68 results on '"Inchan Choi"'
Search Results
2. Optimal Planting Time for Summer Tomatoes (Lycopersicon esculentum Mill.) Cropping in Korea: Growth, Yield, and Photosynthetic Efficiency in a Semi-Closed Greenhouse
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Hyo Jun Bae, Seong-Hoon Kim, Yuseok Jeong, Sungjin Park, Kingsley Ochar, Youngsin Hong, Yun Am Seo, Baul Ko, Jeong Hyang Bae, Dong Soo Lee, and Inchan Choi
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cooling ,light use efficiency ,semi-closed greenhouse ,summer cropping ,tomato ,Botany ,QK1-989 - Abstract
In Korea, greenhouses are traditionally used for crop cultivation in the winter. However, due to diverse consumer demands, climate change, and advancements in agricultural technology, more farms are aiming for year-round production. Nonetheless, summer cropping poses challenges such as high temperatures, humidity from the monsoon season, and low light conditions, which make it difficult to grow crops. Therefore, this study aimed to determine the best planting time for summer tomato cultivation in a Korean semi-closed greenhouse that can be both air-conditioned and heated. The experiment was conducted in the Advanced Digital Greenhouse, built by the National Institute of Agricultural Sciences. The tomato seedlings were planted in April, May, and June 2022. Growth parameters such as stem diameter, flowering position, stem growth rate, and leaf shape index were measured, and harvesting was carried out once or twice weekly per treatment from 65 days to 265 days after planting. The light use efficiency and yield per unit area at each planting time was measured. Tomatoes planted in April showed a maximum of 42.9% higher light use efficiency for fruit production and a maximum of 33.3% higher yield. Furthermore, the growth form of the crops was closest to the reproductive growth type. Therefore, among April, May, and June, April is considered the most suitable planting time for summer cultivation, which is expected to contribute to reducing labor costs due to decreased workload and increasing farm income through increased yields. Future research should explore optimizing greenhouse microclimates and developing crop varieties tailored for summer cultivation to further enhance productivity and sustainability in year-round agricultural practices.
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- 2024
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3. Development of a Real-Time Vespa velutina Nest Detection and Notification System Using Artificial Intelligence in Drones
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Yuseok Jeong, Moon-Seok Jeon, Jaesu Lee, Seung-Hwa Yu, Su-bae Kim, Dongwon Kim, Kyoung-Chul Kim, Siyoung Lee, Chang-Woo Lee, and Inchan Choi
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artificial intelligence ,Vespa velutina nest detection ,unmanned aerial vehicle ,real-time kinematics ,long-term evolution ,YOLOv5 ,Motor vehicles. Aeronautics. Astronautics ,TL1-4050 - Abstract
Vespa velutina is an ecosystem disruptor that causes annual damage worth KRW 170 billion (USD 137 million) to the South Korean beekeeping industry. Due to its strong fertility and high-lying habitat, it is difficult to control. This study aimed to develop a system for the control of V. velutina nests using drones for detection and tracking the real-time location of the nests. Vespa velutina nest image data were acquired in Buan-gun and Wanju-gun (Jeollabuk-do), and artificial intelligence learning was conducted using YOLO-v5. Drone image resolutions of 640, 1280, 1920, and 3840 pixels were compared and analyzed. The 3840-pixel resolution model was selected, as it had no false detections for the verification image and showed the best detection performance, with a precision of 100%, recall of 92.5%, accuracy of 99.7%, and an F1 score of 96.1%. A computer (Jetson Xavier), real-time kinematics module, long-term evolution modem, and camera were installed on the drone to acquire real-time location data and images. Vespa velutina nest detection and location data were delivered to the user via artificial intelligence analysis. Utilizing a drone flight speed of 1 m/s and maintaining an altitude of 25 m, flight experiments were conducted near Gyeongcheon-myeon, Wanju-gun, Jeollabuk-do. A total of four V. velutina nests were successfully located. Further research is needed on the detection accuracy of artificial intelligence in relation to objects that require altitude-dependent variations in drone-assisted exploration. Moreover, the potential applicability of these research findings to diverse domains is of interest.
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- 2023
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4. Deep Learning-Based Portable Image Analysis System for Real-Time Detection of Vespa velutina
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Moon-Seok Jeon, Yuseok Jeong, Jaesu Lee, Seung-Hwa Yu, Su-bae Kim, Dongwon Kim, Kyoung-Chul Kim, Siyoung Lee, Chang-Woo Lee, and Inchan Choi
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honeybee decline ,Vespa velutina ,deep learning ,object detection ,real-time streaming protocol ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
Honeybees pollinate over 75% of the total food resources produced annually, and they produce valuable hive products, such as bee pollen, propolis, and royal jelly. However, species such as the Asian hornet (Vespa velutina) feed on more than 85% of honeybees, causing a decline in their population and considerable damage to beekeepers in Korea. To prevent damage to honeybees, a portable real-time monitoring system was developed that detects V. velutina individuals and notifies users of their presence. This system was designed with a focus on portability and ease of installation, as V. velutina can be found in various areas of apiary sites. To detect V. velutina, an improved convolutional neural network YOLOv5s was trained on 1960 high-resolution (3840×2160) image data. At the confidence threshold of ≥0.600 and intersection over the union of ≥0.500, the performance of the system in terms of detection accuracy, precision, recall, F1 score, and mean average precision was high. A distance-based performance comparison showed that the system was able to detect V. velutina individuals while monitoring three beehives. During a field test of monitoring three beehives, the system could detect 83.3% of V. velutina during their hunting activities and send alarms to registered mobile application users.
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- 2023
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5. From crop specific to variety specific in crop modeling for the smart farm: A case study with blueberry.
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Gyung Deok Han, Jeong Min Choi, Inchan Choi, Yoonha Kim, Seong Heo, and Yong Suk Chung
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Medicine ,Science - Abstract
Facility cultivation has been evolved from greenhouses to smart farms using artificial intelligence (AI) that simulates big data to maximize production. However, the big data for AI in smart farm is not studied well; the effect of differences among varieties within a crop remains unclear. Therefore, the response of two varieties of blueberry, 'Suziblue' and 'Star', to light was tested using SAPD meter in order to demonstrate the environmental responses could be different among varieties within the same species. The results showed that those two varieties had significant differences in SPAD values based on the leaf's position and time, whereas 'Star' did not. This indicates that the effect of light depends on the variety, which implies that other traits and other crops may show similar differences. These results are based on a simple experiment. However, it is enough to elucidate that it is extremely important to characterize responses to the environment not only for each crop but also for each variety to collect data for smart farming to increase accuracy for modeling; consequently, to maximize the efficiency of these facilities.
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- 2022
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6. Mutations in the microRNA172 binding site of SUPERNUMERARY BRACT (SNB) suppress internode elongation in rice
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Hyeonso Ji, Chang-deok Han, Gang-Seob Lee, Ki-Hong Jung, Do-Yu Kang, Jun Oh, Hyoja Oh, Kyeong-Seong Cheon, Song Lim Kim, Inchan Choi, Jeongho Baek, and Kyung-Hwan Kim
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Rice ,Internode elongation ,SNB ,microRNA172 ,Plant culture ,SB1-1110 - Abstract
Abstract Background Internode elongation is an important agronomic trait in rice that determines culm length, which is related to lodging, panicle exsertion, and biomass. sui4 (shortened uppermost internode 4) mutants show reduced internode length and a dwarf phenotype due to shortened internodes; the uppermost internode is particularly severely affected. The present study was performed to identify the molecular nature and function of the SUI4 gene during internode elongation. Results Our previous study showed that the SUI4 gene was mapped to a 1.1-Mb interval on chromosome 7 (Ji et al. 2014). In order to isolate the gene responsible for the sui4 phenotype, genomic DNA resequencing of sui4 mutants and wild-type plants and reciprocal transformation of wild-type and mutant alleles of the putative SUI4 gene was performed. The data revealed that the causative mutation of sui4 was a T to A nucleotide substitution at the microRNA172 binding site of Os07g0235800, and that SUI4 is a new allele of the previously reported gene SUPERNUMERARY BRACT (SNB), which affects flower structure. In order to understand the effect of this mutation on expression of the SUI4/SNB gene, SUI4/SNB native promoter-fuzed GUS transgenics were examined, along with qRT-PCR analysis at various developmental stages. In sui4 mutants, the SUI4/SNB gene was upregulated in the leaves, culms, and panicles, especially when internodes were elongated. In culms, SUI4/SNB was expressed in the nodes and the lower parts of elongating internodes. In order to further explore the molecular nature of SUI4/SNB during internode elongation, RNA-seq and qRT-PCR analysis were performed with RNAs from the culms of sui4 mutants and wild-type plants in the booting stage. The data showed that in sui4 mutants, genes deactivating bioactive gibberellins and cytokinin were upregulated while genes related to cell expansion and cell wall synthesis were downregulated. Conclusion In summary, this paper shows that interaction between SUI4/SNB and microRNA172 could determine internode elongation during the reproductive stage in rice plants. Due to a mutation at the microRNA172 binding site in sui4 mutants, the expression of SUI4/SNB was enhanced, which lowered the activities of cell expansion and cell wall synthesis and consequently resulted in shortened internodes.
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- 2019
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7. Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties
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Kyeong-Seong Cheon, Young-Min Jeong, Hyoja Oh, Jun Oh, Do-Yu Kang, Nyunhee Kim, Eungyeong Lee, Jeongho Baek, Song Lim Kim, Inchan Choi, In Sun Yoon, Kyung-Hwan Kim, Yong Jae Won, Young-il Cho, Jung-Heon Han, and Hyeonso Ji
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temperate japonica rice ,SNP ,high-throughput genotyping ,KASP ,Botany ,QK1-989 - Abstract
Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.
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- 2020
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8. High Throughput Phenotyping for Various Traits on Soybean Seeds Using Image Analysis
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JeongHo BAEK, Eungyeong Lee, Nyunhee Kim, Song Lim Kim, Inchan Choi, Hyeonso Ji, Yong Suk Chung, Man-Soo Choi, Jung-Kyung Moon, and Kyung-Hwan Kim
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rgb image ,seed morphology ,seed color ,seed traits ,breeding ,Chemical technology ,TP1-1185 - Abstract
Data phenotyping traits on soybean seeds such as shape and color has been obscure because it is difficult to define them clearly. Further, it takes too much time and effort to have sufficient number of samplings especially length and width. These difficulties prevented seed morphology to be incorporated into efficient breeding program. Here, we propose methods for an image acquisition, a data processing, and analysis for the morphology and color of soybean seeds by high-throughput method using images analysis. As results, quantitative values for colors and various types of morphological traits could be screened to create a standard for subsequent evaluation of the genotype. Phenotyping method in the current study could define the morphology and color of soybean seeds in highly accurate and reliable manner. Further, this method enables the measurement and analysis of large amounts of plant seed phenotype data in a short time, which was not possible before. Fast and precise phenotype data obtained here may facilitate Genome Wide Association Study for the gene function analysis as well as for development of the elite varieties having desirable seed traits.
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- 2020
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9. RNA-Seq of Plant-Parasitic Nematode Meloidogyne incognita at Various Stages of Its Development
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Inchan Choi, Parthiban Subramanian, Donghwan Shim, Byung-Ju Oh, and Bum-Soo Hahn
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plant parasite ,root-knot nematode ,developmental stages ,RNA-Seq ,transcriptome ,Genetics ,QH426-470 - Published
- 2017
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10. New Parameters for Seedling Vigor Developed via Phenomics
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Song Lim Kim, Yong Suk Chung, Hyeonso Ji, Hongseok Lee, Inchan Choi, Nyunhee Kim, Eungyeong Lee, Jun Oh, Do-Yu Kang, JeongHo BAEK, Gang-Seob Lee, Taek-Ryoun Kwon, and Kyung-Hwan Kim
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plant phenomics ,recombinant inbred line (RIL) ,rice ,initial growth ,QTL ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
Early seedling establishment in rice (Oryza sativa L.), which is measured by primary/secondary tiller, shoot length, biomass, root-related traits, and leaf area index, is an important trait because it helps to compete for light, air, and water for better tolerating various abiotic stresses. Consequently, it can affect the yield. However, there are not many research studies on this subject. Furthermore, previous studies have only measured the target traits once. However, this does not reflect the variation of growth rate during the seedling stage. Thus, two data points, two weeks and four weeks after planting, were used in the current study. As a result, two QTL regions were detected for the growth differences via plant height and green area (reflecting tillering). We expect that these results can be utilized by breeders to evaluate and select vigorous seedlings for their breeding programs.
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- 2019
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11. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective
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Li Shen, Inchan Choi, Eric J. Nestler, and Kyoung-Jae Won
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chromatin modification ,ENCODE ,GENCODE ,transcriptome ,Genetics ,QH426-470 - Abstract
A decade-long project, led by several international research groups, called the Encyclopedia of DNA Elements (ENCODE), recently released an unprecedented amount of data. The ambitious project covers transcriptome, cistrome, epigenome, and interactome data from more than 1,600 sets of experiments in human. To make use of this valuable resource, it is important to understand the information it represents and the techniques that were used to generate these data. In this review, we introduce the data that ENCODE generated, summarize the observations from the data analysis, and revisit a computational approach that ENCODE used to predict gene expression, with a focus on the human transcriptome and its association with chromatin modifications.
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- 2013
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12. The sequence-specific transcription factor c-Jun targets Cockayne syndrome protein B to regulate transcription and chromatin structure.
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Robert J Lake, Erica L Boetefuer, Pei-Fang Tsai, Jieun Jeong, Inchan Choi, Kyoung-Jae Won, and Hua-Ying Fan
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Genetics ,QH426-470 - Abstract
Cockayne syndrome is an inherited premature aging disease associated with numerous developmental and neurological defects, and mutations in the gene encoding the CSB protein account for the majority of Cockayne syndrome cases. Accumulating evidence suggests that CSB functions in transcription regulation, in addition to its roles in DNA repair, and those defects in this transcriptional activity might contribute to the clinical features of Cockayne syndrome. Transcription profiling studies have so far uncovered CSB-dependent effects on gene expression; however, the direct targets of CSB's transcriptional activity remain largely unknown. In this paper, we report the first comprehensive analysis of CSB genomic occupancy during replicative cell growth. We found that CSB occupancy sites display a high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, we found that CSB occupancy is enriched at sites containing the TPA-response element. Consistent with this binding site preference, we show that CSB and the transcription factor c-Jun can be found in the same protein-DNA complex, suggesting that c-Jun can target CSB to specific genomic regions. In support of this notion, we observed decreased CSB occupancy of TPA-response elements when c-Jun levels were diminished. By modulating CSB abundance, we found that CSB can influence the expression of nearby genes and impact nucleosome positioning in the vicinity of its binding site. These results indicate that CSB can be targeted to specific genomic loci by sequence-specific transcription factors to regulate transcription and local chromatin structure. Additionally, comparison of CSB occupancy sites with the MSigDB Pathways database suggests that CSB might function in peroxisome proliferation, EGF receptor transactivation, G protein signaling and NF-κB activation, shedding new light on the possible causes and mechanisms of Cockayne syndrome.
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- 2014
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13. RBPJ, the major transcriptional effector of Notch signaling, remains associated with chromatin throughout mitosis, suggesting a role in mitotic bookmarking.
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Robert J Lake, Pei-Fang Tsai, Inchan Choi, Kyoung-Jae Won, and Hua-Ying Fan
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Genetics ,QH426-470 - Abstract
Mechanisms that maintain transcriptional memory through cell division are important to maintain cell identity, and sequence-specific transcription factors that remain associated with mitotic chromatin are emerging as key players in transcriptional memory propagation. Here, we show that the major transcriptional effector of Notch signaling, RBPJ, is retained on mitotic chromatin, and that this mitotic chromatin association is mediated through the direct association of RBPJ with DNA. We further demonstrate that RBPJ binds directly to nucleosomal DNA in vitro, with a preference for sites close to the entry/exit position of the nucleosomal DNA. Genome-wide analysis in the murine embryonal-carcinoma cell line F9 revealed that roughly 60% of the sites occupied by RBPJ in asynchronous cells were also occupied in mitotic cells. Among them, we found that a fraction of RBPJ occupancy sites shifted between interphase and mitosis, suggesting that RBPJ can be retained on mitotic chromatin by sliding on DNA rather than disengaging from chromatin during mitotic chromatin condensation. We propose that RBPJ can function as a mitotic bookmark, marking genes for efficient transcriptional activation or repression upon mitotic exit. Strikingly, we found that sites of RBPJ occupancy were enriched for CTCF-binding motifs in addition to RBPJ-binding motifs, and that RBPJ and CTCF interact. Given that CTCF regulates transcription and bridges long-range chromatin interactions, our results raise the intriguing hypothesis that by collaborating with CTCF, RBPJ may participate in establishing chromatin domains and/or long-range chromatin interactions that could be propagated through cell division to maintain gene expression programs.
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- 2014
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14. Dynamic Beehive Detection and Tracking System Based on YOLO V5 and Unmanned Aerial Vehicle
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Peng Gao, Kangbeen Lee, Lukas Wiku Kuswidiyanto, Seung-Hwa Yu, Kai Hu, Gaotian Liang, Yufeng Chen, Weixing Wang, Fei Liao, Yu Seok Jeong, Moon-Seok Jeon, Inchan Choi, and Xiongzhe Han
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Mechanical Engineering ,Engineering (miscellaneous) ,Agricultural and Biological Sciences (miscellaneous) ,Computer Science Applications - Published
- 2022
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15. Study on the Technology for Searching Vespa Velutina Nest Using YOLO-v5
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Yu-Seok Jeong, Moon-Seok Jeon, Su-bae Kim, Dongwon Kim, Seung-Hwa Yu, Kyung-Chul Kim, Siyoung Lee, Chang-Woo Lee, and Inchan Choi
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- 2022
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16. High Throughput Phenotyping for Various Traits on Soybean Seeds Using Image Analysis.
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Jeong-Ho Baek, Eungyeong Lee, Nyunhee Kim, Song Lim Kim, Inchan Choi, Hyeonso Ji, Yong Suk Chung, Man-Soo Choi, Jung-Kyung Moon, and Kyung-Hwan Kim
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- 2020
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17. New method for detecting Collectorichum species found in Korea using image analysis
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JeongHo Baek, Nyunhee Kim, JaeYoung Kim, Younguk Kim, Chaewon Lee, Song Lim Kim, Hyeonso Ji, Sang Ryeol Park, Inchan Choi, and Kyung-Hwan Kim
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food and beverages ,Plant Science ,Ecology, Evolution, Behavior and Systematics - Abstract
Colletotrichum acutatum spp. infects various economical crops worldwide and causes massive loss on their yields. Among those, Capsicum spp., which known as chili pepper, is on a critical issue by those pathogens. Due to the lack of their genetic markers in Korea, the unidentifiable various species of C. acutatum obstructs the mechanism studies of these pathogens and the selection of disease resistant breed lines. Therefore, we screened RGB images of the colonization progresses of pathogens to identify the species of Ca40042, K1, NN, AS2, and SW1 by time and temperature. Cultivated pathogens such as Ca40042, K1, and SW1 were detectable on quantified shape and color data of images from specific temperature conditions, while other pathogens were difficult to recognize. Although several limitations exist in identification results of current experiment, but also, we can expect this method can suggest the possibility to replace the genetic marker methods which is now unavailable in Korea.
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- 2022
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18. A Stationary Wavelet Entropy-Based Clustering Approach Accurately Predicts Gene Expression.
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Nha Nguyen, An P. N. Vo, Inchan Choi, and Kyoung-Jae Won
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- 2015
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19. Determination of the Conditions for Image Analysis of Rice Based on a Crop Phenomic Platform
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Chaewon Lee, Inchan Choi, Hongseok Lee, Nyunhee Kim, Eunsook An, Song Lim Kim, Jeongho Baek, Hyeonso Ji, In-Sun Yoon, and Kyung-Hwan Kim
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- 2021
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20. Development of Vespa velutina Monitoring System Based on Deep Learning
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Gookhwan Kim, Kyung-Do Kwon, Kyoung-Chul Kim, Dasom Seo, Inchan Choi, and Youngki Hong
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Vespa velutina ,Computer science ,business.industry ,Deep learning ,Environmental resource management ,Monitoring system ,Artificial intelligence ,business - Published
- 2021
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21. Breeding of a Pink-Colored Multi-Floral Phalaenopsis ‘Tiny Bell’
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Inchan Choi, Hye Ryun An, Pue Hee Park, Pil Man Park, Yae Jin Kim, Su Young Lee, and Hongseok Lee
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Horticulture ,Inflorescence ,Colored ,Phalaenopsis ,Cultivar ,Biology ,biology.organism_classification ,Rural development - Abstract
A new small-type pink-colored Phalaenopsis cultivar, ‘Tiny Bell’, was released by the National Institute of Horticultural and Herbal Science, Rural Development Administration (Korea) in 2018. ‘Tiny Bell’ was derived in 2010 from crossing P. ‘D07PN16’, multi-floral small-type cultivar with pink-colored flowers, and P. ‘D03PN22’, a small-type cultivar with light pink-colored flowers. In the preliminary selection stage in 2014, the cultivar known as ‘10531-53’ was chosen among 120 individual progenies, based on phenotypic standards such as flower color and shape, inflorescence number, and leaf attitude. The stability and uniformity of the cultivar was confirmed through the first and second characteristics tests from 2014 to 2018, and the cultivar was thereafter named ‘Tiny Bell’. ‘Tiny Bell’ has violet pink (RHS, PVGN80A) flowers with a white edge. The dimensions of the f lowers are 3.89 cm ( length) and 4.01 cm (width). T he i nf ol rescence type is a r aceme with m any flowers (19.7 blooms per inflorescence). The leaves of ‘Tiny Bell’ grow horizontally and are 13.1 cm in length and 5.26 cm in width. This new cultivar of Phalaenopsis ‘Tiny Bell’ is well suited as a small-sized potted orchid.
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- 2020
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22. QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing
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Song Lim Kim, Young-Min Jeong, Hyun-Su Park, Inchan Choi, Nyunhee Kim, Eungyeong Lee, In Sun Yoon, Hyeonso Ji, Do-Yu Kang, Kyung-Hwan Kim, Yong Jae Won, Hyoja Oh, Jeong-Ho Baek, Kyeong-Seong Cheon, Youn-Young Lee, and Jun Oh
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0106 biological sciences ,0301 basic medicine ,inorganic chemicals ,Quantitative trait locus ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Germination ,01 natural sciences ,Genome ,Polymorphism, Single Nucleotide ,Japonica ,03 medical and health sciences ,Inbred strain ,INDEL Mutation ,Cleaved amplified polymorphic sequence ,Genetics ,Molecular Biology ,Gene ,Japonica rice ,Plant Proteins ,Pre-harvest sprouting ,biology ,Whole Genome Sequencing ,Chromosome ,food and beverages ,Chromosome Mapping ,Oryza ,General Medicine ,biology.organism_classification ,equipment and supplies ,030104 developmental biology ,bacteria ,Original Article ,Re-sequencing ,010606 plant biology & botany - Abstract
Pre-harvest sprouting (PHS) leads to serious economic losses because of reductions in yield and quality. To analyze the quantitative trait loci (QTLs) for PHS resistance in japonica rice, PHS rates on panicles were measured in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae (PHS resistant) and Unbong40 (PHS susceptible) under two different environmental conditions—field (summer) and greenhouse (winter) environments. Genome re-sequencing of the parental varieties detected 266,773 DNA polymorphisms including 248,255 single nucleotide polymorphisms and 18,518 insertions/deletions. We constructed a genetic map comprising 239 kompetitive allele-specific PCR and 49 cleaved amplified polymorphic sequence markers. In the field environment, two major QTLs, qPHS-3FD and qPHS-11FD, were identified on chromosomes 3 and 11, respectively, whereas three major QTLs, qPHS-3GH, qPHS-4GH, and qPHS-11GH, were identified on chromosomes 3, 4, and 11, respectively, in the greenhouse environment. qPHS-11GH and qPHS-11FD had similar locations on chromosome 11, suggesting the existence of a gene conferring stable PHS resistance effects under different environmental conditions. The QTLs identified in this study can be used to improve the PHS resistance of japonica varieties, and they may improve our understanding of the genetic basis of PHS resistance.
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- 2020
23. Identification of the Capsicum baccatum NLR Protein CbAR9 Conferring Disease Resistance to Anthracnose
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Soohong Kim, Inchan Choi, Doil Choi, Jae Wahng Do, Kyong Sil Lee, Sang Ryeol Park, Seungmin Son, Jae Bok Yoon, Jung-Heon Han, and Jun Oh
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QH301-705.5 ,Virulence ,Nicotiana benthamiana ,Colletotrichum capsici ,Plant disease resistance ,Quantitative trait locus ,Catalysis ,Microbiology ,Inorganic Chemistry ,Physical and Theoretical Chemistry ,Biology (General) ,Molecular Biology ,Gene ,innate immunity ,QD1-999 ,Spectroscopy ,Innate immune system ,biology ,Organic Chemistry ,fungi ,food and beverages ,nucleotide-binding and leucine-rich repeat ,General Medicine ,biology.organism_classification ,Capsicum baccatum ,Computer Science Applications ,Chemistry - Abstract
Anthracnose is caused by Colletotrichum species and is one of the most virulent fungal diseases affecting chili pepper (Capsicum) yield globally. However, the noble genes conferring resistance to Colletotrichum species remain largely elusive. In this study, we identified CbAR9 as the causal locus underlying the large effect quantitative trait locus CcR9 from the anthracnose-resistant chili pepper variety PBC80. CbAR9 encodes a nucleotide-binding and leucine-rich repeat (NLR) protein related to defense-associated NLRs in several other plant species. CbAR9 transcript levels were induced dramatically after Colletotrichum capsici infection. To explore the biological function, we generated transgenic Nicotiana benthamiana lines overexpressing CbAR9, which showed enhanced resistance to C. capsici relative to wild-type plants. Transcript levels of pathogenesis-related (PR) genes increased markedly in CbAR9-overexpressing N. benthamiana plants. Moreover, resistance to anthracnose and transcript levels of PR1 and PR2 were markedly reduced in CbAR9-silenced chili pepper fruits after C. capsici infection. Our results revealed that CbAR9 contributes to innate immunity against C. capsici.
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- 2021
24. Identification of the
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Seungmin, Son, Soohong, Kim, Kyong Sil, Lee, Jun, Oh, Inchan, Choi, Jae Wahng, Do, Jae Bok, Yoon, Jungheon, Han, Doil, Choi, and Sang Ryeol, Park
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fungi ,Quantitative Trait Loci ,food and beverages ,nucleotide-binding and leucine-rich repeat ,NLR Proteins ,Colletotrichum capsici ,Article ,Host-Pathogen Interactions ,Colletotrichum ,Nicotiana benthamiana ,Capsicum ,Capsicum baccatum ,innate immunity ,Disease Resistance ,Plant Diseases - Abstract
Anthracnose is caused by Colletotrichum species and is one of the most virulent fungal diseases affecting chili pepper (Capsicum) yield globally. However, the noble genes conferring resistance to Colletotrichum species remain largely elusive. In this study, we identified CbAR9 as the causal locus underlying the large effect quantitative trait locus CcR9 from the anthracnose-resistant chili pepper variety PBC80. CbAR9 encodes a nucleotide-binding and leucine-rich repeat (NLR) protein related to defense-associated NLRs in several other plant species. CbAR9 transcript levels were induced dramatically after Colletotrichum capsici infection. To explore the biological function, we generated transgenic Nicotiana benthamiana lines overexpressing CbAR9, which showed enhanced resistance to C. capsici relative to wild-type plants. Transcript levels of pathogenesis-related (PR) genes increased markedly in CbAR9-overexpressing N. benthamiana plants. Moreover, resistance to anthracnose and transcript levels of PR1 and PR2 were markedly reduced in CbAR9-silenced chili pepper fruits after C. capsici infection. Our results revealed that CbAR9 contributes to innate immunity against C. capsici.
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- 2021
25. The Capsicum baccatum-Specific Truncated NLR Protein CbCN Enhances the Innate Immunity against Colletotrichum acutatum
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Sang Ryeol Park, Jae Bok Yoon, Jae Wahng Do, Jung-Heon Han, Jun Oh, Seungmin Son, Kyong Sil Lee, Inchan Choi, and Soohong Kim
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0106 biological sciences ,0301 basic medicine ,Colletotrichum acutatum ,QH301-705.5 ,Nicotiana benthamiana ,NLR Proteins ,Genetically modified crops ,Plant disease resistance ,01 natural sciences ,Catalysis ,Inorganic Chemistry ,03 medical and health sciences ,Colletotrichum ,Gene silencing ,Biology (General) ,Physical and Theoretical Chemistry ,QD1-999 ,Molecular Biology ,Gene ,Capsicum baccatum ,Spectroscopy ,Disease Resistance ,Plant Diseases ,Genetics ,biology ,Communication ,Organic Chemistry ,fungi ,food and beverages ,nucleotide-binding and leucine-rich repeat ,General Medicine ,anthracnose resistance ,NPR1 ,biology.organism_classification ,Computer Science Applications ,Chemistry ,030104 developmental biology ,Host-Pathogen Interactions ,Disease Susceptibility ,Capsicum ,010606 plant biology & botany - Abstract
Chili pepper (Capsicumannuum) is an important fruit and spice used globally, but its yield is seriously threatened by anthracnose. Capsicum baccatum is particularly valuable as it carries advantageous disease resistance genes. However, most of the genes remain to be identified. In this study, we identified the C. baccatum-specific gene CbCN, which encodes a truncated nucleotide-binding and leucine-rich repeat protein in the anthracnose resistant chili pepper variety PBC80. The transcription of CbCN was greater in PBC80 than it was in the susceptible variety An-S after Colletotrichum acutatum inoculation. In order to investigate the biological function of CbCN, we generated transgenic tobacco lines constitutively expressing CbCN. Notably, CbCN-overexpressing transgenic plants exhibited enhanced resistance to C. acutatum compared to wild-type plants. Moreover, the expression of pathogenesis-related (PR) genes was remarkably increased in a CbCN-overexpressing tobacco plants. In order to confirm these results in chili pepper, we silenced the CbCN gene using the virus-induced gene silencing system. The anthracnose resistance and expressions of PR1, PR2, and NPR1 were significantly reduced in CbCN-silenced chili peppers after C. acutatum inoculations. These results indicate that CbCN enhances the innate immunity against anthracnose caused by C. acutatum by regulating defense response genes.
- Published
- 2021
26. Breeding of Pink-Colored Big-Lip Phalaenopsis ‘Lovely Angel’
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Oh Keun Kwon, Hongseok Lee, Inchan Choi, Hye Ryun An, Pue Hee Park, Su Young Lee, and Pil Man Park
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Horticulture ,biology ,Inflorescence ,Colored ,Phalaenopsis ,Cultivar ,biology.organism_classification ,Mathematics ,Rural development ,World class - Abstract
A pink big-lip Phalaenopsis cultivar ‘Lovely Angel’ was developed by the National Institute of Horticultural & Herbal Science, Rural Development Administration (Korea) in 2017. ‘Lovely Angel’ was derived by artificial crossing between white-colored cultivar P. ‘Timonthy’ and pink-colored flower with big-lip cultivar P. World Class ‘Big Foot’ in 2009. In 2013, 09056-12 was selected as excellent growth and flowering characteristics, such as flower color, shape, and inflorescence number. The first and second characteristic tests were conducted from 2014 to 2017 to evaluate the stability and uniformity, named thereafter as ‘Lovely Angel’. ‘Lovely Angel’ has violet-pink (RHS, PVG81C) flowers with stripes and big purple lips (RHS, PG78B). The incurved florets measure 6.1 and 5.6 cm in length and width, respectively. The number of florets per inflorescence is 20.6, which is suitably large and abundant, and the inflorescence length of ‘Lovely Angel’ is 31.8 cm. The leaves of ‘Lovely Angel’ grow semi-pendulously and are 18.7 cm in length and 6.8cm in width. The new cultivar ‘Lovely Angel’ can be mainly available for small-type potted flowers.
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- 2019
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27. Kompetitive Allele-Specific PCR Marker Development and Quantitative Trait Locus Mapping for Bakanae Disease Resistance in Korean Japonica Rice Varieties
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Inchan Choi, Yong Jae Won, Jung-Heon Han, Jeong-Ho Baek, Eungyeong Lee, Youn-Young Lee, Hyeonso Ji, Song Lim Kim, In Sun Yoon, Do-Yu Kang, Young-Il Cho, Hyoja Oh, Jun Oh, Kyeong-Seong Cheon, Young-Min Jeong, Kyung-Hwan Kim, and Nyunhee Kim
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0106 biological sciences ,0301 basic medicine ,Molecular breeding ,Genetics ,Candidate gene ,education.field_of_study ,Population ,food and beverages ,Plant Science ,Biology ,Plant disease resistance ,Quantitative trait locus ,01 natural sciences ,Genetic analysis ,03 medical and health sciences ,030104 developmental biology ,Bakanae ,education ,Genotyping ,010606 plant biology & botany ,Biotechnology - Abstract
High-throughput molecular markers with high genotyping accuracy will be helpful for genetic analysis, mapping of interesting genes, and rice breeding program. To develop high-throughput and cost-effective molecular markers for Korean japonica rice varieties, which are closely-related genetically, we designed kompetitive allele-specific polymerase chain reaction (KASP) assays from the sequence data of 13 Korean japonica rice varieties. Of the 504 new KASP assays, 371 (73.6%) showed polymorphisms among the tested varieties. In addition to the 400 previously developed KASP markers, this resulted in 771 KASP markers being applicable for Korean japonica rice varieties. These KASP markers were used to map the quantitative trait loci (QTLs) for rice bakanae disease (BD) resistance. From the results of QTL mapping and determination of the mortality rate of BD in two F2:F3 populations, a major QTL, qFfR1-1, and a novel QTL, qFfR6, were revealed on chromosome 1 in the Junam/Nampyeong F2:F3 population and on chromosome 6 in the Saenuri/Nampyeong F2:F3 population, respectively. Further, the insertion/deletion markers in the qFfR1-1 region were developed to select BD-resistant japonica rice varieties. The 771 developed KASP markers will accelerate the molecular breeding in Korean japonica rice varieties, and the detected QTLs will be helpful in identifying candidate genes for BD resistance.
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- 2019
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28. Mutations in the microRNA172 binding site of SUPERNUMERARY BRACT (SNB) suppress internode elongation in rice
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Song Lim Kim, Do-Yu Kang, Gang-Seob Lee, Chang-deok Han, Kyung-Hwan Kim, Ki-Hong Jung, Hyeonso Ji, Jeong-Ho Baek, Kyeong-Seong Cheon, Inchan Choi, Jun Oh, and Hyoja Oh
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Mutation ,Bract ,Mutant ,Soil Science ,Plant Science ,Biology ,lcsh:Plant culture ,medicine.disease_cause ,Phenotype ,Internode elongation ,Cell biology ,chemistry.chemical_compound ,chemistry ,Cytokinin ,medicine ,Gibberellin ,Original Article ,lcsh:SB1-1110 ,Rice ,SNB ,Agronomy and Crop Science ,Gene ,Plant stem ,microRNA172 - Abstract
Background Internode elongation is an important agronomic trait in rice that determines culm length, which is related to lodging, panicle exsertion, and biomass. sui4 (shortened uppermost internode 4) mutants show reduced internode length and a dwarf phenotype due to shortened internodes; the uppermost internode is particularly severely affected. The present study was performed to identify the molecular nature and function of the SUI4 gene during internode elongation. Results Our previous study showed that the SUI4 gene was mapped to a 1.1-Mb interval on chromosome 7 (Ji et al. 2014). In order to isolate the gene responsible for the sui4 phenotype, genomic DNA resequencing of sui4 mutants and wild-type plants and reciprocal transformation of wild-type and mutant alleles of the putative SUI4 gene was performed. The data revealed that the causative mutation of sui4 was a T to A nucleotide substitution at the microRNA172 binding site of Os07g0235800, and that SUI4 is a new allele of the previously reported gene SUPERNUMERARY BRACT (SNB), which affects flower structure. In order to understand the effect of this mutation on expression of the SUI4/SNB gene, SUI4/SNB native promoter-fuzed GUS transgenics were examined, along with qRT-PCR analysis at various developmental stages. In sui4 mutants, the SUI4/SNB gene was upregulated in the leaves, culms, and panicles, especially when internodes were elongated. In culms, SUI4/SNB was expressed in the nodes and the lower parts of elongating internodes. In order to further explore the molecular nature of SUI4/SNB during internode elongation, RNA-seq and qRT-PCR analysis were performed with RNAs from the culms of sui4 mutants and wild-type plants in the booting stage. The data showed that in sui4 mutants, genes deactivating bioactive gibberellins and cytokinin were upregulated while genes related to cell expansion and cell wall synthesis were downregulated. Conclusion In summary, this paper shows that interaction between SUI4/SNB and microRNA172 could determine internode elongation during the reproductive stage in rice plants. Due to a mutation at the microRNA172 binding site in sui4 mutants, the expression of SUI4/SNB was enhanced, which lowered the activities of cell expansion and cell wall synthesis and consequently resulted in shortened internodes. Electronic supplementary material The online version of this article (10.1186/s12284-019-0324-8) contains supplementary material, which is available to authorized users.
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- 2019
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29. High-throughput phenotyping platform for analyzing drought tolerance in rice
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Nyunhee Kim, In Sun Yoon, Hongseok Lee, Kyeong-Seong Cheon, Ki-Hong Jung, Song Lim Kim, Inchan Choi, Jeong-Ho Baek, Taek-Ryoun Kwon, Kyung-Hwan Kim, Eun-Gyeong Lee, Minsu Kim, and Hyeonso Ji
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Drought stress ,Parameter ,Drought tolerance ,Plant Science ,Biology ,Photosynthetic efficiency ,Fluorescence ,Genetics ,Cultivar ,Water-use efficiency ,Selection, Genetic ,Throughput (business) ,Water content ,Transpiration ,RGB ,business.industry ,fungi ,food and beverages ,Genetic Variation ,Oryza ,NIR ,Biotechnology ,Droughts ,Phenotype ,Agriculture ,IR ,Original Article ,business - Abstract
Main conclusion A new imaging platform was constructed to analyze drought-tolerant traits of rice. Rice was used to quantify drought phenotypes through image-based parameters and analyzing tools. Abstract Climate change has increased the frequency and severity of drought, which limits crop production worldwide. Developing new cultivars with increased drought tolerance and short breeding cycles is critical. However, achieving this goal requires phenotyping a large number of breeding populations in a short time and in an accurate manner. Novel cutting-edge technologies such as those based on remote sensors are being applied to solve this problem. In this study, new technologies were applied to obtain and analyze imaging data and establish efficient screening platforms for drought tolerance in rice using the drought-tolerant mutant osphyb. Red–Green–Blue images were used to predict plant area, color, and compactness. Near-infrared imaging was used to determine the water content of rice, infrared was used to assess plant temperature, and fluorescence was used to examine photosynthesis efficiency. DroughtSpotter technology was used to determine water use efficiency, plant water loss rate, and transpiration rate. The results indicate that these methods can detect the difference between tolerant and susceptible plants, suggesting their value as high-throughput phenotyping methods for short breeding cycles as well as for functional genetic studies of tolerance to drought stress.
- Published
- 2020
30. High Throughput Phenotyping for Various Traits on Soybean Seeds Using Image Analysis
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Man Soo Choi, Song Lim Kim, Yong Suk Chung, Jeong-Ho Baek, Inchan Choi, Eungyeong Lee, Hyeonso Ji, Nyunhee Kim, Kyung-Hwan Kim, and Jung-Kyung Moon
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0106 biological sciences ,Breeding program ,Genotype ,seed traits ,Quantitative Trait Loci ,Biosensing Techniques ,Biology ,lcsh:Chemical technology ,01 natural sciences ,Biochemistry ,Rgb image ,Article ,Analytical Chemistry ,03 medical and health sciences ,Image acquisition ,Humans ,lcsh:TP1-1185 ,Electrical and Electronic Engineering ,Instrumentation ,Throughput (business) ,030304 developmental biology ,0303 health sciences ,seed morphology ,food and beverages ,Phenotype ,Atomic and Molecular Physics, and Optics ,High-Throughput Screening Assays ,Function analysis ,breeding ,Seeds ,Soybeans ,Biological system ,RGB image ,seed color ,010606 plant biology & botany - Abstract
Data phenotyping traits on soybean seeds such as shape and color has been obscure because it is difficult to define them clearly. Further, it takes too much time and effort to have sufficient number of samplings especially length and width. These difficulties prevented seed morphology to be incorporated into efficient breeding program. Here, we propose methods for an image acquisition, a data processing, and analysis for the morphology and color of soybean seeds by high-throughput method using images analysis. As results, quantitative values for colors and various types of morphological traits could be screened to create a standard for subsequent evaluation of the genotype. Phenotyping method in the current study could define the morphology and color of soybean seeds in highly accurate and reliable manner. Further, this method enables the measurement and analysis of large amounts of plant seed phenotype data in a short time, which was not possible before. Fast and precise phenotype data obtained here may facilitate Genome Wide Association Study for the gene function analysis as well as for development of the elite varieties having desirable seed traits.
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- 2020
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31. Development ofPerilla frutescenswith Low Levels of Alpha-Linolenic Acid by Inhibition of a delta 15 desaturase Gene
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Kyeong-Ryeol Lee, Inchan Choi, Hongseok Lee, Song Lim Kim, Jeong-Ho Baek, and Hyeonso Ji, Eun-Gyeong Lee, Jung-Bong Kim, Nyunhee Kim, Myoung Hee Lee, and Kyung-Hwan Kim
- Subjects
0106 biological sciences ,0301 basic medicine ,Delta ,Perilla frutescens ,biology ,alpha-Linolenic acid ,biology.organism_classification ,Perilla ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,RNA interference ,Food science ,Gene ,010606 plant biology & botany ,α-linolenic acid - Published
- 2018
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32. Single Nucleotide Polymorphism (SNP) Discovery and Kompetitive Allele-Specific PCR (KASP) Marker Development with Korean Japonica Rice Varieties
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Youn-Young Lee, Do-Yu Kang, Yong Jae Won, Jeong-Ho Baek, Kyeong-Seong Cheon, Young-Min Jeong, In Sun Yoon, Song Lim Kim, Inchan Choi, Young-Il Cho, Hyeonso Ji, Kyung-Hwan Kim, Jung-Heon Han, Jun Oh, and Hyoja Oh
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0106 biological sciences ,0301 basic medicine ,Genetics ,Kompetitive Allele Specific PCR (KASP) ,Single-nucleotide polymorphism ,Plant Science ,Biology ,01 natural sciences ,Japonica rice ,03 medical and health sciences ,030104 developmental biology ,SNP ,Genotyping ,010606 plant biology & botany ,Biotechnology - Published
- 2018
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33. Detection of Genes Conferring Resistance to the Brown Planthopper (BPH) in Gayabyeo Through Genome Resequencing and Development of Their Selection Markers
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Bo Yoon Seo, Ung-Jo Hyun, Sang Bok Lee, Song Lim Kim, Seok-Chul Suh, Inchan Choi, Eok-Keun Ahn, Seung-Bum Lee, Kyung-Hwan Kim, Hyeonso Ji, and Gang-Seob Lee, and Hyun-Ju Kang
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0106 biological sciences ,0301 basic medicine ,Genetics ,biology ,Resistance (ecology) ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Genome resequencing ,Brown planthopper ,Gene ,Selection (genetic algorithm) ,010606 plant biology & botany - Published
- 2018
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34. Data management for plant phenomics
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Taek-Ryoun Kwon, Inchan Choi, Nita Solehati, Kyung-Hwan Kim, and Song-Lim Kim
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0106 biological sciences ,0301 basic medicine ,Data processing ,business.industry ,Data management ,fungi ,food and beverages ,Hyperspectral imaging ,Plant Science ,Biology ,computer.software_genre ,01 natural sciences ,Field (computer science) ,Biotechnology ,Metadata ,03 medical and health sciences ,030104 developmental biology ,Phenomics ,Data acquisition ,Data quality ,Data mining ,business ,computer ,010606 plant biology & botany - Abstract
Plant phenomics is an area of biology dealing with the analysis of phenotypic traits in plants. It can be cointegrated with other omics like functional genomics, transcriptomics, and metabolomics etc. Phenotypic traits are generated by images of RGB, hyperspectral, near-infrared, thermal, fluorescence imaging and so on. Characterized phenotypes can be revealed in various morphological and physiological measurements of size, growth pattern, biomass and color in plants. The image-base automated plant phenotyping is described as a high throughput plant facility. Despite its advantages like nondestructive phenotyping it has its own limitations such as plant’s complex architectures and environmental conditions at the time of image capture especially in the field. Phenomics generates a large number of images and metadata through phenotyping instruments, so there is a need for proper data processing and managements. Standardized data storage and sharing is also necessary for meaningful data acquisition along with statistical analysis. Processes of data management are largely consisted of data collection, storage, documentation, along with improvement of data quality. In future, plant phenomics must be developed efficiently to store, analyze, protect and share the acquired data. Modern high throughput plant phenotyping could be used effectively in plant improvement programs.
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- 2017
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35. The opening of phenome-assisted selection era in the early seedling stage
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Kyung-Hwan Kim, Inchan Choi, Hongseok Lee, Gang-Seob Lee, Yong Suk Chung, Taek-Ryoun Kwon, Song Lim Kim, Nyunhee Kim, Jeong-Ho Baek, Eungyeong Lee, Hyeonso Ji, and Renato Rodrigues Silva
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0301 basic medicine ,Plant genetics ,lcsh:Medicine ,Biology ,Phenome ,Article ,Plant breeding ,03 medical and health sciences ,0302 clinical medicine ,Phenomics ,Pleiotropism ,lcsh:Science ,Selection (genetic algorithm) ,Multidisciplinary ,lcsh:R ,fungi ,food and beverages ,biology.organism_classification ,030104 developmental biology ,Agronomy ,Seedling ,Shoot ,Trait ,lcsh:Q ,Stage (hydrology) ,030217 neurology & neurosurgery - Abstract
Faster and more efficient breeding cycle is not an option to deal with unpredictable and fast global climate changes. Phenomics for collecting huge number of individuals in accurate manner could be an answer to solve this problem. We collected image data to measure plant height and manual data for shoot length to be compared. QTLs clustered of plant height and shoot length were detected in 2-week old seedlings, which was consistent with many other reports using various genetic resources in matured stage. Further, these traits are highly correlated with yield by pleiotropism or tight linkage of those traits. It implies the “phenome-assisted selection” can be applied for yield trait in rice in the very early stage to shorten the breeding cycle significantly in fast but low-cost manner.
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- 2019
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36. Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by
- Author
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Do-Yu, Kang, Kyeong-Seong, Cheon, Jun, Oh, Hyoja, Oh, Song Lim, Kim, Nyunhee, Kim, Eungyeong, Lee, Inchan, Choi, Jeongho, Baek, Kyung-Hwan, Kim, Nam-Jin, Chung, and Hyeonso, Ji
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resequencing ,quantitative trait locus ,Fusarium ,Quantitative Trait Loci ,food and beverages ,Oryza ,bakanae disease ,genetic map ,Polymorphism, Single Nucleotide ,Genome, Plant ,Article ,Disease Resistance - Abstract
Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, ‘Samgwang’ and ‘Junam’, respectively. Resequencing of ‘Junam’ and ‘Samgwang’ genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, qFfR9, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24–7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the ‘Junam’ and ‘Samgwang’ genome sequence data, and are possibly candidate genes for qFfR9; therefore, qFfR9 could be utilized as a valuable resource for breeding BD-resistant rice varieties.
- Published
- 2019
37. Additional file 3: of Mutations in the microRNA172 binding site of SUPERNUMERARY BRACT (SNB) suppress internode elongation in rice
- Author
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Hyeonso Ji, Chang-Deok Han, Gang-Seob Lee, Jung, Ki-Hong, Do-Yu Kang, Oh, Jun, Hyoja Oh, Kyeong-Seong Cheon, Kim, Song, Inchan Choi, Jeongho Baek, and Kim, Kyung-Hwan
- Abstract
Table S3. qRT-PCR primer sequences (DOCX 14 kb)
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- 2019
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38. Additional file 1: of Mutations in the microRNA172 binding site of SUPERNUMERARY BRACT (SNB) suppress internode elongation in rice
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Hyeonso Ji, Chang-Deok Han, Gang-Seob Lee, Jung, Ki-Hong, Do-Yu Kang, Oh, Jun, Hyoja Oh, Kyeong-Seong Cheon, Kim, Song, Inchan Choi, Jeongho Baek, and Kim, Kyung-Hwan
- Abstract
Table S1. List of SNPs in the SUI4 mapped region of Dongjin plants and sui4 mutants. (DOCX 16 kb)
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- 2019
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39. Breeding of Yellow Small-Type Phalaenopsis ‘Yellow Scent’ with Fragrance
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Inchan Choi, Pue Hee Park, Hongseok Lee, Jong Hee Yoo, Hye Ryun An, Su Young Lee, Pil Man Park, and Oh Keun Kwon
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Horticulture ,Type (biology) ,biology ,Electronic nose ,Phalaenopsis ,biology.organism_classification ,Selection (genetic algorithm) - Published
- 2019
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40. Genome-wide Detection of SNPs between Two Korean Tongil-Type Rice Varieties
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Hyun-Ju Kang, Inchan Choi, Hyeonso Ji, Bo Yoon Seo, Kyung-Hwan Kim, and Eok-Keun Ahn
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0301 basic medicine ,Genetics ,03 medical and health sciences ,030104 developmental biology ,Type (biology) ,Genetic marker ,SNP ,Single-nucleotide polymorphism ,Biology ,Genome - Published
- 2016
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41. Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation
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Kyoung-Jae Won, Karyn L. Sheaffer, Klaus H. Kaestner, Inchan Choi, and Rinho Kim
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0301 basic medicine ,DNA Hydroxymethylation ,Biology ,Epigenesis, Genetic ,Receptors, G-Protein-Coupled ,Mice ,03 medical and health sciences ,Proto-Oncogene Proteins ,Genetics ,Animals ,Gene silencing ,Epigenetics ,Wnt Signaling Pathway ,Cells, Cultured ,Sequence Deletion ,Epigenomics ,Stem Cells ,Wnt signaling pathway ,LGR5 ,Gene Expression Regulation, Developmental ,Cell Differentiation ,DNA Methylation ,Intestinal epithelium ,Cell biology ,DNA-Binding Proteins ,Intestines ,Mice, Inbred C57BL ,030104 developmental biology ,Stem cell ,Research Paper ,Developmental Biology - Abstract
Methylated cytosines are associated with gene silencing. The ten-eleven translocation (TET) hydroxylases, which oxidize methylated cytosines to 5-hydroxymethylcytosine (5hmC), are essential for cytosine demethylation. Gene silencing and activation are critical for intestinal stem cell (ISC) maintenance and differentiation, but the potential role of TET hydroxylases in these processes has not yet been examined. Here, we generated genome-wide maps of the 5hmC mark in ISCs and their differentiated progeny. Genes with high levels of hydroxymethylation in ISCs are strongly associated with Wnt signaling and developmental processes. We found Tet1 to be the most abundantly expressed Tet gene in ISCs; therefore, we analyzed intestinal development in Tet1-deficient mice and determined that these mice are growth-retarded, exhibit partial postnatal lethality, and have significantly reduced numbers of proliferative cells in the intestinal epithelium. In addition, the Tet1-deficient intestine displays reduced organoid-forming capacity. In the Tet1-deficient crypt, decreased expression of Wnt target genes such as Axin2 and Lgr5 correlates with lower 5hmC levels at their promoters. These data demonstrate that Tet1-mediated DNA hydroxymethylation plays a critical role in the epigenetic regulation of the Wnt pathway in intestinal stem and progenitor cells and consequently in the self-renewal of the intestinal epithelium.
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- 2016
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42. Comparative Genomic Analysis for Identification and Characterization of Common Genes among Parasitic Nematodes
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Kang-Hyun Choi, Vimalraj Mani, Chang-Muk Lee, Bum-Soo Hahn, Inchan Choi, Ha Young Chung, Ja Choon Koo, Joon-Soo Sim, and Parthiban Subramanian
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0301 basic medicine ,03 medical and health sciences ,030104 developmental biology ,Identification (biology) ,Comparative genomic analysis ,Computational biology ,Biology ,Gene - Published
- 2016
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43. Exporting South Korea's e-Government Experience
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Inchan Choi and Mark C. Hoffman
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Marketing ,Economic growth ,Public Administration ,Sociology and Political Science ,E-Government ,020204 information systems ,0502 economics and business ,05 social sciences ,0202 electrical engineering, electronic engineering, information engineering ,02 engineering and technology ,Business ,050203 business & management - Published
- 2017
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44. Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties
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Do-Yu Kang, Song Lim Kim, Kyung-Hwan Kim, Eungyeong Lee, Hyeonso Ji, Jung-Heon Han, Inchan Choi, Nyunhee Kim, Yong Jae Won, Young-Il Cho, Jeong-Ho Baek, Jun Oh, In Sun Yoon, Kyeong-Seong Cheon, Hyoja Oh, and Young-Min Jeong
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Molecular breeding ,Genetic diversity ,Ecology ,SNP ,food and beverages ,KASP ,Single-nucleotide polymorphism ,Kompetitive Allele Specific PCR (KASP) ,Plant Science ,Biology ,Quantitative trait locus ,temperate japonica rice ,01 natural sciences ,Article ,high-throughput genotyping ,03 medical and health sciences ,030104 developmental biology ,Gene mapping ,Genetic marker ,Genotyping ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.
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- 2020
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45. RNA-Seq of Plant-Parasitic Nematode Meloidogyne incognita at Various Stages of Its Development
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Parthiban Subramanian, Byung-Ju Oh, Inchan Choi, Donghwan Shim, and Bum-Soo Hahn
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0106 biological sciences ,0301 basic medicine ,root-knot nematode ,lcsh:QH426-470 ,biology ,RNA-Seq ,developmental stages ,biology.organism_classification ,01 natural sciences ,Transcriptome ,lcsh:Genetics ,03 medical and health sciences ,030104 developmental biology ,Nematode ,Botany ,Data Report ,Genetics ,Meloidogyne incognita ,Molecular Medicine ,Root-knot nematode ,plant parasite ,transcriptome ,Genetics (clinical) ,010606 plant biology & botany - Published
- 2017
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46. Mapping of a major quantitative trait locus for bakanae disease resistance in rice by genome resequencing
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Tae Ho Kim, Hyun-Ju Kang, Song Lim Kim, Seung-Bum Lee, Jeong-Ho Baek, Hyeonso Ji, Kyung-Hwan Kim, Inchan Choi, Gang-Seob Lee, and Seok Cheol Suh
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetic Linkage ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Quantitative trait locus ,Plant disease resistance ,01 natural sciences ,Polymorphism, Single Nucleotide ,Japonica ,Chromosomes, Plant ,03 medical and health sciences ,Genotype ,Cleaved amplified polymorphic sequence ,Genetics ,Molecular Biology ,Gene ,Disease Resistance ,biology ,food and beverages ,Chromosome Mapping ,Oryza ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Plant Breeding ,030104 developmental biology ,Bakanae ,010606 plant biology & botany - Abstract
Bakanae disease (BD) has emerged as a serious threat in almost all rice cultivation regions worldwide. Nampyeong is a Korean japonica rice variety known to be resistant to BD. In this study, quantitative trait locus (QTL) mapping was performed with F2 and F3 plants derived from a cross between the Nampyeong variety and a susceptible Korean japonica line, DongjinAD. First, resequencing of Nampyeong and DongjinAD was performed, which identified 171,035 single nucleotide polymorphisms (SNPs) between the two parental varieties. Using these SNPs, 161 cleaved amplified polymorphic sequence (CAPS) markers and six derived CAPS markers were developed; then, a genetic map was constructed from the genotypes of 180 plants from the DongjinAD/Nampyeong F2 plants. The total length of the constructed genetic map was 1386 cM, with an average interval of 8.9 cM between markers. The BD mortality rates of each F3 family were measured by testing 40 F3 progenies using in vitro seedling screening method. QTL analysis based on the genetic map and mortality rate data revealed a major QTL, qFfR1, on rice chromosome 1. qFfR1 was located at 89.8 cM with a logarithm of the odds (LOD) score of 22.7. Further, there were three markers at this point: JNS01033, JNS01037, and JNS01041. A total of 15 genes were identified with annotations related to defense against plant diseases among the 179 genes in the qFfR1 interval at 95% probability, thereby providing potential candidate genes for qFfR1. qFfR1 and its closely linked markers will be useful in breeding rice varieties resistant to BD.
- Published
- 2017
47. A Study of Combustion Instability Mode in Dual Swirl Gas Turbine Combustor by PLIF and Chemiluminescence Measurement
- Author
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Assaad R. Masri, Inchan Choi, Keeman Lee, and Mrinal Juddoo
- Subjects
Work (thermodynamics) ,law ,Chemistry ,Combustor ,Mode (statistics) ,Mechanical engineering ,Combustion instability ,Mechanics ,Acoustic wave ,Combustion chamber ,Instability ,Chemiluminescence ,law.invention - Abstract
Inchan Choi, Keeman Lee, Mrinal Juddoo and A.R. MasriABSTRACTThis paper described an experimental investigations of combustion instability mode in a lean premixed dual swirl combustor for micro-gasturbine system. When such the instability occurs, a strong coupling between pressure oscillations and unsteady heat release excites a self-sustained acoustic wave which results in a loud, annoyed sound and may also lead a structural damage to the combustion chamber. The detailed period of flame behavior and heat release in combustion instability mode have been examined with high speed OH and CH-PLIF system and CH* chemiluminescence measurement, flame tomography with operated at 10 kHz and 6 kHz each. Experiment results suggest that unstable flame behavior has a specific frequency with 200 Hz and this frequency is accords with about 1/2 sub-harmonic of combustor resonance frequency, not funda-mental frequency. This is very interesting phenomenon that have not reported yet from other previous works. Therefore, when a thermo-acoustic instability with Rayleigh criterion occurs, the fact that the period of heat release and flame behavior are different each other was proposed for the first time through this work.
- Published
- 2014
- Full Text
- View/download PDF
48. Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by Fusarium fujikuroi
- Author
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Nyunhee Kim, Nam-Jin Chung, Kyung-Hwan Kim, Do-Yu Kang, Hyoja Oh, Song Lim Kim, Jun Oh, Jeong-Ho Baek, Inchan Choi, Hyeonso Ji, Kyeong-Seong Cheon, and Eun-Gyeong Lee
- Subjects
0106 biological sciences ,0301 basic medicine ,Candidate gene ,Single-nucleotide polymorphism ,Plant disease resistance ,Biology ,Quantitative trait locus ,01 natural sciences ,Catalysis ,lcsh:Chemistry ,Inorganic Chemistry ,03 medical and health sciences ,Centimorgan ,quantitative trait locus ,Cleaved amplified polymorphic sequence ,genetic map ,Physical and Theoretical Chemistry ,lcsh:QH301-705.5 ,Molecular Biology ,Genotyping ,Spectroscopy ,resequencing ,Genetics ,Organic Chemistry ,food and beverages ,General Medicine ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Bakanae ,bakanae disease ,010606 plant biology & botany - Abstract
Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, &lsquo, Samgwang&rsquo, and &lsquo, Junam&rsquo, respectively. Resequencing of &lsquo, genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, qFfR9, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24&ndash, 7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the &lsquo, genome sequence data, and are possibly candidate genes for qFfR9, therefore, qFfR9 could be utilized as a valuable resource for breeding BD-resistant rice varieties.
- Published
- 2019
- Full Text
- View/download PDF
49. New Parameters for Seedling Vigor Developed via Phenomics
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Jeong-Ho Baek, Nyunhee Kim, Hongseok Lee, Hyeonso Ji, Song Lim Kim, Do-Yu Kang, Taek-Ryoun Kwon, Eun-Gyeong Lee, Gang-Seob Lee, Yong Suk Chung, Kyung-Hwan Kim, Jun Oh, and Inchan Choi
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0106 biological sciences ,0301 basic medicine ,QTL ,Tiller (botany) ,initial growth ,Biology ,recombinant inbred line (RIL) ,lcsh:Technology ,01 natural sciences ,lcsh:Chemistry ,plant phenomics ,03 medical and health sciences ,Phenomics ,General Materials Science ,Leaf area index ,lcsh:QH301-705.5 ,Instrumentation ,Fluid Flow and Transfer Processes ,Abiotic component ,Oryza sativa ,lcsh:T ,rice ,Process Chemistry and Technology ,fungi ,General Engineering ,food and beverages ,Sowing ,biology.organism_classification ,lcsh:QC1-999 ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Agronomy ,lcsh:TA1-2040 ,Seedling ,Shoot ,lcsh:Engineering (General). Civil engineering (General) ,lcsh:Physics ,010606 plant biology & botany - Abstract
Early seedling establishment in rice (Oryza sativa L.), which is measured by primary/secondary tiller, shoot length, biomass, root-related traits, and leaf area index, is an important trait because it helps to compete for light, air, and water for better tolerating various abiotic stresses. Consequently, it can affect the yield. However, there are not many research studies on this subject. Furthermore, previous studies have only measured the target traits once. However, this does not reflect the variation of growth rate during the seedling stage. Thus, two data points, two weeks and four weeks after planting, were used in the current study. As a result, two QTL regions were detected for the growth differences via plant height and green area (reflecting tillering). We expect that these results can be utilized by breeders to evaluate and select vigorous seedlings for their breeding programs.
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- 2019
- Full Text
- View/download PDF
50. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis
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Shannon E. Mullican, Kyoung-Jae Won, Dmytro Kobuley, Rohini Sinha, Carly G. K. Ziegler, Frederic D. Bushman, Stephanie Grunberg, Igor E. Brodsky, Mitchell A. Lazar, Theresa Alenghat, Karen L. Joyce, Tram B. Hoang, Meenakshi Bewtra, Paul R. Giacomin, Steven A. Saenz, Meghan A. Wynosky-Dolfi, Inchan Choi, Lisa C. Osborne, Annelise G. Snyder, David Artis, and Gregory F. Sonnenberg
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Adult ,Male ,Paneth Cells ,Inflammation ,Biology ,digestive system ,Histone Deacetylases ,Mice ,Crohn Disease ,Intestinal mucosa ,RNA, Ribosomal, 16S ,Gene expression ,medicine ,Animals ,Homeostasis ,Humans ,Intestinal Mucosa ,Symbiosis ,Regulation of gene expression ,Multidisciplinary ,Bacteria ,Gene Expression Profiling ,HDAC3 ,Cell biology ,Intestines ,Mice, Inbred C57BL ,medicine.anatomical_structure ,Gene Expression Regulation ,Mucosal immunology ,Immunology ,Paneth cell ,Colitis, Ulcerative ,Female ,medicine.symptom ,Signal transduction ,Gene Deletion ,Signal Transduction - Abstract
The development and severity of inflammatory bowel diseases and other chronic inflammatory conditions can be influenced by host genetic and environmental factors, including signals derived from commensal bacteria. However, the mechanisms that integrate these diverse cues remain undefined. Here we demonstrate that mice with an intestinal epithelial cell (IEC)-specific deletion of the epigenome-modifying enzyme histone deacetylase 3 (HDAC3(ΔIEC) mice) exhibited extensive dysregulation of IEC-intrinsic gene expression, including decreased basal expression of genes associated with antimicrobial defence. Critically, conventionally housed HDAC3(ΔIEC) mice demonstrated loss of Paneth cells, impaired IEC function and alterations in the composition of intestinal commensal bacteria. In addition, HDAC3(ΔIEC) mice showed significantly increased susceptibility to intestinal damage and inflammation, indicating that epithelial expression of HDAC3 has a central role in maintaining intestinal homeostasis. Re-derivation of HDAC3(ΔIEC) mice into germ-free conditions revealed that dysregulated IEC gene expression, Paneth cell homeostasis and intestinal barrier function were largely restored in the absence of commensal bacteria. Although the specific mechanisms through which IEC-intrinsic HDAC3 expression regulates these complex phenotypes remain to be determined, these data indicate that HDAC3 is a critical factor that integrates commensal-bacteria-derived signals to calibrate epithelial cell responses required to establish normal host-commensal relationships and maintain intestinal homeostasis.
- Published
- 2013
- Full Text
- View/download PDF
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