• Horticultural Science & Technology
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• v.35 no.2
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• pp.232-242
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• 2017

The goal of marker-assisted backcrossing (MAB) is to significantly reduce the number of breeding generations required by using genome-based molecular markers to select for a particular trait; however, MAB systems have only been developed for a few vegetable crops to date. Among the types of molecular markers, SNPs (single-nucleotide polymorphisms) are primarily used in the analysis of genetic diversity due to their abundance throughout most genomes. To develop a MAB system in Chinese cabbage, a high-throughput (HT) marker system was used, based on a previously developed set of 468 SNP probes (BraMAB1, Brassica Marker Assisted Backcrossing SNP 1). We selected a broad-spectrum TuMV (Turnip mosaic virus) resistance (trs) Chinese cabbage line (SB22) as a donor plant, constructing a $BC_1F_1$ population by crossing it with the TuMV-susceptible 12mo-682-1 elite line. Foreground selection was performed using the previously developed trsSCAR marker. Background selection was performed using 119 SNP markers that showed clear polymorphism between donor and recipient plants. The background genome recovery rate (% recurrent parent genome recovery; RPG) was good, with three of 75 $BC_1F_1$ plants showing a high RPG rate of over 80%. The background genotyping result and the phenotypic similarity between the recurrent parent and $BC_1F_1$ showed a correlation. The plant with the highest RPG recovery rate was backcrossed to construct the $BC_2F_1$ population. Foreground selection and background selection were performed using 169 $BC_2F_1$ plants. This study shows that, using MAB, we can recover over 90% of the background genome in only two generations, highlighting the MAB system using HT markers as a highly efficient Brassica rapa backcross breeding system. This is the first report of the application of a SNP marker set to the background selection of Chinese cabbage using HT SNP genotyping technology.

• 한국전산유체공학회:학술대회논문집
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• 2009.11a
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• pp.1-1
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• 2009

In this presentation, I talk about various fluid simulation methods that have been developed for computer graphics special effects since 1996. They are all based on CFD but sacrifice physical reality for visual plausability and time. But as the speed of computer increases rapidly and the capability of GPU (graphics processing unit) improves, methods for more physical realism have been tried. In this talk, I will focus on four aspects of fluid simulation methods for computer graphics: (1) particle level-set methods, (2) particle-based simulation, (3) methods for exact satisfaction of incompressibility constraint, and (4) GPU-based simulation. (1) Particle level-set methods evolve the surface of fluid by means of the zero-level set and a band of massless marker particles on both sides of it. The evolution of the zero-level set captures the surface in an approximate manner and the evolution of marker particles captures the fine details of the surface, and the zero-level set is modified based on the particle positions in each step of evolution. (2) Recently the particle-based Lagrangian approach to fluid simulation gains some popularity, because it automatically respects mass conservation and the difficulty of tracking the surface geometry has been somewhat addressed. (3) Until recently fluid simulation algorithm was dominated by approximate fractional step methods. They split the Navier-Stoke equation into two, so that the first one solves the equation without considering the incompressibility constraint and the second finds the pressure which satisfies the constraint. In this approach, the first step introduces error inevitably, producing numerical diffusion in solution. But recently exact fractional step methods without error have been developed by fluid mechanics scholars), and another method was introduced which satisfies the incompressibility constraint by formulating fluid in terms of vorticity field rather than velocity field (by computer graphics scholars). (4) Finally, I want to mention GPU implementation of fluid simulation, which takes advantage of the fact that discrete fluid equations can be solved in parallel.

• Mycobiology
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• v.32 no.1
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• pp.6-10
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• 2004

White and brown strains of Flammulina velutipes were inter-crossed. All $F_1$ showed light-brown fruitbody, suggesting that a gene for the brown fruitbody was incompletely dominant against the white one. And backcross experiment showed that more than two genes were involved in color determination. To isolate a molecular marker linked to fruitbody color, a set of primers was designed from a sequence of clones derived by a bulked segregant analysis. These markers showed a specific band which co-segregated with brown fruitbody forming strains.

• Mycobiology
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• v.47 no.4
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• pp.466-472
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• 2019

For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders' rights.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1232-1246
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• 2021

Recently, the cattle genome sequence has been completed, followed by developing a commercial single nucleotide polymorphism (SNP) chip panel in the animal genome industry. In order to increase statistical power for detecting quantitative trait locus (QTL), a number of animals should be genotyped. However, a high-density chip for many animals would be increasing the genotyping cost. Therefore, statistical inference of genotype imputation (low-density chip to high-density) will be useful in the animal industry. The purpose of this study is to investigate the effect of the reference population size and marker density on the imputation accuracy and to suggest the appropriate number of reference population sets for the imputation in Hanwoo cattle. A total of 3,821 Hanwoo cattle were divided into reference and validation populations. The reference sets consisted of 50k (38,916) marker data and different population sizes (500, 1,000, 1,500, 2,000, and 3,600). The validation sets consisted of four validation sets (Total 889) and the different marker density (5k [5,000], 10k [10,000], and 15k [15,000]). The accuracy of imputation was calculated by direct comparison of the true genotype and the imputed genotype. In conclusion, when the lowest marker density (5k) was used in the validation set, according to the reference population size, the imputation accuracy was 0.793 to 0.929. On the other hand, when the highest marker density (15k), according to the reference population size, the imputation accuracy was 0.904 to 0.967. Moreover, the reference population size should be more than 1,000 to obtain at least 88% imputation accuracy in Hanwoo cattle.

• Journal of Korea Multimedia Society
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• v.21 no.12
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• pp.1396-1406
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• 2018

Lane detection is a key function in developing autonomous vehicle technology. In this paper, we propose a lane marker detection algorithm robust to environmental variation targeting low cost embedded computing devices. The proposed algorithm consists of two phases: initialization phase which is slow but has relatively higher accuracy; and the tracking phase which is fast and has the reliable performance in a limited condition. The initialization phase detects lane markers using a set of filters utilizing the various features of lane markers. The tracking phase uses Kalman filter to accelerate the lane marker detection processing. In a tracking phase, we measure the reliability of the detection results and switch it to initialization phase if the confidence level becomes below a threshold. By combining the initialization and tracking phases we achieved high accuracy and acceptable computing speed even under a low cost computing resources in which we cannot use the computing intensive algorithm such as deep learning approach. Experimental results show that the detection accuracy is about 95% on average and the processing speed is about 20 frames per second with Raspberry Pi 3 which is low cost device.

• Radiation Oncology Journal
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• v.22 no.1
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• pp.69-75
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• 2004

Purpose : A new fiduciary plate and orientation marker have been devised to assist the quality assurance (QA) procedures for port films in radiation therapy department. The plate is used in conjunction with the film/cassette combination during weekly QA procedures, at Seoul National University Hospital (SNUH), in order to verify treatment fields in high radiation therapy. Materials and Methods : A new fiduciary plate was fabricated using an acrylic plate, cerrobend, standard blocking tray and mercury. The acrylic plate had the dimension of $1{\times}25{\times}25$ cm, with two fiduciary markers. The plate was rigidly attached onto the standard blocking tray, thus making it easier to set the fiduciary plate to the center on the radiation field on the linear accelerator. The plate had two 2-mm vertical and horizontal lines, with the minor scales in 2-cm steps. The orientation marker was a small mercury filled disk, which was inserted into the plate. Results : The geometrical structure of the lines in the plate makes it easier to correlate two different images between the simulation and port films. The marker clearly indicated the orientation of the film, for example, the anterior, posterior, left, right and various oblique orientations, without the placement of a conventional orientation marker. Also, the new orientation marker could easily be applied to the simulator by placing the small orientation marker onto the image intensifier or in front of the film/cassette holder. Conclusions : The new fiduciary plate appears to be useful in verifying the treatment fields, and the new orientation marker makes the film orientation simple, which is expected to lower the block fabrication errors.

• Horticultural Science & Technology
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• v.32 no.4
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• pp.535-543
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• 2014

Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang $F_1$-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.

• Journal of the Society of Naval Architects of Korea
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• v.51 no.1
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• pp.58-66
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• 2014

Numerical simulations for the flows containing free surface remain difficult problems because the drastic differences of physical properties of water and air, The difference of densities makes the solution instable in particular. For the stabilities of the solutions, the most typical methods to simulate free surface flows, such as Volume Of Fluid(VOF) and Level-Set(LS) methods, impose transient zones where the physical prosperities are continuously distributed. The thickness of the transient zone is the source of the numerical errors. The other side, marker-density method does not use such a transient zone. In the traditional marker-density method, however, the air velocities of free surface cells are extrapolated from the water velocity, and the pressures on the free surface are extrapolated from the air pressures for the stability of the solution. In this study, the marker-density method is modified for the decrease of such numerical errors. That is, the pressure on the free surface is determined to coincide with the pressure gradient terms of the governing equations, and the velocity of free surface cells are calculated with the governing equations. Two-dimensional steady spilling breakers behind of a submersed hydrofoil and three-dimensional spilling breaker near a wedge shaped ship model are simulated using INHAWAVE-II including the modified marker-density(MMD) method. The results are compared with the results of Fluent V6.3 including VOF method and several published research results.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2013.05a
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• pp.1419-1420
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• 2013