장애 환자를 분류 할 수 있었으며, 더 적은 차원에서도 분류가 가능했다. 이는 혈액 유전자 발현을 이용해 경도 인지장애 단계를 예측한 첫 번째 연구이며, 인지능력 저하에 따른 혈액 유전자 발현의 연관성을 확인하고 향후 조기 진단, 치료 표적 탐색에 기여한다.

• Horticultural Science & Technology
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• v.28 no.4
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• pp.664-671
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• 2010

A genetic linkage map was constructed using 188 $F_9$ RILs derived from a cross between $Solanum$ $lycopersicum$ H7996 (resistant to bacterial wilt) and $S.$ $pimpinellifolium$ WVa700 (highly susceptible to bacterial wilt). The map consisted of 361 markers including 260 DArTs, 74 AFLPs, 4 RFLPs, 1 SNP, and 22 SSRs. The resulting linkage map was comprised of 13 linkage groups covering 2042.7 cM. The genetic linkage map had an average map distance between markers of 5.7 cM, with an average DArT marker density of 1/7.9 cM. Based on the distribution of anchor SSR markers, 11 linkage groups were assigned to 10 chromosomes of tomato except chromosomes 5 and 12. The DArT markers were distributed across the genome in a similar way as other markers and showed the highest frequency of clustering (38.8%) at ${\leq}$ 0.5 cM intervals between adjacent markers, which is 3 times higher than AFLPs (13.5%). The present study is the first utilization of DArT markers in tomato linkage map construction.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2002.11b
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• pp.50-50
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• 2002

배추무사마귀병 저항성 유전 양식을 증명하기 위해서 CR계 F1에서 유래된 F2 세대를 포장시험과 유묘 검정을 실시하였다. F$_2$ 세대의 7 집단은 단인자우성으로 3:1의 분리비를 보였고, 5 집단은 중복 유전자가 관여하는 9:7의 유전 분리비를 보였다. 배추무사마귀병 저항성 유전자와 연관된 DNA 마커를 개발하기 위하여 CR-Saerona F$_2$ 집단을 배추무사마귀병 발병포장에서 재배하여 저항성 평가를 하였다. 220개의 임의의 프라이머를 이용하여 BSA-RAPD (Bulked segregant analysis-Randomly amplified polymorphic DNA)를 수행하였지만 CR-Saerona F2 집단에서 배추무사마귀병 저항성 유전자와 꼭 들어맞는 DNA 마커는 발견되지 않았다. 300개의 임의의 프라이머를 이용하여 CR-Saerona에서 유래된 F$_2$ 세대를 QTL 분석하였다. 저항성 정도는 발병지수에 따라 조사되었고 QTL 분석을 위해 one-way ANOVA 테스트를 하였다. 통계분석 결과 두 프라이머(K16-1, L2-2)가 저항성과의 상관관계를 보여 주었으나 유의성은 인정되지 않았다.

• Journal of Plant Biotechnology
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• v.39 no.1
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• pp.33-48
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• 2012

As a scientific curiosity to understand the structure and the function of crops and experimental efforts to apply it to plant breeding, genetic maps have been constructed in various crops. Especially, in the case of Brassica crop, genetic mapping has been accelerated since genetic information of model plant $Arabidopsis$ was available. As a result, the whole $B.$ $rapa$ genome (A genome) sequencing has recently been done. The genome sequences offer opportunities to develop molecular markers for genetic analysis in $Brassica$ crops. RFLP markers are widely used as the basis for genetic map construction, but detection system is inefficiency. The technical efficiency and analysis speed of the PCR-based markers become more preferable for many form of $Brassica$ genome study. The massive sequence informative markers such as SSR, SNP and InDels are also available to increase the density of markers for high-resolution genetic analysis. The high density maps are invaluable resources for QTLs analysis, marker assisted selection (MAS), map-based cloning and comparative analysis within $Brassica$ as well as related crop species. Additionally, the advents of new technology, next-generation technique, have served as a momentum for molecular breeding. Here we summarize genetic and genomic resources and suggest their applications for the molecular breeding in $Brassica$ crop.

• Journal of the Korean Data and Information Science Society
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• v.26 no.6
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• pp.1397-1407
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• 2015

Individual phenotype is mostly influenced by genetic factors as well as the effects of environmental factors. Therefore, adjustment of environmental factors are needed in order to see more clearly the effects of genetic factors that we are interested in gene screening study related to Hanwoo's economic trait. The purpose of this study is to propose new statistical model that was adjusted environmental factor and identify adjustment effect in a superior gene marker screening study for producing high quality Hanwoo. First, statistical model including both genetic factor and environmental factor establishes and adjusted value of economic trait find by removing effect of environmental factor such as age, breeding farm. Finally, we identify superior gene marker combination and compare accuracy by applying MDR to data of before and after adjustment. Economic trait is used C18:1, SFA, MUFA, MS, CWT, BFT and SNP marker is used 6 markers of LPL that were identified as more excellent SNP marker than the others among 49 markers through fatty acid composition and economic trait performance test.

• Journal of Life Science
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• v.20 no.2
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• pp.208-212
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• 2010

The low and high temperature stress might affect the yield and quality of many crop species. Alternative oxidase (AOX) gene is known as factors related to stress resistance in plants. In order to develop molecular markers related to stress resistance in Chinese cabbage, fifteen ESTs sharing sequence similarity to arabidopsis AOX genes were found using Brassica rapa EST database from NCBI. The polymorphic DNA sequences using the ESTs were then screened between Chinese cabbage, 'Chiifu' and 'Kenshin'. We found four ESTs that have either insertion or deletion between the two cultivars. These polymorphic sites were then targeted for development of the four PCR based molecular markers. These molecular markers developed in this study could be useful for a test of their relationship with abiotic stress resistance in Chinese cabbage.