• Molecules and Cells
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• v.42 no.2
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• Korean Journal of Plant Resources
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• v.36 no.3
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• pp.237-255
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• 2023

Variations in phenotypic traits are important for onion genetic improvement. The aim of this study was to identify the phenotypic traits of temporary genetic resources and the best accessions for the development of onion breeding programs. Sixteen phenotypic traits of 79 onion accessions were studied. The descriptive statistics of phenotypic traits exhibited a high variation in onion accessions. Among the 79 evaluated accessions, 64.55% had a large bulb neck width and 44.30% had a circular bulb shape. Principal component analysis showed that six principal components (PCs) accounted for 72.65% of the total variation. The main factors contributing to PC1 were bulb weight, equatorial and bulb polar diameters, plant height, and degree of splitting into bulblets, whereas those contributing to PC2 were the bulb color of the epidermal cells of the fleshy scales and color of the dry skin on the bulb. The accessions were classified into three groups-clusters 1, 2, and 3. Cluster 2 accessions were the most suitable for selecting large and circular bulb-shaped onion cultivars. The phenotypic variation observed in this study may help to select potential accessions for breeding new onion cultivars.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.11
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• pp.102-108
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• 2020

This study was conducted to investigate the genetic diversity and genetic taxonomic relationships between Korean native black goat (KNBG) populations and crossbred goats. The 45,658 common single nucleotide polymorphisms present in the KNBG strain and crossbred goat were used for the analysis. The expected and observed heterozygosity (which can be indicators of genetic diversity) were in the order of crossbred, Gyeongsang National University, Jangsu, then the Tongyeong strains. The variance component represents the degree of genetic diversity between groups. The highest variance (19.98 %) was between the Dangjin and Gyeongsang National University strains. The lowest variance (8.87 %) was between the Jangsu and Tongyeong strains. In addition, the genetic distance between the populations showed that Jangsu and Tongyeong formed one branch (they were very similar genetically). The Dangjin and the Gyeongsang National University strains appeared to form a second branch. Furthermore, the crossbred formed one branch with the Dangjin and the Gyeongsang National University strains. Therefore, the results of this study can be used as basic data to reduce unnecessary inbreeding and genetic resource flow between the KNBG populations. The basic data indicates the uniqueness of the genetic resources of the domestic lineage. These findings provide a basis for differentiating KNBG and Crossbred goats to use to improve the desirable characteristics of this species.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.9
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• pp.1245-1251
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• 2006

This study was carried out to determine the genetic relationships among seven west African goat breeds : Casamance Goat (Kolda, Senegal), Labe Goat (Fouta Djallon, Guinea), three Sahel Goat (Djoloff, Senegal ; Maradi, Niger; Gorgol, Mauritania) red Sokoto Goat (Maradi, Niger) and Guera goat (Atar, Mauritania).The polymorphism of six microsatellites and the ${\alpha}_{s1}$-casein locus was analysed. The six microsatellite loci were polymorphic with a mean number of alleles ranging from 2.71 to 4.0. At the ${\alpha}_{s1}$-casein locus, A and B were the most frequent alleles, which are known to be associated with a high level of protein synthesis. A neighbour-joining tree and a Principal Component Analysis were performed and the reliability of both methods was tested. Our study shows that the genetic relationships among the breeds analysed correspond to their geographical distribution and in addition, that the Labe Goat is strongly separated from the other breeds. Among the seven markers used, four have an effect on the distribution of breeds while three seem to be non-informative.

• Interdisciplinary Bio Central
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• v.6 no.1
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• pp.1.1-1.6
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• 2014

A growing body of evidence shows that most psychological traits are polygenic, that is they involve the action of many genes with small effects. However, the study of selection has disproportionately been on one or a few genes and their associated sweep signals (rapid and large changes in frequency). If our goal is to study the evolution of psychological variables, such as intelligence, we need a model that explains the evolution of phenotypes governed by many common genetic variants. This study illustrates simple statistical tools to detect signals of recent polygenic selection: a) ANOVA can be used to reveal significant deviation from random distribution of allele frequencies across racial groups. b) Principal component analysis can be used as a tool for finding a factor that represents the strength of recent selection on a phenotype and the underlying genetic variation. c) Method of correlated vectors: the correlation between genetic frequencies and the average phenotypes of different populations is computed; then, the resulting correlation coefficients are correlated with the corresponding alleles' genome-wide significance. This provides a measure of how selection acted on genes with higher signal to noise ratio. Another related test is that alleles with large frequency differences between populations should have a higher genome-wide significance value than alleles with small frequency differences. This paper fruitfully employs these tools and shows that common genetic variants exhibit subtle frequency shifts and that these shifts predict phenotypic differences across populations.

• Journal of Plant Biotechnology
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• v.34 no.3
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• pp.201-205
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• 2007

To determine whether pattern recognition based on metabolite fingerprinting for whole cell extracts of higher plants is applied to discriminate plants genetically, leaf samples of eight cultivars of Catharanthus roseus were subjected to Fourier transform infrared spectroscopy (FT-IR). FT-IR fingerprint region data were analyzed by principal component analysis (PCA). Major peaks as biomarkers were identified as the most significant contributors to distinguish samples by using genetic programming. A hierarchical dendrogram based on the results from PCA separated the eight cultivars into two major groups in the same manner as the dendrograms based on genetic fingerprinting methods such as RAPD and AFLP. A slight difference between the dendrograms was found only in branching pattern within each subgroup. Therefore, we conclude that the hierarchical dendrogram based on PCA of the FT-IR data represents the most probable chemotaxonomical relationship between cultivars, which is in general agreement with the genetic relationship determined by conventional DNA fingerprinting methods.

• Journal of Ecology and Environment
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• v.35 no.4
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• pp.301-306
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• 2012

Determination of the minimum population size is an important component for the ex situ conservation of an endangered species. Here, we present the identification of collection strategies that most efficiently captured the genetic diversity of Brasenia schreberi J.F. Gmelin (water-shield) in natural populations from the mainland (MGC) and Jeju Island (JNS) of South Korea, using amplified fragment length polymorphism (AFLP) markers. A total of 313 and 383 polymorphic bands were detected in the MGC and JNS populations, respectively. All of the 140 sampled ramets were distinguishable by the presence of distinct AFLP phenotypes. According to the simulation of the individual sampling by maximization sampling, 25 and 28 individuals captured all of the genetic diversity in the MGC population (mainland of South Korea) and the JNS population (Jeju Island), respectively. The level of genetic diversity of the core collections was similar to the entire collection, indicating that the core collections very well represent the diversity of the entire collection. We therefore suggest a management unit of B. schreberi based on the genetic information for assessing the minimum population size for its ex situ conservation.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.4 no.3
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• pp.242-247
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• 2003

This paper deals with an optimal design methodology for an automatic transmission lever using a genetic algorithm. A component of an automatic transmission lever has been designed sequentially in the industry, but the study presents a new design method to consider the design parameters of components simultaneously. A genetic algorithm approach is described to determine a set of design parameters for an automatic transmission lever. We have attempted to model the design problem with the objective of minimizing the angle variation of detent spring subject to constraints such as modulus of elasticity of steel, geometry of shift pipe. and stiffness of spring. The proposed method can give the better design alternative.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.8
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• pp.1090-1094
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• 2015

The aim of the study was to select traits that may constitute a prospective criterion for breeding value prediction of young horses. The results of 1,232 starts of 894 four-, five-, six-, and seven-year-old horses, obtained during jumping championships for young horses which had not been evaluated in, alternative to championships, training centres were analyed. Nine traits were chosen of those recorded: ranking in the championship, elimination (y/n), conformation, rating of style on day one, two, and three, and penalty points on day one, two, and three of a championship. (Co)variance components were estimated via the Gibbs sampling procedure and adequate (co)variance component ratios were calculated. Statistical classifications were trait dependent but all fitted random additive genetic and permanent environment effects. It was found that such characteristics as penalty points and jumping style are potential indicators of jumping ability, and the genetic variability of the traits was within the range of 14% to 27%. Given the low genetic correlations between the conformation and other results achieved on the parkour, the relevance of assessment of conformation in four-years-old horses has been questioned.

• Journal of Genetic Medicine
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• v.6 no.2
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• pp.121-130
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• 2009

Medical Research Center, Seoul National University College of Medicine, Seoul, Korea To analyze a wide variety of polymorphisms in patients with endometriosis is important since this disease has a strong genetic component. Until now, more than 30 Korean studies have been performed in order to elucidate the possible role of specific polymorphisms in the susceptibility to endometriosis. The most meaningful polymorphisms in Korean patients with endometriosis came from studies investigating GSTM1, AhRR, ER-alpha, VEGF, AHSG, and TNF-alpha. However, following studies should be made to confirm the consistency of the data to have some implications in the prediction of endometriosis. In this review, we also present the future direction of the association studies in complex trait disease such as endometriosis.