• 한국균학회소식:학술대회논문집
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• 2018.05a
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• pp.22-22
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• 2018

Fungal genome sequencing and assembly have been trivial in these days. Genome analysis relies on high quality of gene prediction and annotation. Automatic fungal genome annotation pipeline is essential for handling genomic sequence data accumulated exponentially. However, building an automatic annotation procedure for fungal genomes is not an easy task. FunGAP (Fungal Genome Annotation Pipeline) is developed for precise and accurate prediction of gene models from any fungal genome assembly. To make high-quality gene models, this pipeline employs multiple gene prediction programs encompassing ab initio, evidence-, and homology-based evaluation. FunGAP aims to evaluate all predicted genes by filtering gene models. To make a successful filtering guide for removal of false-positive genes, we used a scoring function that seeks for a consensus by estimating each gene model based on homology to the known proteins or domains. FunGAP is freely available for non-commercial users at the GitHub site (https://github.com/CompSynBioLab-KoreaUniv/FunGAP).

• Journal of Aquaculture
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• v.18 no.2
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• pp.130-132
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• 2005

Genomics research has two ultimate applied goals: to Isolate and clone genes of economic importance for bio-technology and gene-assisted selection (GAS), and to locate and use markers for marker-assisted selection (MAS) in selective breeding programs. To this end, we have identified linked markers for feed conversion efficiency growth rate, and disease resistance to enteric septicemia of catfish (ESC). Three microsatellite markers Ip266, Ip384, and Ip607 were identified to be linked to feed conversion efficiency. Similarly one marker each was identified to be linked to growth rate (Ip607) and disease resistance to ESC (Ip477). Ip607 marker linked to both growth rate and feed conversion efficiency, indicating that the QTL for both growth rate and feed conversion efficiency may either be the same or located in the same chromosomal region in the catfish genome. On phenotypic evaluation, certain traits such as growth rate can be accurately evaluated by body weight evaluation while other traits such as disease resistance can be quite complex. The linked DNA markers will be highly useful for MAS programs and for directing further efforts of genomic mapping for important quantitative traits.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8227-8233
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• 2016

Background: To investigate polymorphisms in heat shock proteins A1B and A1L (HOM) and associated risk of oesophageal carcinoma in Northeast India. Materials and Methods: The study includes oesophageal cancer (ECA) patients attending general outpatient department (OPD) and endoscopic unit of Gauhati Medical College. Patients were diagnosed based on endoscopic and histopathological findings. Genomic DNA was typed for HSPA1B1267 and HSPA1L2437 SNPs using the polymerase chain reaction with restriction fragment length polymorphisms. Results: A total of 78 cases and 100 age-sex matched healthy controls were included in the study with a male: female ratio of 5:3 and a mean age of $61.4{\pm}8.5years$. Clinico-pathological evaluation showed 84% had squamous cell carcinoma and 16% were adenocarcinoma. Dysphagia grades 4 (43.5%) and 5 (37.1%) were observed by endoscopic and hispathological evaluation. The frequency of genomic variation of A1B from wild type A/A to heterozygous A/G and mutant G/G showed a positive association [chi sq=19.9, p=<0.05] and the allelic frequency also showed a significant correlation [chi sq=10.3, with cases vs. controls, OR=0.32, $p{\leq}0.05$]. The genomic variation of A1L from wild T/T to heterozygous T/C and mutant C/C were found positively associated [chi sq=7.02, p<0.05] with development of ECA. While analyzing the allelic frequency, there was no significant association [chi sq=3.19, OR=0.49, p=0.07]. Among all the risk factors, betel quid [OR=9.79, Chi square=35.0, p<0.05], tobacco [OR=2.95, chi square=10.6, p<0.05], smoking [OR=3.23, chi square=10.1, p<0.05] demonstrated significant differences between consumers vs. non consumers regarding EC development. Alcohol did not show any significant association [OR=1.34, chi square=0.69, p=0.4] independently. Conclusions: It can be concluded that the present study provides marked evidence that polymorphisms of HSP70 A1B and HSP70 A1L genes are associated with the development of ECA in a population in Northeast India, A1B having a stronger influence. Betel quid consumption was found to be a highly significant risk factor, followed by smoking and tobacco chewing. Although alcohol was not a potent risk factor independently, alcohol consumption along with tobacco, smoking and betel nut was found to contribute to development of ECA.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.737-750
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• 2015

This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard's genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation ($r{\geq}0.80$). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

• Journal of Animal Science and Technology
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• v.53 no.1
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• pp.1-6
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• 2011

This simulation study was performed to investigate the accuracy of the estimated breeding value by using genomic information (GEBV) by way of Bayesian framework. Genomic information by way of single nucleotide polymorphism (SNP) from a chromosome with length of 100cM were simulated with different marker distance (0.1cM, 0.5cM), heritabilities (0.1, 0.5) and half sibs families (20 heads, 4 heads). For generating the simulated population in which animals were inferred to genomic polymorphism, we assumed that the number of quantitative trait loci (QTL) were equal with the number of no effect markers. The positions of markers and QTLs were located with even and scatter distances, respectively. The accuracies of estimated breeding values by way of indicating correlations between true and estimated breeding values were compared on several cases of marker distances, heritabilities and family sizes. The accuracies of breeding values on animals only having genomic information were 0.87 and 0.81 in marker distances of 0.1cM and 0.5cM, respectively. These accuracies were shown to be influenced by heritabilities (0.87 at $h^2$ =0.10, 0.94 at $h^2$ =0.50). According to half sibs' family size, these accuracies were 0.87 and 0.84 in family size of 20 and 4, respectively. As half sibs family size is high, accuracy of breeding appeared high. Based on the results of this study it is concluded that the amount of marker information, heritability and family size would influence the accuracy of the estimated breeding values in genomic selection methodology for animal breeding.

• Journal of Animal Science and Technology
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• v.55 no.5
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• pp.399-403
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• 2013

This study was conducted to investigate the basic concept of multiple trait effective daughter contribution (MTEDC) for dairy cattle sires and calculate effective daughter contribution (EDC) by applying a five lactation multiple trait model using milk yield test records of daughters for the Multiple-trait Across Country Evaluation (MACE). Milk yield data and pedigree information of 301,551 cows that were the progeny of 2,046 Korean and imported dairy bulls were collected from the National Agricultural Cooperative Federation and used in this study. For MTEDC approximation, the reliability of the breeding value was separated based on parents average, own yield deviation and mate adjusted progeny contribution. EDC was then calculated by lactation using these reliabilities. The average number of recorded daughters per sire by lactations were 140.57, 94.24, 55.14, 29.20 and 14.06 from the first to fifth lactation, respectively. However, the average EDC per sire by lactation using the five lactation multiple trait model was 113.49, 89.28, 73.56, 54.02 and 35.08 from the first to fifth lactation, respectively, while the decrease of EDC in late lactations was comparably lower than the average number of recorded daughters per sire. These findings indicate that the availability of daughters without late lactation records is increased by genetic correlation using the multiple trait model. Owing to the relatedness between the EDC and reliability of the estimated breeding value for sire, understanding the MTEDC algorithm and continuous monitoring of EDC is required for correct MACE application of the five lactation multiple trait model.

• Applied Biological Chemistry
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• v.48 no.4
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• pp.331-334
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• 2005

In this study, the effects of five extraction methods for raw and processed corns were compared with respect to the integrity, yields and quality of DNA extracted from them and the results were assessed by PCR analysis. From the comparison of five extraction methods, DNA integrity showed a similar pattern. Amounts of genomic DNA obtained from the five extraction methods varies from $0.25{\mu}g\;to\;234{\mu}g$ per 1 g sample. The DNA yield extracted with CTAB method and DNeasy Plant Maxi kit is greater than that obtained from other extraction methods. These results would be applicable for the selection of an adequate extraction method for specific samples.

• Genomics & Informatics
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• v.18 no.1
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• pp.4.1-4.6
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• 2020

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE-association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.

• Environmental Mutagens and Carcinogens
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• v.18 no.1
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• pp.15-21
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• 1998

Transgenic animal and cell line models which are recently developed and used in toxicology fields combined with molecular biological technique, are powerful tools to study the mechanism of mutation in vivo and in vitro, respectively. Transgenic models, which have exogenous DNA incorporated into their genome, carry recoverable shuttle vector containing reporter genes to assess endogenous effects or alteration in specific genes related to disease processes. The lac I and lac Z gnee most widely used as a mutational target in transgenic systems. The assay is performed by treatment with putative mutagenic agents, isolation of genomic DNA from cells or tissues, exposure the isolated DNA to in vitro packaging extract, plating and sequencing. The results from these processes provide not only mutant frequency as quantitative evaluation but also mutational spectrum as qualitative evaluation of various agents. Therefore we introduce and review the principle, detailed procedure and application of transgenic mutagenesis assay system in toxicology fields especially in mutagenesis and carcinogenesis.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.107-112
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• 2013

With the progress of NGS technologies, large genome data have been exploded recently. To analyze such data effectively, the assistance of HPC technique is necessary. In this paper, we organized a genome analysis pipeline to call SNP from NGS data. To organize the pipeline efficiently under HPC environment, we analyzed the CPU utilization pattern of each pipeline steps. We found that sequence alignment is computing centric and suitable for parallelization. We also analyzed the performance of parallel open source alignment tools and found that alignment method utilizing many-core processor can improve the performance of genome analysis pipeline.