• BMB Reports
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• 제40권1호
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• pp.95-99
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• 2007

Bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci were identified to facilitate bovine QTL fine mapping research. A total of 692,763 bovine SNPs was extracted from 39,432 UniGene clusters, and 53,446 candidate SNPs were found to be a depth >3. In order to validate the in silico SNPs experimentally, 186 animals representing 14 breeds and 100 mixed breeds were analyzed. Genotyping of 40 randomly selected candidate SNPs revealed that 43% of these SNPs ranged in frequency from 0.009 to 0.498. To identify non-synonymous SNPs and to correct for possible frameshift errors in the ESTs at the predicted SNP positions, we designed a program that determines coding regions by protein-sequence referencing, and identified 17,735 nsSNPs. The SNPs and bovine quantitative traits loci informations were integrated into a bovine SNP data: BcSNPdb (http://snugenome.snu.ac.kr/BtcSNP/). Currently there are 43 different kinds of quantitative traits available. Thus, these SNPs would serve as valuable resources for exploiting genomic variation that influence economically and agriculturally important traits in cows.

• Journal of Plant Biotechnology
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• 제43권3호
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• pp.261-271
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• 2016

세계적인 과수작물로서의 경제적 중요성에도 불구하고, 감귤 생산은 주로 자연교잡 실생이나 눈 돌연변이로부터의 선발 또는 단순 품종 도입 등을 통해 이루어지고 있는 실정이다. 긴 유년기, 다배성, 자가불화합성과 같은 감귤 고유의 식물학적 특성, 주요 형질들(병저항성, 수량성, 품질 등)의 QTL에 의한 조절 등은 전통 육종을 통한 우수 품종의 개발을 어렵게 하는 요인이다. 지구 온난화에 의한 생산 여건의 급격한 변화, 소비자 요구 다양화 등은 고품질 감귤의 조기 선발과 안정적 생산, 품종 다양화, 육종 비용 절감 등을 위한 체계적인 감귤 분자육종 프로그램의 도입을 요구하고 있다. 동위효소를 이용한 최초의 감귤 연관지도 작성이 이루어진 이래, 다양한 분자표지를 이용한 연관지도 작성, 생물(CTV, CiLV, ABS, 선충] 및 비생물적(염분, 저온) 스트레스, 아포믹시스, 다배성, 과실착색(카로티노이드, 안토시아닌), 무종자, 웅성불임, 신맛 적음, 생식, 형태(나무, 잎, 꽃, 열매 등), 과실 품질, 종자수, 수량성, 조기 착과 등과 연관된 분자표지 발굴, QTL 맵핑 등이 이루어졌다. CTV 저항성과 적육(안토시아닌 축적) 형질에 대해서는 유전자 클로닝이 이루어졌고, 교배 육종 효율 증대 및 비용 절감을 위해 교잡배와 주심배를 구분하기 위한 다수의 simple sequence repeat (SSR) 분자표지가 개발되었다. 최근, 스위트오렌지와 '클레멘타인' 만다린에 대한 고품질의 표준 유전체가 완성되어 유전체 기반 감귤 분자육종을 위한 토대가 마련되었다. 표준 유전체 정보를 토대로 대규모 분자표지(SNP, SSR, InDel) 기반의 표준 연관 및 물리지도 작성, 비교 유전체 지도 작성, gene annotation, 전사체 분석 등이 활발히 이루어지고 있다. 감귤 유전자원 및 핵심집단에 대해 표준 유전체 기반 비교 유전체 분석, GBS (genotyping-by-sequencing), GWAS (genome wide association study) 등을 통해 감귤의 다양한 형질과 연관된 분자마커 발굴 및 개발, 유용/변이 유전자 클로닝 등에 관한 연구가 가속화될 것으로 전망된다. 또한 표적 유전체 교정 및 VIGS (virus-induced gene silencing) 기술도 유전자 마커의 검증을 비롯한 감귤 분자육종 프로그램에 활발히 이용될 것이다.

• Genes and Genomics
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• 제40권12호
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• pp.1351-1361
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• 2018

A new cold tolerant germplasm resource named glutinous rice 89-1 (Gr89-1, Oryza sativa L.) can overwinter using axillary buds, with these buds being ratooned the following year. The overwintering seedling rate (OSR) is an important factor for evaluating cold tolerance. Many quantitative trait loci (QTLs) controlling cold tolerance at different growth stages in rice have been identified, with some of these QTLs being successfully cloned. However, no QTLs conferring to the OSR trait have been located in the perennial O. sativa L. To identify QTLs associated with OSR and to evaluate cold tolerance. 286 $F_{12}$ recombinant inbred lines (RILs) derived from a cross between the cold tolerant variety Gr89-1 and cold sensitive variety Shuhui527 (SH527) were used. A total of 198 polymorphic simple sequence repeat (SSR) markers that were distributed uniformly on 12 chromosomes were used to construct the linkage map. The gene ontology (GO) annotation of the major QTL was performed through the rice genome annotation project system. Three main-effect QTLs (qOSR2, qOSR3, and qOSR8) were detected and mapped on chromosomes 2, 3, and 8, respectively. These QTLs were located in the interval of RM14208 (35,160,202 base pairs (bp))-RM208 (35,520,147 bp), RM218 (8,375,236 bp)-RM232 (9,755,778 bp), and RM5891 (24,626,930 bp)-RM23608 (25,355,519 bp), and explained 19.6%, 9.3%, and 11.8% of the phenotypic variations, respectively. The qOSR2 QTL displayed the largest effect, with a logarithm of odds score (LOD) of 5.5. A total of 47 candidate genes on the qOSR2 locus were associated with 219 GO terms. Among these candidate genes, 11 were related to cell membrane, 7 were associated with cold stress, and 3 were involved in response to stress and biotic stimulus. OsPIP1;3 was the only one candidate gene related to stress, biotic stimulus, cold stress, and encoding a cell membrane protein. After QTL mapping, a total of three main-effect QTLs-qOSR2, qOSR3, and qOSR8-were detected on chromosomes 2, 3, and 8, respectively. Among these, qOSR2 explained the highest phenotypic variance. All the QTLs elite traits come from the cold resistance parent Gr89-1. OsPIP1;3 might be a candidate gene of qOSR2.

• Asian-Australasian Journal of Animal Sciences
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• 제20권10호
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• pp.1473-1477
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• 2007

Four-and-a-half LIM-only protein 3 (FHL3) is a member of the LIM protein superfamily and can participate in mediating protein-protein interaction by binding one another through their LIM domains. In this study, the 5'- and 3'- cDNA ends were characterized by RACE (Rapid Amplification of the cDNA Ends) methodology in combination with in silico cloning based on the partial cDNA sequence obtained. Bioinformatics analysis showed FHL3 protein contained four LIM domains and four LIM zinc-binding domains. In silico mapping assigned this gene to the gene cluster MTF1-INPP5B-SF3A3-FHL3-CGI-94 on pig chromosome 6 where several QTL affecting intramuscular fat and eye muscle area had previously been identified. Transcription of the FHL3 gene was detected in spleen, liver, kidney, small intestine, skeletal muscle, fat and stomach, with the greatest expression in skeletal muscle. The A/G polymorphism in exon II was significantly associated with birth weight, average daily gain before weaning, drip loss rate, water holding capacity and intramuscular fat in a Landrace-derived pig population. Together, the present study provided the useful information for further studies to determine the roles of FHL3 gene in the regulation of skeletal muscle cell growth and differentiation in pigs.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2015년도 춘계학술대회 및 임시총회
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• pp.29-29
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• 2015

Clubroot disease is caused by the soil-born obligate plant pathogen Plasmodiophora brassicae. This pathogen can infect all cruciferous vegetables and oil crops, including Brassica rapa, B. oleracea, B. napus, and other Brassica species. Clubroot disease is now considered to be a major problem in Chinese cabbage production in China, Korea, and Japan. We collected several hundreds of P. brassicae infected galls from Korea, and isolated the single spore from the collection. For establishment of novel isolation, and mass-propagation methods for singe spore isolates of P. brassicae pathogen, we developed new filtration method using both cellulose nitrate filter and syringe filter. Accurate detection of P. brassicae pathogen in the field was done by using real-time PCR in the potential infested soil. When we tested the different pathogenicity on commercial Chinese cabbage varieties, P. brassicae from collected galls showed various morphological patterns about clubroot symptom on roots. To date, 8 CR loci have been identified in the B. rapa genome using the quantitative trait loci (QTL) mapping approach, with different resistant sources and isolates. We are trying to develop the molecular marker systems for detect all 8 CR resistant genes. Especially for the study on the interaction between pathogens and CR loci which are not well understood until now, genome wide association studies are doing using the sequenced inbred lines of Chinese cabbage to detect the novel CR genes.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.13-13
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• 2017

By the progress of genome sequencing, infrastructures for marker-assisted breeding (MAB) of rice came to be established. Fine mapping and gene isolation have been conducted using the breeding materials derived from natural variations and artificial mutants. Such genetic analysis by the genome-wide dense markers provided us the knowledge about the many genes controlling important traits. We identified several genes or quantitative trait loci (QTL) for heading date, blast resistance, eating quality, high-temperature stress tolerance, and so on. NILs of each gene controlling heading date contribute to elongate the rice harvest period. Determination of precise gene location of blast resistance gene pi21, allowed us to overcome linkage drag, co-introduction of undesirable eating quality. We could also breed the first practical rice cultivar in Japan with a brown planthopper resistance gene bph11 in the genetic back-ground of an elite cultivar. Discovery of major and minor QTLs for good eating quality allowed us to fine-tune of eating quality according to the rice planting area or usage of rice grain. Many rice cultivars have bred efficiently by MAB for several traits, or by marker-assisted backcross breeding through chromosome segment substitution lines (CSSLs) using genetically diverse accessions. We are also systematically supporting the crop breeding of other sectors by MAB or by providing resources such as CSSLs. It is possible to pyramid many genes for important traits by using MAB, but is still difficult to improve the yielding ability. We are performing a Genomic Selection (GS) for improvement of rice biomass and grain yield. We are also trying to apply the genome editing technology for high yield rice breeding.

• Molecules and Cells
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• 제20권2호
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• pp.201-209
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• 2005

We have constructed an AFLP-based linkage map of Japanese red pine (Pinus densiflora Siebold et Zucc.) using haploid DNA samples of 96 megagametophytes from a single maternal tree, selection clone Kyungbuk 4. Twenty-eight primer pairs generated a total of 5,780 AFLP fragments. Five hundreds and thirteen fragments were verified as genetic markers with two alleles by their Mendelian segregation. At the linkage criteria LOD 4.0 and maximum recombination fraction 0.25(${\theta}$), a total of 152 markers constituted 25 framework maps for 19 major linkage groups. The maps spanned a total length of 2,341 cM with an average framework marker spacing of 18.4 cM. The estimated genome size was 2,662 cM. With an assumption of equal marker density, 82.2% of the estimated genome would be within 10 cM of one of the 230 linked markers, and 68.1% would be within 10 cM of one of the 152 framework markers. We evaluated map completeness in terms of LOD value, marker density, genome length, and map coverage. The resulting map will provide crucial information for future genomic studies of the Japanese red pine, in particular for QTL mapping of economically important breeding target traits.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.27-27
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• 2022

(-)-Epicatechin (EC), a primary form of flavan-3ol and a building block of proanthocyanidins, has health benefits as it is a potent antioxidant. So far, no quantitative trait loci (QTLs) associated with EC have yet been identified in soybean. In this study, QTLs for EC and hilum color were identified in recombinant inbred lines (RILs) derived from the varieties Jinpung and IT109098 using high-resolution single nucleotide polymorphism linkage mapping. This revealed two major QTLs for EC content, qEC06 and qEC08. qEC06 spanned the T Locus encoding flavonoid 3'-hydroxylase. qEC08, located near the I locus on Chr08, was also a major QTL for hilum color; however, allelic stacking of qEC08 and I revealed no relationship between I and EC content. RILs with IT 109098 alleles at both qEC06 and qEC08 had higher EC content than other lines. These results will enable the production of soybean varieties with high EC content via marker-assisted selection.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.34-34
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• 2022

Capacity building for bioinformatics could be achieved with the systematic training of research staff and higher degree students in the current best practices for analysis of data from 'omic-type experiments. It is anticipated that the KOICA-University of the Philippines Los Baños - International Rice Research Insitute Agricultural Genomics Research Center activities will focus on the use of next generation sequencing technology for genome sequencing and annotation, genome variant discovery for use in GWAS and QTL mapping, and transcriptome analysis of organisms important to agriculture and food security. Such activities require that researchers have high levels of knowledge and skills in bioinformatics in order to gain insights from the results of the experiments performed. In this talk the bioinformatic tools/solutions and online training materials already available will be presented, as well the upcoming resources under development in support of the project.

• 한국육종학회지
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• 제51권4호
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• pp.395-403
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• 2019

우리나라의 도열병 균계에 내구저항성을 보이는 자포니카 벼 품종 팔공의 저항성 유전좌위를 분석한 결과, 팔공 allele에 의한 저항성 관련 putative QTLs가 2번, 4번, 7번, 11번 염색체상에서 9개 좌위들이 확인되었다. 팔공의 allele에 의한 도열병 저항성 연관 유전자좌들 중 qBn2.3 (Ch r. 2), qBn4.2 (Ch r. 4), qBn11.1 및 qBn11.2 (Ch r. 11) 등 4개 좌위는 표현형 변이의 28-56.7%를 설명하는 major QTL이었고, 이들 좌위에서는 1-4개의 저항성 관련 유전자들이 위치하는 것으로 보고되었다. 팔공 allele의 5개 QTLs qBn2.1, qBn2.4 (Ch r. 2), qBn4.1 (Chr. 4), qBn7.1 및 qBn7.2 (Ch r. 7) 등은 표현형 변이를 9.7-18.8% 설명하였으며, 이들 좌위들 중 2번 염색체상의 qBn2.1를 제외한 4개 QTLs 좌위에서는 다른 유전자의 보고가 없어 팔공 고유의 도열병 저항성 관련 유전 요소들로 추정 된다. 팔공의 도열병 내구 저항성은 2번, 4번, 7번, 11번 염색체상의 9개 QTLs들의 상호 작용에 의한 것으로 생각되며, 특히 목도열병 내구 저항성 유전자 Pb1이 위치하는 것으로 보고된 좌위의 qBn11.2는 표현형 변이 56.7%를 설명하였고 내구저항성에서 중요한 역할을 하는 것으로 생각된다. 팔공의 줄무늬잎마름병 저항성은 qBn11.2 좌위의 Stvb-i 유전자에 의한 것으로 생각된다.