• Asian-Australasian Journal of Animal Sciences
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• 제30권4호
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• pp.462-469
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• 2017

Objective: The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods: Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results: We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion: Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.

• 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.

• Molecules and Cells
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• 제25권3호
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• pp.417-427
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• 2008

Comparison of maps and QTLs between populations may provide us with a better understanding of molecular maps and the inheritance of traits. We developed and used two reciprocal $BC_1F_1$ populations, IP/DS//IP and IP/DS//DS, for QTL analysis. DS (Dasanbyeo) is a Korean tongil-type cultivar (derived from an indica x japonica cross and similar to indica in its genetic make-up) and IP (Ilpumbyeo) is a Korean japonica cultivar. We constructed two molecular linkage maps corresponding to each backcross population using 196 markers for each map. The length of each chromosome was longer in the IP/DS//IP population than in the IP/DS//DS population, indicating that more recombinants were produced in the IP/DS//IP population. Distorted segregation was observed for 44 and 19 marker loci for the IP/DS//IP and IP/DS//DS populations, respectively; these were mostly skewed in favor of the indica alleles. A total of 36 main effect QTLs (M-QTLs) and 15 digenic epistatic interactions (E-QTLs) were detected for the seven traits investigated. The phenotypic variation explained (PVE) by M-QTLs ranged from 3.4% to 88.2%. Total PVE of the M-QTLs for each trait was significantly higher than that of the E-QTLs. The total number of M-QTLs identified in the IP/DS//IP population was higher than in the IP/DS//DS population. However, the total PVE by the M-QTLs and E-QTLs together for each trait was similar in the two populations, suggesting that the two $BC_1F_1$ populations are equally useful for QTL analysis. Maps and QTLs in the two populations were compared. Eleven new QTLs were identified for SN, SF, GL, and GW in this study, and they will be valuable in marker-assisted selection, particularly for improving grain traits in tongil-type varieties.

• Animal Bioscience
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• 제36권6호
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• pp.861-868
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• 2023

Objective: Loin muscle area (LMA) is an important target trait of pig breeding. This study aimed to identify single nucleotide polymorphisms (SNPs) and genes associated with LMA in the Duroc×(Landrace×Yorkshire) crossbred pigs (DLY). Methods: A genome-wide association study was performed using the Illumina 50K chip to map the genetic marker and genes associated with LMA in 511 DLY pigs (255 boars and 256 sows). Results: After quality control, we detected 35,426 SNPs, including six SNPs significantly associated with LMA in pigs, with MARC0094338 and ASGA0072817 being the two key SNPs responsible for 1.77% and 2.48% of the phenotypic variance of LMA, respectively. Based on previous research, we determined two candidate genes (growth hormone receptor [GHR] and 3-oxoacid Co A-transferase 1 [OXCT1]) that are associated with fat deposition and muscle growth and found further additional genes (MYOCD, ARHGAP44, ELAC2, MAP2K4, FBXO4, FBLL1, RARS1, SLIT3, and RANK3) that are presumed to have an effect on LMA. Conclusion: This study contributes to the identification of the mutation that underlies quantitative trait loci associated with LMA 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 LMA regulation.

• 한국환경생태학회지
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• 제30권6호
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• pp.929-938
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• 2016

본 연구에서는 희귀수종인 가침박달의 외부형태학적 형질을 재검토하여 기존 문헌 및 선행 연구와의 차이를 파악하였으며, 식물상 문헌 및 표본정보를 통해 국내 분포도를 작성하였다. 또한 토양의 이화학적 특성을 분석하여 외부형태형질과 토양 조건과의 상관성을 고찰하였다. 가침박달 자생지 토양분석 결과, 유기물함량 3.25-29.83%, 전질소함량 0.15-1.14%, 유효인산 3.0-156mg/kg, 치환성 $K^+$ $0.39-1.49cmol^+/kg$, 치환성 $Ca^{2+}$ $2.48-38.07cmol^+/kg$, 치환성 $Mg^{2+}$ $0.77-18.29cmol^+/kg$, 양이온치환용량 $7.3-23.0cmol^+/kg$으로 확인되었으며, 토양 pH는 4.6-7.1인 것으로 조사되었다. 대구 앞산 집단의 경우, 유기물함량, 전질소, 양이온치환용량이 가장 높았고, 화서의 길이가 길고, 꽃의 수가 많아 다른 지역에 비해 유의성 있게 차이를 나타냈다(P < 0.001). 또한, 집단의 유전적거리와 지리적 거리, 일부 외부형태형질의 차이를 통해 이들의 상관성을 확인할 수 있었다. 희귀 수종인 가침박달의 생육특성을 파악하고, 서식지 내 보존을 위해 외부형태형질, 유전적 구조, 생육상태, 식생구조, 환경특성 등 다양한 데이터의 종합적 고찰이 필요하다.

• 환경영향평가
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• 제26권1호
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• pp.44-56
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• 2017

지속가능한 발전은 도시의 효율적인 개발과 경제, 사회, 환경적 측면의 보전을 목표로 하기 때문에 중요하다. 그러나 우리나라의 빠른 도시화로 경제적 발전은 이루었지만 자원의 비효율적인 배분현상을 경험하게 되었고 이는 토지이용 배분도 예외가 아니다. 토지이용 배분의 문제가 어려운 이유는 다양한 목적을 고려해야하기 때문이며 이는 다목적 최적화의 방법에서 그 해결책을 찾을 수가 있다. 본 연구에서는 생태적으로 보존이 잘 되어있으며 인구 증가가 일어나고 있는 경기도 양평지역의 양평읍과 그 일대를 대상지로 선정하였다. 그리고 넓은 공간 탐색에 유리하고 토지이용 배분의 문제에서 널리 사용되고 있는 유전 알고리즘을 사용하였다. 유전알고리즘(GA)는 더 좋은 자손을 얻기 위하여 염색체의 교차 및 돌연변이의 과정을 거치는 적자생존의 원리가 작용하는 진화의 단계가 그 출발점이다. 본 연구는 변이의 방식에 변화를 주었으며 공간적 목적, 토지이용 전환 최소화, 생태계 보전 최대화, 경제적 이익 최대화라는 네 가지 목적과 특정 토지이용의 면적제한과 고정지역 설정이라는 제약요건을 두고 최적 안을 도출해내었다. 생태적으로 보존시켜야 할 곳에는 시가지가 형성되지 않았고, 시가지 면적 증가율이 높은 결과는 최적화의 방향인 '경제적 이익의 최대화'라는 점과 상응하였다. 적합도 값이 최소인 지점이 수렴지점임을 고려했을 때, 1500세대 부근에서 최적화가 일어났음을 알 수 있었다. 본 연구의 결과는 양평읍과 그 일대에 적용시킬 수 있는 효과적인 지원방안을 마련하는데 도움이 될 수 있을 것으로 판단된다.

• 한국환경생태학회지
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• 제31권2호
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• pp.188-201
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• 2017

경상북도 울진군에 위치한 소광리 산림유전자원보호구역 산림식생의 조성 및 구조적 특성을 파악하기 위하여 ZM학파의 식물사회학적 연구방법으로 총 272개 식생자료를 수집한 후, 표비교법과 TWINSPAN법을 병용하여 산림식생 유형을 구분하고 그 생태적 특성을 분석하였다. 산림식생 유형은 모두 7개 유형이 구분되었으며, 신갈나무, 소나무, 진달래, 싸리 등이 특징짓는 '사면 능선형'과 층층나무, 들메나무, 산뽕나무, 산수국 등이 특징짓는 '계곡 요(凹)지형'의 두 그룹으로 대별되었다. 식생단위의 구성 체계는 2개 군락군, 4개 군락, 그리고 6개 아군락으로 나타났다. 구분된 산림식생 유형별 단위면적당 구성종의 총피도, 중요치, 종다양성 등의 구성적 특성도 파악하였다. 산림식생의 공간분포 특성을 파악하기 위하여 1/5,000 대축척 현존상관식생도를 작성하였다. 보호구역의 핵심 보호대상 군락인 금강소나무 우점 임분은 자연적 및 인위적 영향으로 그 조성과 구조적 특성에 있어 이미 잠재자연식생인 신갈나무림의 아형 (subtype)으로 나타나고 있어 향후 보호구역 금강소나무림의 지속적인 자기유지를 유도하는 적절한 보전대책 수립이 시급히 필요해 보였다.

• Molecules and Cells
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• 제28권3호
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• pp.201-207
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• 2009

Silibinin is a polyphenolic flavonoid compound isolated from milk thistle (Silybum marianum), with known hepatoprotective, anticarcinogenic, and antioxidant effects. Herein, we show that silibinin inhibits receptor activator of $NF-{\kappa}B$ ligand (RANKL)-induced osteoclastogenesis from RAW264.7 cells as well as from bone marrow-derived monocyte/macrophage cells in a dose-dependent manner. Silibinin has no effect on the expression of RANKL or the soluble RANKL decoy receptor osteoprotegerin (OPG) in osteoblasts. However, we demonstrate that silibinin can block the activation of $NF-{\kappa}B$, c-Jun N-terminal kinase (JNK), p38 mitogen-activated protein (MAP) kinase, and extracellular signal-regulated kinase (ERK) in osteoclast precursors in response to RANKL. Furthermore, silibinin attenuates the induction of nuclear factor of activated T cells (NFAT) c1 and osteoclast-associated receptor (OSCAR) expression during RANKL-induced osteoclastogenesis. We demonstrate that silibinin can inhibit $TNF-{\alpha}$-induced osteoclastogenesis as well as the expression of NFATc1 and OSCAR. Taken together, our results indicate that silibinin has the potential to inhibit osteoclast formation by attenuating the downstream signaling cascades associated with RANKL and $TNF-{\alpha}$.

• Genomics & Informatics
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• 제6권4호
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• pp.231-234
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• 2008

Precise and reliable identification of CNV is still important to fully understand the effect of CNV on genetic diversity and background of complex diseases. SNP marker has been used frequently to detect CNVs, but the analysis of SNP chip data for identifying CNV has not been well established. We compared various normalization methods for CNV analysis and suggest optimal normalization procedure for reliable CNV call. Four normal Koreans and NA10851 HapMap male samples were genotyped using Affymetrix Genome-Wide Human SNP array 5.0. We evaluated the effect of median and quantile normalization to find the optimal normalization for CNV detection based on SNP array data. We also explored the effect of Robust Multichip Average (RMA) background correction for each normalization process. In total, the following 4 combinations of normalization were tried: 1) Median normalization without RMA background correction, 2) Quantile normalization without RMA background correction, 3) Median normalization with RMA background correction, and 4) Quantile normalization with RMA background correction. CNV was called using SW-ARRAY algorithm. We applied 4 different combinations of normalization and compared the effect using intensity ratio profile, box plot, and MA plot. When we applied median and quantile normalizations without RMA background correction, both methods showed similar normalization effect and the final CNV calls were also similar in terms of number and size. In both median and quantile normalizations, RMA backgroundcorrection resulted in widening the range of intensity ratio distribution, which may suggest that RMA background correction may help to detect more CNVs compared to no correction.

• The Korean Journal of Physiology and Pharmacology
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• 제19권2호
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• pp.141-149
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• 2015

"G protein-coupled receptor 40" (GPR40), a receptor for long-chain fatty acids, mediates the stimulation of glucose-induced insulin secretion. We examined the profiles of differential gene expression in GPR40-activated cells treated with linoleic acid, and finally predicted the integral pathways of the cellular mechanism of GPR40-mediated insulinotropic effects. After constructing a GPR40-overexpressing stable cell line (RIN-40) from the rat pancreatic ${\beta}$-cell line RIN-5f, we determined the gene expression profiles of RIN-5f and RIN-40. In total, 1004 genes, the expression of which was altered at least twofold, were selected in RIN-5f versus RIN-40. Moreover, the differential genetic profiles were investigated in RIN-40 cells treated with $30{\mu}M$ linoleic acid, which resulted in selection of 93 genes in RIN-40 versus RIN-40 treated with linoleic acid. Based on the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG, http://www.genome.jp/kegg/), sets of genes induced differentially by treatment with linoleic acid in RIN-40 cells were found to be related to mitogen-activated protein (MAP) kinase- and neuroactive ligand-receptor interaction pathways. A gene ontology (GO) study revealed that more than 30% of the genes were associated with signal transduction and cell proliferation. Thus, this study elucidated a gene expression pattern relevant to the signal pathways that are regulated by GPR40 activation during the acute period. Together, these findings increase our mechanistic understanding of endogenous molecules associated with GPR40 function, and provide information useful for identification of a target for the management of type 2 diabetes mellitus.