Search

Genetic resources are the cornerstone of our food supply and play a pivotal role in developing new crop varieties that ensure sustainable agricultural production amid the challenges of climate change [...]

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Background: Histone variants play further important roles in DNA packaging and controlling gene expression. However, our understanding about their composition and their functions is limited. Results: Integrating proteomic and genomic approaches, we performed a comprehensive analysis of the epigenetic landscapes containing the four histone variants H3.1, H3.3, H2A.Z, and macroH2A. These histones were FLAG-tagged in HeLa cells and purified using chromatin immunoprecipitation (ChIP). By adopting ChIP followed by mass spectrometry (ChIP-MS), we quantified histone post-translational modifications (PTMs) and histone variant nucleosomal ratios in highly purified mononucleosomes. Subsequent ChIP followed by next-generation sequencing (ChIP-seq) was used to map the genome-wide localization of the analyzed histone variants and define their chromatin domains. Finally, we included in our study large datasets contained in the ENCODE database. We newly identified a group of regulatory regions enriched in H3.1 and the histone variant associated with repressive marks macroH2A. Systematic analysis identified both symmetric and asymmetric patterns of histone variant occupancies at intergenic regulatory regions. Strikingly, these directional patterns were associated with RNA polymerase II (PolII). These asymmetric patterns correlated with the enhancer activities measured using global run-on sequencing (GRO-seq) data. Conclusions: Our studies show that H2A.Z and H3.3 delineate the orientation of transcription at enhancers as observed at promoters. We also showed that enhancers with skewed histone variant patterns well facilitate enhancer activity. Collectively, our study indicates that histone variants are deposited at regulatory regions to assist gene regulation. [ABSTRACT FROM AUTHOR]

Background: Recent mapping of 5-hydroxymethylcytosine (5hmC) provides a genome-wide view of the distribution of this important chromatin mark. However, the role of 5hmC in specific regulatory regions is not clear, especially at enhancers. Results: We found a group of distal transcription factor binding sites highly enriched for 5-hdroxymethylcytosine (5hmC), but lacking any known activating histone marks and being depleted for nascent transcripts, suggesting a repressive role for 5hmC in mouse embryonic stem cells (mESCs). 5-formylcytosine (5fC), which is known to mark poised enhancers where H3K4me1 is enriched, is also observed at these sites. Furthermore, the 5hmC levels were inversely correlated with RNA polymerase II (PolII) occupancy in mESCs as well as in fully differentiated adipocytes. Interestingly, activating H3K4me1/2 histone marks were enriched at these sites when the associated genes become activated following lineage specification. These putative enhancers were shown to be functional in embryonic stem cells when unmethylated. Together, these data suggest that 5hmC suppresses the activity of this group of enhancers, which we termed “silenced enhancers”. Conclusions: Our findings indicate that 5hmC has a repressive role at specific proximal and distal regulatory regions in mESCs, and suggest that 5hmC is a new epigenetic mark for silenced enhancers. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]