• 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.

• Asian-Australasian Journal of Animal Sciences
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• 제15권9호
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• pp.1250-1256
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• 2002

A novel fine-mapping method exploiting linkage disequilibrium (LD) was applied to better refine the quantitative trait loci (QTL) positions for milk production traits on bovine chromosome 14 in the pedigree comprising 22 paternal half-sib families of a Black-and-White Holstein-Friesian grand-daughter design in the Netherlands for a total of 1,034 sons. The chromosome map was constructed with the 31 genetic markers spanning 90 Kosambi cM with the average inter-marker distance of 3.5 cM. The linkage analyses, in which the effects of sire QTL alleles were assumed random and the random factor of the QTL allelic effects was incorporated into the Animal Model, found the QTL for milk, fat, and protein yield and fat and protein % with the Lod scores of 10.9, 2.3, 6.0, 25.4 and 3.2, respectively. The joint analyses including LD information by use of multi-marker haplotypes highly increased the evidence of the QTL (Lod scores were 25.1, 20.9, 11.0, 85.7 and 17.4 for the corresponding traits, respectively). The joint analyses including DGAT markers in the defined haplotypes again increased the QTL evidence and the most likely QTL positions for the five traits coincided with the position of the DGAT gene, supporting the hypothesis of the direct causal involvement of the DGAT gene. This study strongly indicates that the exploitation of LD information will allow additional gains of power and precision in finding and localising QTL of interest in livestock species, on the condition of high marker density around the QTL region.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2005년도 추계학술발표회 요지
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• pp.266-267
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• 2005

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.116-116
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• 2017

Low-temperature is one of the environmental stress factors that affect plant growth and development and consequently limit crop productivity. The control of seed germination under low-temperature is organized by many genes which are called quantitative trait loci (QTLs). High germination rate for low-temperature is an important factor of growing rice. Previously, we identified a major QTL controlling low-temperature germinability in rice using 96 introgression lines (ILs) derived from a cross between Oryza rufipogon (Rufi) and the Korean japonica cultivar, 'Hwaseongbyeo (HS)'. A $BC_3F_7$ line (TR5) showed better low-temperature germinability than its recurrent parent. TR5 was crossed with HS to develop a segregating F2:3 populations for the target QTL. Six SSR markers polymorphic between HS and Rufi were used to screen and fine map the qLTG1. The qLTG1 on chromosome 1, which accounted for 55.5% of the total phenotypic variation, confirmed that Rufi allele enhanced the low-temperature germinability. Intervals between markers CRM16 and CRM15, four candidate genes were identified. The identified candidate genes, which are encoded by a protein of unknown function, showed their direct involvement on seed germination at low-temperature. To identify genes targeted by qLTG1, we investigated the expression profiles of these candidate genes and germination behavior of qLTG1 under different stress conditions and compared to HS, Rufi, and TR5 at $13{\pm}2^{\circ}C$ for 3 days after incubation. Furthermore, transgenic rice plants will also be developed to conduct a detailed investigation on low-temperature germinability. Hence, the QTL for low-temperature germinability would be useful in rice breeding programs especially in the development of lines possessing low-temperature germinability.

• 한국통계학회:학술대회논문집
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• 한국통계학회 2003년도 춘계 학술발표회 논문집
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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.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.103-103
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• 2017

Vigorous root growth at the seedling stage in dry direct-seeded conditions is considered as a critical trait because it is involved in seedling emergence, early vegetative vigour, nutrient uptake as well as drought tolerance. In this study, we performed QTL mapping using the recombinant inbred lines obtained from the cross between Tongil-type Dasan and temperate japonica TR22183 (DT-RILs) to identify QTL underlying early root development. TR22183, which was previously reported to have high nitrogen utility and cold tolerance, showed vigorous root growth at the seedling stage in semi-drought conditions. Root length, fresh weight and dry weight of TR22183 were significantly higher than in Dasan. By QTL analysis with genotyping-by-sequencing method, we identified two QTLs for root fresh weight (RFW) in chromosome 7 and root dry weight (RDW) in chromosome 8, explaining phenotypic variances of 13.5% and 10.6%, respectively. These QTLs would be used to develop rice varieties adapted to direct-seeded cultivating system.

• 한국육종학회지
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• 제41권4호
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• pp.429-436
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• 2009

We conducted a QTL analysis of grain quality traits using 117 $BC_3F_4$ and $BC_3F_5$ lines developed from a cross between Ilpumbyeo and Moroberekan. Genotypes of 117 $BC_3F_5$ lines were determined using 134 simple sequence repeat (SSR) markers. A linkage map constructed using 134 SSR markers was employed to characterize quantitative trait loci (QTL). The 117 $BC_3F_4$ and $BC_3F_5$ lines were evaluated for eleven grain quality traits in 2005 and 2006. A total of 18 QTLs were identified for eleven traits, and the phenotypic variance explained by each QTL ranged from 9.9% to 35.2%. Moroberekan alleles contributed positive effects in the Ilpumbyeo background at two QTL loci for 1,000 grain weight. Four QTLs, two for chalky rice and one each for 1,000 grain weight and head rice were consistently detected in two consecutive years indicating that these QTLs are stable. Clusters of QTLs were observed in three chromosome regions. One cluster harboring five QTLs including head rice and brown rice ratio near SSR markers RM190 and RM314 was detected on chromosome 6. Another cluster harboring grain weight and white belly was detected on chromosome 2. Increase in white belly at this locus might be due to the increase in grain weight due to the presence of the Moroberekan allele. The Moroberekan alleles at two QTL loci, gw3 and gw4 associated with increased grain weight might be useful in breeding programs to develop high-yielding cultivars.

• Journal of Animal Science and Technology
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• 제45권6호
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• pp.939-948
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• 2003

본 연구는 돼지의 염색체 6번에 존재하는 주요 경제형질에 관여하는 양적형질 유전자좌위(Quantitative trait loci; QTL)를 밝히기 위하여 초위성체 마커를 이용하여 유전자지도를 작성하였다. 기준집단의 조성은 재래돼지 수컷 5마리와 Landrace 암컷 9마리를 자연교미하여 생산된 F$_1$의 동복 자손별로 수컷 1두를 임의적으로 선발하여 암컷 2두 이상과 전형매 교배시켜 F$_2$ 240두를 생산하였고 QTL 분석에는 F$_2$ 183두만을 이용하였다. 기준집단의 표현형 성적은 3주령체중, 등지방두께, 도축 24시간 후의 pH, 전단력, 조단백질 함량 등을 조사 분석하였다. F$_2$ 집단은 재래돼지와 Landrace의 두 종의 평균성적을 갖고 있었으며, 개체간 표현형적 변이가 매우 높아서 경제형질과 연관된 QTL을 탐색하기 적절한 기준집단이라고 평가되었다. 연관지도는 29개의 초위성체 마커와 1개의 PCR-RFLP 마커(AMPKα2)를 이용하여 작성하였으며, 연관지도상의 염색체 길이는 169.3cM이었고, 마커간 평균 간격은 6.05cM이었다. 염색체 6번에서 경제형질과 연관된 유의적인 QTL은 모두 5개가 탐색 되었다. 3주령 체중과 연관된 QTL이 5cM 위치에서 탐색되었으며, 전단력, 도축 24시간 후 pH, 등지방두께, 조단백질 함량 등의 육질관련 QTL이 서로 다른 위치에서 5% 수준의 통계적 유의성이 확인되었다.

• Plant Resources
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• 제3권3호
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• pp.184-193
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• 2000

Soybean [Glycine max (L.) Merr.] seed weight is a important trait in cultivar development. Objective of this study was to identify and confirm quantitative trait loci (QTLs) for seed weight variation in the F2 and F2:3 generations. QTLs for seed weight were identified in F2 and F2:3 generations using interval mapping (MapMaker/QTL) and single-factor analysis of variance (ANOVA). In the F2 plant generation (i.e., F3 seed), three markers, OPL9a, OPM7a, and OPAC12 were significantly (P<0.01) associated with seed weight QTLs. In the F2:3 plant row generation (i.e., F4 seed), five markers, OPA9a, OPG19, OPL9b, OPP11, and Sat_085 were significantly (P<0.01) associated with seed weight QTLs. Two markers, OPL9a and OPL9b were significantly (P<0.05) associated with seed weight QTLs in both generations. Two QTLs on USDA soybean linkage group C1 and R were identified in both F2 and F2:3 generations using interval mapping. The linkage group C1 QTL explained 16% of the variation in seed weight in both generations, and the linkage group R QTL explained 39% and 41% of the variation for F2 and F2:3 generation, respectively. The linkage group C2 QTL identified in F2:3 generation explained 14.9% of variation. Linkage groups C1, C2 and R had previously been identified as harbouring seed size QTLs. The consistency of QTLs across generations and populations indicates that marker-assisted selection is possible in a soybean breeding program.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.187-187
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• 2022

Purple-discoloration of the uppermost leaves has been observed in some soybean cultivars in recent years. The purpose of this study was to characterize the novel phenotypic changes between the uppermost and middle leaves via multiple approaches. First, quantitative trait loci mapping was conducted to detect loci associated with the novel phenotype using 85 recombinant inbred lines (RILs) of the 'Daepung' × PI 96983 population. 180K SNP data, a major quantitative trait locus (QTL) was identified at around 60 cM of chromosome 6, which accounts for 56% of total phenotypic variance. The genomic interval is about ~700kb, and a list of annotated genes includes the T-gene which is known to control pubescence and seed coat color and is presumed to encode flavonoid 35-hydroxylase (F3'H). Based on Hyperspectral imaging, the reflectance at 528-554 nm wavelength band was extremely reduced in the uppermost leaves compared to the middle (green leaves), which is presumed die to the accumulation of anthocyanins. In addition, purple-discolored leaf tissues were observed and compared to normal leaves using a transmission electronic microscope (TEM). Base on observations of the cell organelles, the purple-discolored uppermost leaves had many pigments formed in the epidermal cells unlike the normal middle leaves, and the cell wall thickness was twice as thick in the discolored leaves. The thickness of the thylakoid layer in the chloroplast the number of starch grains, the size of starch all decreased in the discolored leaves, while the number of plastoglobule and mitochondria increased.