• BMB Reports
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• v.49 no.9
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• pp.514-519
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• 2016

Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.50 no.2
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• pp.97-104
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• 2005

Mass selection (MS) is an efficient selection method to directly improve highly heritable traits. In the present study, two cycles of MS for ear length were conducted on two sweet corn populations, BC2-l0 and $BC1-10{\times}Syn-II$ after introgression of exotic germplasm. The improved populations generated from these selections were evaluated in comparison with the base populations at two locations, to determine the genetic gains and performance of the improved populations. The two base populations showed varied average realized responses to MS. In BC2-l0 derived population, the realized responses were $9.1\%$ in BC2-l0 C1 and $1.2\%$ in BC2-l0 C2, whereas in$BC1-10{\times}Syn-II$ derived population, the realized responses were$ 5.6\%$ in $BC1-10{\times}Syn-II$ C1 and $2.9\%$ in $BC1-10{\times}Syn-II$ C2. All the improved populations showed longer ears than their respective base populations and the check varieties. Ear length, which was used as the selection criterion in this study, showed high broad-sense heritability in the BC2-l0 and $BC1-10{\times}Syn-II$ derived populations, while fresh ear yield revealed low heritability, indicating that selection for ear length in these populations would be more effective than direct selection for yield. Results of this study indicate that MS conducted on BC2­10 and $BC1-10{\times}Syn-II$ had significantly increased ear length and fresh ear yield in both populations. The improved populations obtained would serve as better germplasm sources and further selection in these populations could offer better responses.

• Journal of Animal Science and Technology
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• v.53 no.6
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• pp.511-516
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• 2011

Fas gene known to associate with intramuscular fat content in Korean cattle was selected for DNA marker development. Fas (APO-1, CD95), a member of the tumor necrosis factor (TNF) receptor superfamily, is a cell membrane protein that mediates apoptosis (programmed cell death). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers at genomic level. Of this gene to search for SNP, sequences of whole exon and 1kb range of both front and back of the gene using 24 cattle were determined by direct-sequencing methods. As a result, 16 SNPs in exon, 37 SNPs in intron and 2 SNPs in promoter region, a total of 55 SNPs were discovered. In these SNPs, thirty-one common polymorphic sites were selected considering their allele frequencies, haplotype-tagging status and Linkage Disequilibrium (LD) for genotyping in larger-scale subjects. Selected SNPs were confirmed genotype through SNaPshot method (n=274) and were examined for possible genetic association of Fas polymorphisms with carcass weight (CWT), eye muscle area (EMA), and backfat thickness (BF). So, the SNP have been identified significant g.-12T>G, g.1112T>G and g.32548T>C. These results suggest that polymorphism of Fas gene was associated with meat quality traits in Hanwoo.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.56 no.1
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• pp.14-17
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• 2011

Dwarfuess and Kunitz trypsin inhibitor (KTI) protein in soybean is useful traits for basic studies. df2 and ti gene control dwarfness and the expression of Kunitz trypsin inhibitor (KTI) protein in soybean, respectively. The objective of this research was to verify genetic linkage or independent inheritance of df2 and ti loci in soybean. The $F_2$ population was made by cross combination between "Gaechuck#2" (Df2Df2titi genotype, KTI protein absence and a normal growth type) and T210 (df2df2TiTi genotype, a dwarf growth type and KTI protein present). A total of 258 $F_2$ seeds were analyzed for the segregation of KTI protein using SDS-PAGE. And so, 198 $F_2$ plants were recorded for the segregation of dwarfness. The segregation ratio of 3 : 1 for Ti locus (201 Ti_ : 57 titi) and Df2 locus (143 Df2_ : 55 df2df2) was observed. Segregation ratio of 9 : 3 : 3 : 1 (116 Ti_Df2_: 44 Ti_df2df2: 27 titiDf2_: 11 titidf2df2) between df2 gene and ti gene was observed ($x^2$=3.53, P = 0.223). These results showed that df2 gene was inherited independently with the ti gene in soybean.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.1
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• pp.24-28
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• 2009

This study was conducted to evaluate the growth characters and yield components of 18 collected sesame cultivars to get basic information on the variation for the sesame breeding using principal component analysis. All characters except days to flowering, days to maturity and 1,000 seed weight showed significantly different. Seed weight per 10 are showed higher coefficient of variance. Capsule bearing stem length and liter weight showed positive correlation with seed yield per 10 are. The principal components analysis grouped the estimated sesame cultivars into four main components which accounted for 83.7% of the total variation at the eigenvalue and its contribution to total variation obtained from principal component analysis. The first principal component ($Z_1$) was applicable to increase plant height, capsule bearing stem length and 1,000-seed weight. The second principal component ($Z_2$) negatively correlated with days to flowering and maturity by which it was applicable to shorten flowering and maturity date of sesame. At the scatter diagram, Yangbaek, Ansan, M1, M2, M4, M7 and M9 were classified as same group, but M10, Yanghuk, Kanghuk, M5, M6, M12 and M13 were classified as different group. This results would be helpful for sesame breeder to understand genetic relationship of some agronomic characters and select promising cross lines for the development of new sesame variety.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.47
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• pp.175-185
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• 2002

Rapeseed(Brassica napus L.) is an important oil crop as a vegetable oil, concentrated feed and industrial materials. The name "canola" was registered in 1979 by the Western Canadian Oilseed Crushers Association to describe "double-low" varieties. Double low indicates that the processed oil contains less than 2% erucic-acid and the meal less than 3mg/g of glucosinolates. Today annual worldwide production of rapeseed is approximately 35 million tons on 24 million hectares. China accounts for 33% of the world production and the European Economic Community for nearly 32%. Canola ranks 3rd in production among the world's oilseed crops following soybeans, sunflowers, peanuts and cottonseed. The recent advances in genomics and in gene function studies has allowed us to understand the detailed genetic basis of many complex traits, such as flowering time, height, and disease resistance. The manipulation of seed oil content via transgene insertion has been one of the earliest successful applications of modern biotechnology in agriculture. For example, the first transgenic crop with a modified seed composition to be approved for unrestricted commercial cultivation in the US was a lauric oil, rape-seed, grown in 1995. There were also some significant early successes, mostly notably the achievement of 40% to 60% lauric acid content in rapeseed oil, which normally accumulates little or no lauric acid. The name "$\textrm{Laurical}^{TM}$" was registered in 1995 by Calgene Inc. Nevertheless, attempts to achieve high levels of other novel fatty acids in seed oils have met with much less success and there have been several reports that the presence of novel fatty acids in transgenic plants can sometimes lead to the induction of catabolic pathways which break down the novel fatty acid, i.e. the plant recognizes the "strange" fatty acid and, far from tolerating it, may even actively eliminate it from the seed oil. It is likely that, in the future, transgenic oil crops and newly domesticated oil crops will both be developed in order to provide the increased amount and diversity of oils which will be required for both edible and industrial use. It is important that we recognize that both approaches have both positive and negative points. It will be a combination of these two strategies that is most likely to supply the increasing demands for plant oils in the 21st century and beyond.ant oils in the 21st century and beyond.

• Journal of Animal Science and Technology
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• v.52 no.3
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• pp.167-174
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• 2010

The objectives of this study were to quantify the combination values of the principal components and factors calculated using body measurements of Hanwoo (Korean Cattle) and estimate their heritabilities. The technique of multivariate analysis was used to reduce a large number of variables to a smaller number of new variables and characterize cattle according to body shape. The analyses were performed using 1,979 cattle at 12 months of age and 936 cattle at 24 months of age. The data for the analyses was obtained from progeny tests performed on Korean Cattle for 6 years from 2003 to 2008. The phenotypic correlations among these traits were estimated to range from 0.32 to 0.90 at 12 months of age and from 0.21 to 0.82 at 24 months of age. The first principal components (PC1s) indicated a weighed average of overall body measurements, accounting for 99.91% of the total variation for both periods of test. The two first PCs had positive coefficients for all body measurements. The major sources of PC, such as chest girth (CG), body length (BL), rump height (RH), and wither height (WH) were similar for both test periods. The heritabilities for PC1, the first factor score (FS1), and the second factor score (FS2) were estimated by multivariate REML method. The estimated heritabilities for PC1, FS1, and FS2 were 0.33, 0.38, and 0.40, respectively, at 12 months of age and 0.26, 0.76, and 0.58 at 24 months of age. Further studies are needed to determine whether the heritabilities of FS1 and FS2 at 24 months of age were overestimated.

• Journal of Microbiology and Biotechnology
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• v.26 no.11
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• pp.1891-1907
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• 2016

Yeasts that are present in marine environments have evolved to survive hostile environments that are characterized by high exogenous salt content, high concentrations of inhibitory compounds, and low soluble carbon and nitrogen levels. Therefore, yeasts isolated from marine environments could have interesting characteristics for industrial applications. However, the application of marine yeast in research or industry is currently very limited owing to the lack of a suitable isolation method. Current methods for isolation suffer from fungal interference and/or low number of yeast isolates. In this paper, an efficient and non-laborious isolation method has been developed and successfully isolated large numbers of yeasts without bacterial or fungal growth. The new method includes a three-cycle enrichment step followed by an isolation step and a confirmation step. Using this method, 116 marine yeast strains were isolated from 14 marine samples collected in the UK, Egypt, and the USA. These strains were further evaluated for the utilization of fermentable sugars (glucose, xylose, mannitol, and galactose) using a phenotypic microarray assay. Seventeen strains with higher sugar utilization capacity than the reference terrestrial yeast Saccharomyces cerevisiae NCYC 2592 were selected for identification by sequencing of the ITS and D1/D2 domains. These strains belonged to six species: S. cerevisiae, Candida tropicalis, Candida viswanathii, Wickerhamomyces anomalus, Candida glabrata, and Pichia kudriavzevii. The ability of these strains for improved sugar utilization using seawater-based media was confirmed and, therefore, they could potentially be utilized in fermentations using marine biomass in seawater media, particularly for the production of bioethanol and other biochemical products.

• Genomics & Informatics
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• v.12 no.4
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• pp.187-194
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• 2014

Metabolic syndrome (METS) is a disorder of energy utilization and storage and increases the risk of developing cardiovascular disease and diabetes. To identify the genetic risk factors of METS, we carried out a genome-wide association study (GWAS) for 2,657 cases and 5,917 controls in Korean populations. As a result, we could identify 2 single nucleotide polymorphisms (SNPs) with genome-wide significance level p-values (< $5{\times}10^{-8}$), 8 SNPs with genome-wide suggestive p-values ($5{\times}10^{-8}{\leq}$ p < $1{\times}10^{-5}$), and 2 SNPs of more functional variants with borderline p-values ($5{\times}10^{-5}{\leq}$ p < $1{\times}10^{-4}$). On the other hand, the multiple correction criteria of conventional GWASs exclude false-positive loci, but simultaneously, they discard many true-positive loci. To reconsider the discarded true-positive loci, we attempted to include the functional variants (nonsynonymous SNPs [nsSNPs] and expression quantitative trait loci [eQTL]) among the top 5,000 SNPs based on the proportion of phenotypic variance explained by genotypic variance. In total, 159 eQTLs and 18 nsSNPs were presented in the top 5,000 SNPs. Although they should be replicated in other independent populations, 6 eQTLs and 2 nsSNP loci were located in the molecular pathways of LPL, APOA5, and CHRM2, which were the significant or suggestive loci in the METS GWAS. Conclusively, our approach using the conventional GWAS, reconsidering functional variants and pathway-based interpretation, suggests a useful method to understand the GWAS results of complex traits and can be expanded in other genomewide association studies.

• Genomics & Informatics
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• v.12 no.4
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• pp.181-186
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• 2014

Genome-wide association studies have proven the highly polygenic architecture of complex diseases or traits; therefore, single-locus-based methods are usually unable to detect all involved loci, especially when individual loci exert small effects. Moreover, the majority of associated single-nucleotide polymorphisms resides in non-coding regions, making it difficult to understand their phenotypic contribution. In this work, we studied epistatic interactions associated with three common diseases using Korea Association Resource (KARE) data: type 2 diabetes mellitus (DM), hypertension (HT), and coronary artery disease (CAD). We showed that epistatic single-nucleotide polymorphisms (SNPs) were enriched in enhancers, as well as in DNase I footprints (the Encyclopedia of DNA Elements [ENCODE] Project Consortium 2012), which suggested that the disruption of the regulatory regions where transcription factors bind may be involved in the disease mechanism. Accordingly, to identify the genes affected by the SNPs, we employed whole-genome multiple-cell-type enhancer data which discovered using DNase I profiles and Cap Analysis Gene Expression (CAGE). Assigned genes were significantly enriched in known disease associated gene sets, which were explored based on the literature, suggesting that this approach is useful for detecting relevant affected genes. In our knowledge-based epistatic network, the three diseases share many associated genes and are also closely related with each other through many epistatic interactions. These findings elucidate the genetic basis of the close relationship between DM, HT, and CAD.