• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1537-1544
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• 2015

Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l'Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.

• Asian-Australasian Journal of Animal Sciences
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• 제20권9호
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• pp.1334-1341
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• 2007

This study identified hepatic differentially expressed genes (DEGs) affecting the marbling of muscle. Most dietary nutrients bypass the liver and produce plasma lipoproteins. These plasma lipoproteins transport free fatty acids to the target tissue, adipose tissue and muscle. We examined hepatic genes differentially expressed in a differential-display reverse transcription-polymerase chain reaction (ddRT-PCR) analysis comparing high- and low-marbled Hanwoo steers. Using 60 arbitrary primers, we found 13 candidate genes that were upregulated and five candidate genes that were downregulated in the livers of high-marbled Hanwoo steers compared to low-marbled individuals. A BLAST search for the 18 DEGs revealed that 14 were well characterized, while four were not annotated. We examined four DEGs: ATP synthase F0, complement component CD, insulin-like growth factor binding protein-3 (IGFBP3) and phosphatidylethanolamine binding protein (PEBP). Of these, only two genes (complement component CD and IGFBP3) were differentially expressed at p<0.05 between the livers of high- and low-marbled individuals. The mean mRNA levels of the PEBP and ATP synthase F0 genes did not differ significantly between the livers of high- and low-marbled individuals. Moreover, these DEGs showed very high inter-individual variation in expression. These informative DEGs were assigned to the bovine chromosome in a BLAST search of MS marker subsets and the bovine genome sequence. Genes related to energy metabolism (ATP synthase F0, ketohexokinase, electron-transfer flavoprotein-ubiquinone oxidoreductase and NADH hydrogenase) were assigned to BTA 1, 11, 17, and 22, respectively. Syntaxin, IGFBP3, decorin, the bax inhibitor gene and the PEBP gene were assigned to BTA 3, 4, 5, 5, and 17, respectively. In this study, the in silico physical maps provided information on the specific location of candidate genes associated with economic traits in cattle.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.93-93
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• 2017

To develop rice cultivars with increased biomass and grain yield, superior lodging resistance is an essential trait. The new breeding approach can be adopted for the improvement of stem lodging resistance by enhancing culm strength. The resistance to breaking type lodging is attributed to bending moment of basal culm (M), which is composed of the section modulus (SM) and bending stress (BS). The resistance to the bending type lodging is attributed to flexural rigidity (FR) of stem, which is composed of the secondary moment of inertia (SMI) and Young's modulus (YM). Starch and cell wall components such as cellulose, hemicellulose and lignin also play a significant role in physical strength of culm, and thus affect lodging. Leaf Star has a superior lodging resistance due to its thick and stiff culm because of its high M and FR compared with Koshihikari. Furthermore, Leaf Star contains high densities of hemicellulose, cellulose and low lignin density in culm compared with Koshihikari. In this study, we performed QTL analysis for these traits associated with culm strength, using 94 recombinant inbred lines (RILs, $F_8$), derived from a cross between Leaf Star and Koshihikari. The SM in the RILs showed a continuous distribution. QTLs for SM were detected on chrs.2, 3 and 10. Leaf Star alleles increased SM on chrs. 2 and 3, but Koshihikari allele increased on chr.10. These QTLs overlapped with those QTLs identified using backcrossed inbred line derived from a cross between Chugoku 117 and Koshihikari, the parents of Leaf Star. The FR in Leaf Star was higher than that in Koshihikari due to the larger SMI and YM. 3 QTLs for SMI were detected on chrs.2, 3 and 10. Leaf Star alleles increased SMI on chrs.2 and 3, and Koshihikari alleles increased on chr.10. One QTL on chr.3 and two QTLs on chr.5 for hollocelulose content were detected with Leaf Star alleles contribution. Moreover, two QTLs were detected for hemicellulose density on chrs.3 and 5. Leaf Star allele increased hemicellulose density on chr.5, and Koshihikari allele increased on chr.3. Furthermore, two QTLs for cellulose density were detected on chr.5, and one QTL on chr.2. For starch content, one QTL on chr.3 and two QTLs on chr.5 with Leaf Star alleles contribution were detected. TULK-6 carrying a chromosome segment of Leaf Star on chr.5 in the Koshihikari genetic background showed higher densities of starch and hemicellulose than those in Koshihikari. These results suggest that the detected QTLs for culm strength could be utilized for the improvement of lodging resistance in rice by marker-assisted selection.

• 원예과학기술지
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• 제30권3호
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• pp.286-293
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• 2012

고추에 있어서 Tobamovirus 저항성은 고추 염색체 11번 긴 팔 끝부분에 위치한 L 유전자좌의 다섯 개 대립유전자($L^0$, $L^1$, $L^2$, $L^3$, and $L^4$)에 의해 조절된다고 알려져 있다. 표현형 분석 없이 L 대립유전자를 구분할 수 있는 분자표지를 개발하기 위해서 다섯 개의 고추 판별 계통{Capsicum annuum Early California Wonder(ECW, $L^0L^0$), C. annuum Tisana($L^1L^1$), C. annuum Criollo de Morelos 334(CM334,$L^2L^2$), Capsicum chinense PI 159236($L^3L^3$), and Capsicum chacoense PI 260429($L^4L^4$)}을 식물재료로 사용하였다. 대립유전자 특이적 분자표지는 고추 판별 계통에 대해 $L^3$ 연관 분자표지(189D23M, A339, and 253A1R)와 BAC 염기서열(FJ597539 and FJ597541)의 PCR 증폭산물 염기서열을 비교 분석하여 개발되었다. 총 53개의 상용 고추 품종 중 48개에서 분자표지에 의한 추정 유전자형과 Tobamovirus{Tobacco mosaic virus(pathotype 0, $P_0$), Tomato mosaicvirus($P_1$), and Pepper mild mottle virus($P_{1,2}$)} 접종 표현형과 일치했다. 결과적으로 본 연구에서 개발된 분자표지는 고추 육종에 있어서 TMV 저항성 도입에 필요한 선발마커로 충분히 활용될 수 있을 것이다.

• 식물조직배양학회지
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• 제22권3호
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• pp.121-126
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• 1995

현사시나무 4배체의 약배양에 의하여 2배체 식물을 얻을 수 있었다. 약배양에 의한 캘러스 유도에는 2,4-D가 효과적 인 것으로 나타났다. 증식된 캘러스로부터 식물체 재분화를 위해서는 16시간의 광조건하에 6-8 $\mu$M의 zeatin 처리가 가장 좋은 반응을 보였는데 이때 얻어진 줄기수는 평균 7.7개 였다. 재분화된 식물체는 MS 기본배지에서 쉽게 뿌리를 유기시킬 수 있었으며, 이들 식물체는 폿트묘로 육성하여 온실 및 포지로 이식하였다. 약배양유래의 300클론에 대한 생육상태를 조사한 결과 삽목묘에 비하여 33%는 생장이 저해됨을, 47%는 생장이 더 좋은 것으로 나타났으며, 그중 20%는 삽목묘에 비해 직경이 5배 이상되는 거대 엽을 가지고 있었다. 염색체 수는 대체로 2배체성 혹은 4배성을 띠고 있었으며, RAPD marker를 이용하여 DNA polymorphism을 본 결과 약배양 유래의 몇몇 식물체에 있어 서 밴드 형태적인 차이를 나타내는 개체를 발견할 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권4호
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• pp.480-488
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• 2018

Objective: Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population. Methods: We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models. Results: After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development. Conclusion: This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.

• Journal of Animal Science and Technology
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• 제53권1호
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• pp.15-22
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• 2011

자돈의 생시 체중은 자돈의 이유 체중 및 생존율에도 크게 영향을 미친다. 또한 출하 시까지 돼지의 성장률 뿐만아니라 출하 일령 단축 및 출하 체중과도 밀접한 연관성이 있는 것으로 알려져 있다. 본 연구는 돼지 7번 염색체의 PGK 2 (phosphoglycerate kinase 2) 유전자의 promoter 영역 및 transcription 영역에 해당하는 DNA 염기서열을 유전체 구조분석을 통해 20개의 SNP (Single Nucleotide Polymorpism)를 발굴하였고, 발굴된 SNP 중 PGK 2 유전자의 전사 조절 영역 내 g.122 T>G 다형을 재래돼지와 Landrace를 이용한 $F_2$ 집단 268두 자돈의 성장 형질과의 연관성 분석을 실시한 결과, 생시 체중(p<0.01) 및 3주령 체중(p<0.001)에서 통계적으로 고도의 유의적 연관성이 있음을 확인 할 수 있었다. 따라서 본 연구를 통하여 확인된 PGK 2 유전자의 promoter 영역 내 성장 형질 관련 SNP는 건강한 자돈 및 종돈을 조기 선발하기 위한 유전자 marker로 활용 가능성을 제시하였다.

• Journal of Crop Science and Biotechnology
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• 제10권4호
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• pp.265-276
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• 2007

The 13 major blast resistance(R) genes against Magnaporthe grisea were screened in a number of Korean rice varieties using molecular markers. Of the 98 rice varieties tested, 28 were found to contain the Pia gene originating from Japanese japonica rice genotypes. The Pib gene from BL1 and BL7 was incorporated into 39 Korean japonica varieties, whereas this same gene from the IRRI-bred indica varieties was detected in all Tongil-type varieties. We also found that 17 of the japonica varieties contained the Pii gene. The Pii gene in Korean rice varieties originates from the Korean japonica variety Nongbaeg, and Japanese japonica varieties Hitomebore, Inabawase, and Todorokiwase. The Pi5 gene, which clusters with Pii on chromosome 9, was identified only in Taebaeg. Thirty-four varieties were found to contain alleles of the resistance gene Pita or Pita-2. The Pita gene in japonica varieties was found to be inherited from the Japanese japonica genotype Shimokita, and the Pita-2 gene was from Fuji280 and Sadominori. Seventeen japonica and one Tongil-type varieties contained the Piz gene, which in the japonica varieties originates from Fukuhikari and 54BC-68. The Piz-t gene contained in three Tongil-type varieties was derived from IRRI-bred indica rice varieties. The Pi9(t) gene locus that is present in Korean japonica and Tongil-type varieties was not inherited from the original Pi9 gene from wild rice Oryza minuta. The Pik-multiple allele genes Pik, Pik-m, and Pik-p were identified in 24 of the varieties tested. In addition, the Pit gene inherited from the indica rice K59 strain was not found in any of the Korean japonica or Tongil-type varieties tested.

• Molecules and Cells
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• 제20권3호
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• pp.385-391
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• 2005

As a first step towards identifying genes involving in the signal transduction pathways mediating rice blast resistance, we isolated 3 mutants lines that showed enhanced susceptibility to rice blast KJ105 (91-033) from a T-DNA insertion library of the japonica rice cultivar, Hwayeong. Since none of the susceptible phenotypes co-segregated with the T-DNA insertion we adapted a map-based cloning strategy to isolate the gene(s) responsible for the enhanced susceptibility of the Hwayeong mutants. A genetic mapping population was produced by crossing the resistant wild type Hwayeong with the susceptible cultivar, Nagdong. Chi-square analysis of the $F_2$ segregating population indicated that resistance in Hwayeong was controlled by a single major gene that we tentatively named Pi-hy. Randomly selected susceptible plants in the $F_2$ population were used to build an initial map of Pi-hy. The SSLP marker RM2265 on chromosome 2 was closely linked to resistance. High resolution mapping using 105 $F_2$ plants revealed that the resistance gene was tightly linked, or identical, to Pib, a resistance gene with a nucleotide binding sequence and leucine-rich repeats (NB-LRR) previously isolated. Sequence analysis of the Pib locus amplified from three susceptible mutants revealed lesions within this gene, demonstrating that the Pi-hy gene is Pib. The Pib mutations in 1D-22-10-13, 1D-54-16-8, and 1C-143-16-1 were, respectively, a missense mutation in the conserved NB domain 3, a nonsense mutation in the 5th LRR, and a nonsense mutation in the C terminus following the LRRs that causes a small deletion of the C terminus. These findings provide evidence that NB domain 3 and the C terminus are required for full activity of the plant R gene. They also suggest that alterations of the resistance gene can cause major differences in pathogen specificity by affecting interactions with an avirulence factor.

• 한국응용곤충학회지
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• 제40권4호
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• pp.337-344
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• 2001

The house fly (Musca domestica L.) strains were derived from the Yumenoshima III strain by selecting with cypermethrin and methomyl for 19 and 16 generations, respectively. The resulting strains, cypermethrin resistance strain (Cyp-R19) and methomyl resistance strain (Met-R16), showed high level of resistance by 12906 and 51 times, respectively, comparing with the susceptible SRS strain. The Cyp-R19 strain was resistant to synthetic pyrethroids such as deltamethrin, esfenvalerate, fenpropathrin, $\beta$-cyfluthrin, showing > 11000, 1231, 103, 292 times higher $LD_{50}$ values than the SRS strain, respectively. It was also resistant to 3 organophosphates and 2 carbamates such as fenitrothion, profenofos, pyridaphenthion, benfuracarb, methomyl, showing resistance ratios fo 51, 17, 49, 39 and 62 comparing to SRS strain. The Met-R16 strain was resistant to synthetic carbamate benfuracarb, showing 6 times higher $LD_{50}$ value than SRS strain. It was also resistant to 4 organophosphates such as acephate, fenitrothion, profenofos and pyridaphenthion, showing > 40, 103, 19, 60 times higher $LD_{50}$ value. It was also resistant to 5 pyrethroids and a pyrrole such as cypermethrin, deltamethrin, esfenvalerate, fenpropathrin, $\beta$-cyfluthrin and chlorfenapyr, showing 3030, 249, 4063, 34, 330 and 86 times higher $LD_{50}$ values than the SRS strain. Cyp-R14 strain which was selected for 14 generations by cypermethrin and developed 11014 times higher resistance to the SRS strain was used in the dominance and linkage group analysis. Cypermethrin resistance inheritance was incompletely dominant in house fly as judged by the reciprocal cross between the resistant and susceptible strains. The linkage group analysis for the major factors responsible for this resistance was carried out by the$ F_1$male-backcross method, using susceptible multi-chromosomal marker aabys strain. The major factors for cypermethrin resistance were located on the 1st, the 3rd and the 4th chromosomes, and the effect of the 3rd chromosome was most prominent.