• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.4
• /
• pp.462-469
• /
• 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
• /
• v.20 no.3
• /
• pp.385-391
• /
• 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
• /
• v.25 no.3
• /
• pp.417-427
• /
• 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
• /
• v.36 no.6
• /
• pp.861-868
• /
• 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.

• Korean Journal of Environment and Ecology
• /
• v.30 no.6
• /
• pp.929-938
• /
• 2016

This study reviewed the external morphological characteristics of a rare species, Exochorda serratifolia S.Moore, in South Korea through a comparison of its previous records. Also, a distribution map of this species was made using previous data on flora and voucher specimens. Furthermore, the soil characteristics of Exochorda serratifolia S.Moore was analysed in order to determine the correlation between external morphological features and soil characteristics. At the study sites, soil organic matter, total nitrogen, available phosphates, exchangeable potassium, exchangeable calcium, exchangeable magnesium, cation exchange capacity and soil pH were found to be in the ranges of 3.25-29.83%, 0.15-1.14%, 3.0-156 mg/kg, $0.39-1.49cmol^+/kg$, $2.48-38.07cmol^+/kg$, $0.77-18.29cmol^+/kg$, $7.3-23.0cmol^+/kg$ and 4.6-7.1 respectively. The soil condition surrounding the population of Exochorda serratifolia S.Moore in Mt. Ap-san (Daegu) was found to have higher percentages of organic matter, total nitrogen, and cation exchange capacity than the soil condition of other populations. Moreover, the length of inflorescence and the number of flowers in this population were significantly higher than the populations studied in other areas (P < 0.001). We also identified a significant correlation between genetic, geographic distance and several morphological characteristics. A comprehensive review of various data on Exochorda serratifolia S.Moore such as external morphological characteristics, genetic structure, growth conditions, vegetation properties, and environmental characteristics is required to understand its growth characteristics and conserve this rare species.

• Journal of Environmental Impact Assessment
• /
• v.26 no.1
• /
• pp.44-56
• /
• 2017

Sustainable development is important because the ultimate objective is efficient development combining the economic, social, and environmental aspects of urban conservation. Despite Korea's rapid urbanization and economic development, the distribution of resources is inefficient, and land-use is not an exception. Land use distribution is difficult, as it requires considering a variety of purposes, whose solutions lie in a multipurpose optimization process. In this study, Yangpyeong-eup, Yangpyeong, Gyeonggi-do, is selected, as the site has ecological balance, is well-preserved, and has the potential to support population increases. Further, we have used the genetic algorithm method, as it helps to evolve solutions for complex spatial problems such as planning and distribution of land use. This study applies change to the way of mutation. With four goals and restrictions of area, spatial objectives, minimizing land use conversion, ecological conservation, maximizing economic profit, restricting area to a specific land use, and setting a fixed area, we developed an optimal planning map. No urban areas at the site needed preservation and the high urban area growth rate coincided with the optimization of purpose and maximization of economic profit. When the minimum point of the fitness score is the convergence point, we found optimization occurred approximately at 1500 generations. The results of this study can support planning at Yangpyeong-eup.ausative relationship between the perception of improving odor regulation and odor acceptance.

• Korean Journal of Environment and Ecology
• /
• v.31 no.2
• /
• pp.188-201
• /
• 2017

Based on a total of 272 vegetation data collected by the ZM school phytosociological study method, the composition and structural characteristics of the forest vegetation in the Sogwang-ri forest genetic resource reservoir located in Uljin-gun, Gyeongsangbuk-do were compared using the table comparison method and the TWINSPAN method, And their ecological characteristics were analyzed. The types of forest vegetation were classified into 7 types, and it was divided into two major groups, 'Slope and Ridge type', which characterized by Quercus mongolica, Pinus densiflora for. erecta, Lespedeza bicolor etc. and 'valley and concave slope', which characterized by Cornus controversa, Fraxinus mandshurica, Morus bombycis, Hydrangea serrata for. acuminata etc. The hierarchy of the vegetation unit was 2 community groups, 4 communities, and 6 subcommunities. The structural characteristics such as the total percent cover, species importance value, species diversity of the constituent species per unit area($/100m^2$) of each type of forest vegetation were also identified. In order to understand the spatial distribution of forest vegetation, 1/5,000 large-scale physiognomic vegetation map was created by the uppermost dominant species. The composition and structural characteristics of Geumgang pine(P. densiflora for. erecta) forest, which is a core community of protected area by natural and anthropogenic influences, appear as a subtype of Quercus mongolica forest, which is a potential natural vegetation, Appropriate maintenance measures seemed urgently needed.

• Molecules and Cells
• /
• v.28 no.3
• /
• pp.201-207
• /
• 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
• /
• v.6 no.4
• /
• pp.231-234
• /
• 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
• /
• v.19 no.2
• /
• pp.141-149
• /
• 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.