• Asian-Australasian Journal of Animal Sciences
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• v.14 no.12
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• pp.1665-1669
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• 2001

A QTL was localized near S0120 on porcine chromosome 18. The QTL was significant (p<0.05) for average daily gain (ADG) of body weight and backfat thickness (BFT). The estimates of additive and dominance effects for the QTL were 0.0135 kg/day (p<0.001) and 0.0138 kg/day (p>0.5) for ADG and 1.6115 mm (p<0.001) and 0.9281 mm (p>0.05) for BFT. The location of this QTL coincided with a few growth hormone pathway genes. This study suggested that a QTL allele probably resulted from a mutation responsible for physiological lipase deficiency favoring obesity. This QTL might be important to obesity as well as growth in pigs.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.73-73
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• 2019

Angelica gigas Nakai (Korean danggui), a member of the Umbelliferae family, is a Korean traditional medicinal plant whose roots have been used for treating gynecological diseases. Transcriptomics is the study of the transcriptome, which is the complete set of RNA transcripts that are produced by the genome, using high-throughput methods, such as microarray analysis. In this study, transcriptome analysis of A.gigas Nakai was carried out. Transcriptome sequencing and assembly was carried out by using Illumina Hiseq 2500, Velvet and Oases. A total of 109,591,555 clean reads of A. gigas Nakai was obtained after trimming adaptors. The obtained reads were assembled with an average length of 1,154 bp, a maximum length of 13,166 bp, a minimum length of 200 pb, and N50 of 1,635 bp. Functional annotation and classification was performed using NCBI NR, InterprotScan, KOG, KEGG and GO. Candidate genes for phenylpropanoid biosynthesis were obtanied from A.gigas transcriptome and the genes and its proteins were confirmed through the NCBI homology BLAST searches, revealing high identity with other othologous genes and proteins from various plants pecies. In RNA sequencing analysis using an Illumina Next-Seq2500 sequencer, we identified a total 94,930 transcripts and annotated 71,281 transcripts, which provide basic information for further research in A.gigas Nakai. Our transcriptome data reveal that several differentially expressed genes related to flower color in A.gigas Nakai. The results of this research provide comprehensive information on the A.gigas Nakai genome and enhance our understanding of the flower color related gene pathways in this plant.

• Interdisciplinary Bio Central
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• v.4 no.1
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• pp.1.1-1.7
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• 2012

Background: The F-box proteins represent one of the largest families of proteins in eukaryotes. Apart from being a component of the ubiquitin (Ub)/26 S proteasome pathways, their regulatory roles in other cellular and developmental pathways have also been reported. One interesting feature of the genes encoding the proteins of this particular family is their variable selection patterns across different lineages. This resulted in the presence of lineage specific F-box proteins across different species. Findings: In this study, 48 non-redundant F-box proteins in E. siliculosus have been identified by a homology based approach and classified into three classes based on their variable C-terminal domains. A greater number of the F-box proteins have domains similar to the ones identified in other species. On the other hand, when the proteins having unknown or no C-terminal domain (as predicted by InterProScan) were analyzed, it was found that some of them have the polyglutamine repeats. To gain evolutionary insights on the genes encoding the F-box proteins, their selection patterns were analyzed and a strong positive selection was observed which indicated the adaptation potential of the members of this family. Moreover, four lineage specific F-box genes were found in E. siliculosus with no identified homolog in any other species. Conclusions: This study describes a genome wide in silico analysis of the F-box proteins in E. siliculosus which sheds light on their evolutionary patterns. The results presented in this study provide a strong foundation to select candidate sequences for future functional analysis.

• The Journal of Internal Korean Medicine
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• v.30 no.3
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• pp.594-603
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• 2009

Objectives : ICH breaks down blood vessels within the brain parenchyma, which finally leads to neuronal loss, drugs to treat ICH have not yet been established. In this experiment, we measured the effect of Woowhangchongshim-won (WWCSW) on intracerebral hemorrhage (ICH) in rat using microarray technology. Methods : We measured the effect of WWCSW on ICH in rat using microarray technology. ICH was induced by injection of collagenase type IV, and total RNA was isolated. Image files of microarray were measured using a ScanArray scanner, and the criteria of the threshold for up- and down-regulation was 2 fold. Hierarchical clustering was implemented using CLUSTER and TREEVIEW program, and for Ontology analysis. GOSTAT program was applied in which p-value was calculated by Chi square or Fisher's exact test based on the total array element. Results : WWCSW-treatment restored the gene expression altered by ICH-induction in brain to the levels of 76.0% and 70.1% for up- and down-regulated genes, respectively. Conclusion : Co-regulated genes by ICH model of rat could be used as molecular targets for therapeutic effects of drug including WWCSW. That is, the presence of co-regulated genes may represent the importance of these genes in ICH in the brain and the change of expression level of these co-regulated genes would also indicate the functional change of brain tissue.

• Genomics & Informatics
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• v.3 no.1
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• pp.15-23
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• 2005

Background MicroRNAs (miRNAs) are a class of noncoding RNAs found in various organisms such as plants and mammals. However, most of the mRNAs regulated by miRNAs are unknown. Furthermore, miRNA targets in genomes cannot be identified by standard sequence comparison since their complementarity to the target sequence is imperfect in general. In this paper, we propose a kernel-based method for the efficient prediction of miRNA targets. To help in distinguishing the false positives from potentially valid targets, we elucidate the features common in experimentally confirmed targets. Results The performance of our prediction method was evaluated by five-fold cross-validation. Our method showed 0.64 and 0.98 in sensitivity and in specificity, respectively. Also, the proposed method reduced the number of false positives by half compared with TargetScan. We investigated the effect of feature sets on the classification of miRNA targets. Finally, we predicted miRNA targets for several miRNAs in the Caenorhabditis elegans (C. elegans) 3' untranslated region (3' UTR) database. Condusions The targets predicted by the suggested method will help in validating more miRNA targets and ultimately in revealing the role of small RNAs in the regulation of genomes. Our algorithm for miRNA target site detection will be able to be improved by additional experimental­knowledge. Also, the increase of the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.8
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• pp.1088-1097
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• 2005

Main objectives of this study were to investigate accuracy, bias and power of linear and threshold model segregation analysis methods for detection of major genes in categorical traits in farm animals. Maximum Likelihood Linear Model (MLLM), Bayesian Linear Model (BALM) and Bayesian Threshold Model (BATM) were applied to simulated data on normal, categorical and binary scales as well as to disease data in pigs. Simulated data on the underlying normally distributed liability (NDL) were used to create categorical and binary data. MLLM method was applied to data on all scales (Normal, categorical and binary) and BATM method was developed and applied only to binary data. The MLLM analyses underestimated parameters for binary as well as categorical traits compared to normal traits; with the bias being very severe for binary traits. The accuracy of major gene and polygene parameter estimates was also very low for binary data compared with those for categorical data; the later gave results similar to normal data. When disease incidence (on binary scale) is close to 50%, segregation analysis has more accuracy and lesser bias, compared to diseases with rare incidences. NDL data were always better than categorical data. Under the MLLM method, the test statistics for categorical and binary data were consistently unusually very high (while the opposite is expected due to loss of information in categorical data), indicating high false discovery rates of major genes if linear models are applied to categorical traits. With Bayesian segregation analysis, 95% highest probability density regions of major gene variances were checked if they included the value of zero (boundary parameter); by nature of this difference between likelihood and Bayesian approaches, the Bayesian methods are likely to be more reliable for categorical data. The BATM segregation analysis of binary data also showed a significant advantage over MLLM in terms of higher accuracy. Based on the results, threshold models are recommended when the trait distributions are discontinuous. Further, segregation analysis could be used in an initial scan of the data for evidence of major genes before embarking on molecular genome mapping.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.176-182
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• 2019

Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles ($n_e$) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient ($F_{IS}$) value (-0.15). Principal component analysis of estimated genetic distance ($F_{ST}$) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise $F_{ST}$ values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance ($F_{ST}$ values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). $F_{ST(C-E)}$ was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance ($F_{ST}$<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.

• Journal of Ginseng Research
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• v.43 no.4
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• pp.572-579
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• 2019

Background: Panax ginseng has been used in traditional medicine to strengthen the body and mental well-being of humans for thousands of years. Many elite ginseng cultivars have been developed, and ginseng cultivation has become well established during the last century. However, heat stress poses an important threat to the growth and sustainable production of ginseng. Efforts have been made to study the effects of high temperature on ginseng physiology, but knowledge of the molecular responses to heat stress is still limited. Methods: We sequenced the transcriptomes (RNA-Seq) of two ginseng cultivars, Chunpoong (CP) and Yunpoong (YP), which are sensitive and resistant to heat stress, respectively, after 1- and 3-week heat treatments. Differential gene expression and gene ontology enrichment along with profiled chlorophyll contents were performed. Results: CP is more sensitive to heat stress than YP and exhibited a lower chlorophyll content than YP. Moreover, heat stress reduced the chlorophyll content more rapidly in CP than in YP. A total of 329 heat-responsive genes were identified. Intriguingly, genes encoding chlorophyll a/b-binding proteins, WRKY transcription factors, and fatty acid desaturase were predominantly responsive during heat stress and appeared to regulate photosynthesis. In addition, a genome-wide scan of photosynthetic and sugar metabolic genes revealed reduced transcription levels for ribulose 1,5-bisphosphate carboxylase/oxygenase under heat stress, especially in CP, possibly attributable to elevated levels of soluble sugars. Conclusion: Our comprehensive genomic analysis reveals candidate loci/gene targets for breeding and functional studies related to developing high temperature-tolerant ginseng varieties.

• Animal Bioscience
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• v.37 no.5
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• pp.832-838
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• 2024

Objective: The use of molecular genetic methods in pig breeding can significantly increase the efficiency of breeding and breeding work. We applied the F_st (fixsacion index) method, the main focus of the work was on the search for common options related to the number of born piglets and the weight of born piglets, since today the urgent task is to prevent a decrease in the weight of piglets at birth while maintaining high fertility of sows. Methods: One approach is to scan the genome, followed by an assessment of Fst and identification of selectively selected regions. We chose Large White sows (n = 237) with the same conditions of keeping and feeding. The data were collected from the sows across three farrowing. For genotyping, we used GeneSeek GGP Porcine HD Genomic Profiler v1, which included 68,516 single nucleotide polymorphisms evenly distributed with an average spacing of 25 kb (Illumina Inc, San Diego, CA, USA). Results: Based on the results of the Fst analysis, 724 variants representing selection signals for the signs BALWT, BALWT1, NBA, and TNB (weight of piglets born alive, average weight of the 1st piglets born alive, total number born alive, total number born). At the same time, 18 common variants have been identified that are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive characteristics in sows. Conclusion: Our work resulted in identification of variants associated with the reproductive characteristics of pigs. Moreover, we identified, variants which are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive performance in sows.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.34 no.5
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• pp.509-517
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• 2008

DNA damage accumulates in cells as a result of exposure to exogenous agents such as benzopyrene, cigarette smoke, ultraviolet light, X-ray, and endogenous chemicals including reactive oxygen species produced from normal metabolic byproducts. DNA damage can also occur during aberrant DNA processing reactions such as DNA replication, recombination, and repair. The major of DNA damage affects the primary structure of the double helix; that is, the bases are chemically modified. These modification can disrupt the molecules'regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. DNA repair genes and proteins scan the global genome to detect and remove DNA damage and damage to single nucleotides. Direct reversal of DNA damage, base excision repair, double strand break. DNA repair are known relevant DNA repair mechanisms. Four different mechanisms are distinguished within excision repair: direct reversal, base excision repair, nucleotide excision repair, and mismatch repair. Genetic variation in DNA repair genes can modulate DNA repair capacity and alter cancer risk. The instability of a cell to properly regulate its proliferation in the presence of DNA damage increase risk of gene mutation and carcinogenesis. This article aimed to review mechanism of excision repair and to understand the relationship between genetic variation of excision repair genes and head and neck cancer.