• Title/Summary/Keyword: Genetic Approach

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Genetic Diversity of Polydora haswelli (Polychaeta, Spionidae) in Korean Shellfish using cox1 Marker (cox1 분자마커를 이용한 한국산 패류 천공성 다모류 Polydora haswelli (Polychaeta, Spionidae) 유전자 다양성 발굴)

  • Lee, Soon Jeong;Kim, Seung Min;Kwon, Mun Gyeong;Lee, Sang-Rae
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.54 no.5
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    • pp.685-690
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    • 2021
  • Harmful shell-boring species of the genus Polydora (Polychaeta: Spionidae) were frequently reported from commercially important mollusk species in Korea, Japan and China. The traditional approach based on the morphological characteristics showed limitations for species discrimination among shell-boring species. Therefore, DNA barcoding was adopted to identify Polydora species using molecular markers. Two Polydora species (P. haswelli and P. hoplura) in abalone shells were reported from our previous molecular phylogenetic study. In this study, we additionally reported the presence of shell-boring Polydora haswelli in commercially sold shellfish. The taxon-specific cox1 marker used in this study successfully allowed the isolation of P. haswelli from cockle Scapharca subcrenata, mussel Mytilus galloprovincialis, oyster Crassostrea gigas and scallop Argopecten irradians. Polydora hoplura was not found in these shellfish species. The genetic variations were found on the intraspecific level of P. haswelli and the same genotype was also detected in different shellfish species. This result can provide information on a new host and accurate parasitic Polydora species. Moreover, this report can be used as the biodiversity data of Polydora species on the invasion and transition of harmful Polydora species in mollusk aquaculture farms.

The Development and Selection of SSR Markers for Identification of Peanut (Arachis hypogaea L.) Varieties in Korea

  • Han, Sang-Ik;Bae, Suk-Bok;Ha, Tae Joung;Lee, Myong-Hee;Jang, Ki-Chang;Seo, Woo-Duck;Park, Geum-Yong;Kang, Hang-Won
    • Korean Journal of Breeding Science
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    • v.43 no.2
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    • pp.133-138
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    • 2011
  • The groundnut or cultivated peanut (Arachis hypogaea L.) in Korea consists of 36 domestic varieties which have been developed and registered as cultivars for the public during last 25 years. To screen and identify of Korean peanut varieties and genetic resources, we present a simple and reliable method. A methodology based on simple sequence repeat (SSR) markers developed and widely used for prominent gene identification and variety discrimination. For identification of those 36 Korean peanut varieties, 238 unique peanut SSR markers were selected from some previously reported results, synthesized and used for polymerase chain reaction (PCR). Data were taken through acryl amide gel electrophoresis and changed into proper formats for application of data mining analysis using Biomine (all-in-one functional genomics data mining program). Consequently, twelve SSR primers were investigated and revealed the differences between those 36 varieties. These primer pairs amplified 27 alleles with an average of 2.3 allele per primer pair. In addition, those results showed genetic relationship by classification method within 36 varieties. The approach described here could be applied to monitoring of our varieties and adapting to peanut breeding program.

Evolutionary Computation-based Hybird Clustring Technique for Manufacuring Time Series Data (제조 시계열 데이터를 위한 진화 연산 기반의 하이브리드 클러스터링 기법)

  • Oh, Sanghoun;Ahn, Chang Wook
    • Smart Media Journal
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    • v.10 no.3
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    • pp.23-30
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    • 2021
  • Although the manufacturing time series data clustering technique is an important grouping solution in the field of detecting and improving manufacturing large data-based equipment and process defects, it has a disadvantage of low accuracy when applying the existing static data target clustering technique to time series data. In this paper, an evolutionary computation-based time series cluster analysis approach is presented to improve the coherence of existing clustering techniques. To this end, first, the image shape resulting from the manufacturing process is converted into one-dimensional time series data using linear scanning, and the optimal sub-clusters for hierarchical cluster analysis and split cluster analysis are derived based on the Pearson distance metric as the target of the transformation data. Finally, by using a genetic algorithm, an optimal cluster combination with minimal similarity is derived for the two cluster analysis results. And the performance superiority of the proposed clustering is verified by comparing the performance with the existing clustering technique for the actual manufacturing process image.

Structural system identification by measurement error-minimization observability method using multiple static loading cases

  • Lei, Jun;Lozano-Galant, Jose Antonio;Xu, Dong;Zhang, Feng-Liang;Turmo, Jose
    • Smart Structures and Systems
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    • v.30 no.4
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    • pp.339-351
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    • 2022
  • Evaluating the current condition of existing structures is of primary importance for economic and safety reasons. This can be addressed by Structural System Identification (SSI). A reliable static SSI depends on well-designed sensor configuration and loading cases, as well as efficient parameter estimation algorithms. Static SSI by the Measurement Error-Minimizing Observability Method (MEMOM) is a model-based deterministic static SSI method that could estimate structural parameters from static responses. In the current state of the art, this method is only applicable when structures are subjected to one loading case. This might lead to lack of information in some local regions of the structure (such as the null curvatures zones). To address this issue, the SSI by MEMOM using multiple loading cases is proposed in this work. Observability equations obtained from different loading cases are concatenated simultaneously and an optimization procedure is introduced to obtain the estimations by minimizing the discrepancy between the predicted response and the measured one. In addition, a Genetic-Algorithm (GA)-based Optimal Sensor Placement (OSP) method is proposed to tackle the OSP problem under multiple static loading cases for the very first time. In this approach, the Fisher Information Matrix (FIM)'s determinant is used as the metric of the goodness of sensor configurations. The numerical examples of a 3-span continuous bridge and a 13-story frame, are analyzed to validate the applicability of the extended SSI by MEMOM and the GA-based OSP method.

Genome-wide association study for the free amino acid and nucleotide components of breast meat in an F2 crossbred chicken population

  • Minjun Kim;Eunjin Cho;Jean Pierre Munyaneza;Thisarani Kalhari Ediriweera;Jihye Cha;Daehyeok Jin;Sunghyun Cho;Jun Heon Lee
    • Journal of Animal Science and Technology
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    • v.65 no.1
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    • pp.57-68
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    • 2023
  • Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat. Measurements of FAA and NT components were recorded at the age of 10 weeks from 764 and 767 birds, respectively, using a White leghorn and Yeonsan ogye crossbred F2 chicken population. For genotyping, we used 60K Illumina single-nucleotide polymorphism (SNP) chips. We found a total of nine significant SNPs for five FAA traits (arginine, glycine, lysine, threonine content, and the essential FAAs and one NT trait (inosine content), and six significant genomic regions were identified, including three regions shared among the essential FAAs, arginine, and inosine content traits. A list of potential candidate genes in significant genomic regions was detected, including the KCNRG, KCNIP4, HOXA3, THSD7B, and MMUT genes. The essential FAAs had significant gene regions the same as arginine. The genes related to arginine content were involved in nitric oxide metabolism, while the inosine content was possibly affected by insulin activity. Moreover, the threonine content could be related to methylmalonyl-CoA mutase. The genes and SNPs identified in this study might be useful markers in chicken selection and breeding for chicken meat flavor.

The Prediction Ability of Genomic Selection in the Wheat Core Collection

  • Yuna Kang;Changsoo Kim
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2022.10a
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    • pp.235-235
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    • 2022
  • Genome selection is a promising tool for plant and animal breeding, which uses genome-wide molecular marker data to capture large and small effect quantitative trait loci and predict the genetic value of selection candidates. Genomic selection has been shown previously to have higher prediction accuracies than conventional marker-assisted selection (MAS) for quantitative traits. In this study, the prediction accuracy of 10 agricultural traits in the wheat core group with 567 points was compared. We used a cross-validation approach to train and validate prediction accuracy to evaluate the effects of training population size and training model.As for the prediction accuracy according to the model, the prediction accuracy of 0.4 or more was evaluated except for the SVN model among the 6 models (GBLUP, LASSO, BayseA, RKHS, SVN, RF) used in most all traits. For traits such as days to heading and days to maturity, the prediction accuracy was very high, over 0.8. As for the prediction accuracy according to the training group, the prediction accuracy increased as the number of training groups increased in all traits. It was confirmed that the prediction accuracy was different in the training population according to the genetic composition regardless of the number. All training models were verified through 5-fold cross-validation. To verify the prediction ability of the training population of the wheat core collection, we compared the actual phenotype and genomic estimated breeding value using 35 breeding population. In fact, out of 10 individuals with the fastest days to heading, 5 individuals were selected through genomic selection, and 6 individuals were selected through genomic selection out of the 10 individuals with the slowest days to heading. Therefore, we confirmed the possibility of selecting individuals according to traits with only the genotype for a shorter period of time through genomic selection.

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Genome-wide association studies to identify quantitative trait loci and positional candidate genes affecting meat quality-related traits in pigs

  • Jae-Bong Lee;Ji-Hoon Lim;Hee-Bok Park
    • Journal of Animal Science and Technology
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    • v.65 no.6
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    • pp.1194-1204
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    • 2023
  • Meat quality comprises a set of key traits such as pH, meat color, water-holding capacity, tenderness and marbling. These traits are complex because they are affected by multiple genetic and environmental factors. The aim of this study was to investigate the molecular genetic basis underlying nine meat quality-related traits in a Yorkshire pig population using a genome-wide association study (GWAS) and subsequent biological pathway analysis. In total, 45,926 single nucleotide polymorphism (SNP) markers from 543 pigs were selected for the GWAS after quality control. Data were analyzed using a genome-wide efficient mixed model association (GEMMA) method. This linear mixed model-based approach identified two quantitative trait loci (QTLs) for meat color (b*) on chromosome 2 (SSC2) and one QTL for shear force on chromosome 8 (SSC8). These QTLs acted additively on the two phenotypes and explained 3.92%-4.57% of the phenotypic variance of the traits of interest. The genes encoding HAUS8 on SSC2 and an lncRNA on SSC8 were identified as positional candidate genes for these QTLs. The results of the biological pathway analysis revealed that positional candidate genes for meat color (b*) were enriched in pathways related to muscle development, muscle growth, intramuscular adipocyte differentiation, and lipid accumulation in muscle, whereas positional candidate genes for shear force were overrepresented in pathways related to cell growth, cell differentiation, and fatty acids synthesis. Further verification of these identified SNPs and genes in other independent populations could provide valuable information for understanding the variations in pork quality-related traits.

Exploring Efficient Solutions for the 0/1 Knapsack Problem

  • Dalal M. Althawadi;Sara Aldossary;Aryam Alnemari;Malak Alghamdi;Fatema Alqahtani;Atta-ur Rahman;Aghiad Bakry;Sghaier Chabani
    • International Journal of Computer Science & Network Security
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    • v.24 no.2
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    • pp.15-24
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    • 2024
  • One of the most significant issues in combinatorial optimization is the classical NP-complete conundrum known as the 0/1 Knapsack Problem. This study delves deeply into the investigation of practical solutions, emphasizing two classic algorithmic paradigms, brute force, and dynamic programming, along with the metaheuristic and nature-inspired family algorithm known as the Genetic Algorithm (GA). The research begins with a thorough analysis of the dynamic programming technique, utilizing its ability to handle overlapping subproblems and an ideal substructure. We evaluate the benefits of dynamic programming in the context of the 0/1 Knapsack Problem by carefully dissecting its nuances in contrast to GA. Simultaneously, the study examines the brute force algorithm, a simple yet comprehensive method compared to Branch & Bound. This strategy entails investigating every potential combination, offering a starting point for comparison with more advanced techniques. The paper explores the computational complexity of the brute force approach, highlighting its limitations and usefulness in resolving the 0/1 Knapsack Problem in contrast to the set above of algorithms.

Evaluation of genetic differentiation and search for candidate genes for reproductive traits in pigs

  • Elena Romanets;Siroj Bakoev;Timofey Romanets;Maria Kolosova;Anatoly Kolosov;Faridun Bakoev;Olga Tretiakova;Alexander Usatov;Lyubov Getmantseva
    • 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 Fst (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.

Development of Intelligent ATP System Using Genetic Algorithm (유전 알고리듬을 적용한 지능형 ATP 시스템 개발)

  • Kim, Tai-Young
    • Journal of Intelligence and Information Systems
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    • v.16 no.4
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    • pp.131-145
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    • 2010
  • The framework for making a coordinated decision for large-scale facilities has become an important issue in supply chain(SC) management research. The competitive business environment requires companies to continuously search for the ways to achieve high efficiency and lower operational costs. In the areas of production/distribution planning, many researchers and practitioners have developedand evaluated the deterministic models to coordinate important and interrelated logistic decisions such as capacity management, inventory allocation, and vehicle routing. They initially have investigated the various process of SC separately and later become more interested in such problems encompassing the whole SC system. The accurate quotation of ATP(Available-To-Promise) plays a very important role in enhancing customer satisfaction and fill rate maximization. The complexity for intelligent manufacturing system, which includes all the linkages among procurement, production, and distribution, makes the accurate quotation of ATP be a quite difficult job. In addition to, many researchers assumed ATP model with integer time. However, in industry practices, integer times are very rare and the model developed using integer times is therefore approximating the real system. Various alternative models for an ATP system with time lags have been developed and evaluated. In most cases, these models have assumed that the time lags are integer multiples of a unit time grid. However, integer time lags are very rare in practices, and therefore models developed using integer time lags only approximate real systems. The differences occurring by this approximation frequently result in significant accuracy degradations. To introduce the ATP model with time lags, we first introduce the dynamic production function. Hackman and Leachman's dynamic production function in initiated research directly related to the topic of this paper. They propose a modeling framework for a system with non-integer time lags and show how to apply the framework to a variety of systems including continues time series, manufacturing resource planning and critical path method. Their formulation requires no additional variables or constraints and is capable of representing real world systems more accurately. Previously, to cope with non-integer time lags, they usually model a concerned system either by rounding lags to the nearest integers or by subdividing the time grid to make the lags become integer multiples of the grid. But each approach has a critical weakness: the first approach underestimates, potentially leading to infeasibilities or overestimates lead times, potentially resulting in excessive work-inprocesses. The second approach drastically inflates the problem size. We consider an optimized ATP system with non-integer time lag in supply chain management. We focus on a worldwide headquarter, distribution centers, and manufacturing facilities are globally networked. We develop a mixed integer programming(MIP) model for ATP process, which has the definition of required data flow. The illustrative ATP module shows the proposed system is largely affected inSCM. The system we are concerned is composed of a multiple production facility with multiple products, multiple distribution centers and multiple customers. For the system, we consider an ATP scheduling and capacity allocationproblem. In this study, we proposed the model for the ATP system in SCM using the dynamic production function considering the non-integer time lags. The model is developed under the framework suitable for the non-integer lags and, therefore, is more accurate than the models we usually encounter. We developed intelligent ATP System for this model using genetic algorithm. We focus on a capacitated production planning and capacity allocation problem, develop a mixed integer programming model, and propose an efficient heuristic procedure using an evolutionary system to solve it efficiently. This method makes it possible for the population to reach the approximate solution easily. Moreover, we designed and utilized a representation scheme that allows the proposed models to represent real variables. The proposed regeneration procedures, which evaluate each infeasible chromosome, makes the solutions converge to the optimum quickly.