UAV telephotography elucidates floristic variability and beta diversity of island cliffs under grazing interventions.

Cliffs contain one of the least known plant communities, which has been overlooked in biodiversity assessments due to the inherent inaccessibility. Our study adopted the unmanned aerial vehicle (UAV) with the telephoto camera to remotely clarify floristic variability across unreachable cliffs. Studied cliffs comprised 17 coastal and 13 inland cliffs in Gageodo of South Korea, among which 9 and 5 cliffs were grazed by the introduced cliff-dwelling goats. The UAV telephotography showed 154 and 166 plant species from coastal and inland cliffs, respectively. Inland cliffs contained more vascular plant species (P < 0.001), increased proportions of fern and woody species (P < 0.05), and decreased proportion of herbaceous species (P < 0.001) than coastal cliffs. It was also found that coastal and inland cliffs differed in the species composition (P < 0.001) rather than taxonomic beta diversity (P = 0.29). Furthermore, grazed coastal cliffs featured the elevated proportions of alien and annual herb species than ungrazed coastal cliffs (P < 0.05). This suggests that coastal cliffs might not be totally immune to grazing if the introduced herbivores are able to access cliff microhabitats; therefore, such anthropogenic introduction of cliff-dwelling herbivores should be excluded to conserve the native cliff plant communities.

Asymbiotic Seed Germination and In Vitro Seedling Development of the Endangered Orchid Species Cypripedium guttatum.

Cypripedium guttatum is a highly restricted terrestrial orchid that faces increasing endangerment owing to its habitat destruction and illegal collection. Compared to epiphytic orchids, terrestrial orchids such as C. guttatum have harder seed coats and more demanding in vitro germination conditions. This study aimed to develop an effective in vitro propagation system for C. guttatum to aid in its conservation. Seeds from mature capsules were subjected to various conditions, including sterilization using 1% sodium hypochlorite (NaOCl) and different light conditions, culture media, hormones, and organic supplements, to assess germination and early seedling development in vitro. Sterilization with 1% NaOCl significantly improved the germination rate, especially under dark conditions. Germination initiation occurred at 2 and 3 months in orchid seed sowing medium (OSM) and Murashige and Skoog (MS) medium, respectively. The addition of 1 mg/L naphthaleneacetic acid (NAA) further enhanced germination. However, the inclusion of organic supplements, such as apple and banana homogenates, in the culture medium led to substantial growth inhibition after 12 months. Notably, orchid maintenance medium (OMM) without organic additives proved to be the most suitable for seedling growth. The results of this study show that sterilization, appropriate light, and optimal NAA concentrations are beneficial for seed germination.

Development of InDel markers for interspecific hybridization between hill pigeons and feral pigeons based on whole-genome re-sequencing.

Interspecific hybridization occurs among birds, and closely related sister taxa tend to hybridize at a high rate. Genomic hybridization markers are useful for understanding the patterns and processes of hybridization and for conserving endangered species in captivity and the wild. In this study, we developed genomic hybridization markers for the F1 progeny of the sister taxa feral pigeons (Columba livia var. domestica) and endangered hill pigeons (Columba rupestris) (family Columbidae). Using whole-genome re-sequencing data, we performed genome-wide analysis for insertion/deletion (InDel) polymorphisms and validated using primers. We conducted polymerase chain reaction (PCR) and agarose gel electrophoresis to identify species-specific InDels. We produced eight F1 hybrids of hill and feral pigeons, and their samples were tested by re-performing analyses and sequencing using 11 species-specific InDel polymorphisms. Eight InDel markers simultaneously amplified two DNA fragments from all F1 hybrids, and there was no abnormality in the sequencing results. The application of genomic tools to detect hybrids can play a crucial role in the assessment of hybridization frequency in the wild. Moreover, systematic captive propagation efforts with hybrids can help control the population decline of hill pigeons.

Association between ranitidine use with potential NDMA impurities and risk of cancer in Korea.

N-Nitrosodimethylamine (NDMA) detected above the acceptable level in ranitidine products has been a great global concern. To examine the risk of cancer among people treated with ranitidine, we conducted a cohort study using the National Health Insurance Service-National Sample Cohort data (2002-2015) of South Korea. Patients were aged 40 or above as of January 2004 and began receiving ranitidine or other histamine-2 receptor antagonist (H2RA), active comparator, without a history of H2RAs prescription during the prior 2-years. The lag time was designated up to 6 years. The outcomes were an overall incident cancer risk and the risk of major single cancers during the follow-up. The association between ranitidine use and cancer risk was examined by Cox regression model. After exclusion and propensity score matching, 25,360 patients were available for analysis. The use of ranitidine was not associated with the overall cancer risk and major individual cancers [overall cancer: incidence rate per 1000 person-years, 2.9 vs 3.0 among the ranitidine users and other H2RAs users, respectively; adjusted hazard ratio (HR) and 95% confidence interval (95% CI) for all cancers, 0.98 (0.81-1.20)]. The higher cumulative exposure to ranitidine did not increase the cancer risk. Given the insufficient follow-up period, these findings should be interpreted carefully.

Endangered plant species under differing anthropogenic interventions: how to preserve Pterygopleurum neurophyllum in Wondong wetland?

Endangered wetland plants are important as the potential keystone species and mediators for plant-soil interactions. Establishing conservation strategies for endangered plants is also prioritized because of the elevating extinction risk by human-induced wetland disturbances. The present study examined the factors controlling the incidence of Pterygopleurum neurophyllum, the endangered wetland plant experiencing severe habitat loss throughout Northeast Asia. Here, P. neurophyllum populations and their surrounding environments were addressed in the last natural Korean habitat to assess the possible influential factors (vegetation coverage, species richness, exotic plant species, coarse rock content, soil bulk density, and soil electroconductivity and pH) under anthropogenic wetland interventions (with or without soil disturbance). Our results showed that P. neurophyllum occurred 6 out of 32 plots in the study area. All P. neurophyllum were found in Miscanthus-dominated area, but preferred microhabitats featuring reduced vegetation coverage, increased species richness, and undisturbed soils under vegetation removal. Multimodel inference also indicated that vegetation coverage (relative importance = 1.00) and coarse rock content (relative importance = 0.70) were the major influential factors for P. neurophyllum population size, and the surviving P. neurophyllum were strictly limited to where both of them were kept lowered. Furthermore, the wetland intervention with soil disturbance had a negative effect on P. neurophyllum by creating the rocky and compacted soil surface as a result of land reclamation treatments. Conversely, the wetland intervention without soil disturbance enhanced the P. neurophyllum incidence by decreasing vegetation coverage of the overcrowding competitive plants. Overall findings reflect that the strategies to counteract habitat loss and manage the overly dense competitive plants should be necessary for conserving P. neurophyllum, as well as other wetland plants threatened by the human-induced disturbances and excessive competition intensities.

Population genetic structure and conservation management of hill pigeons (Columba rupestris) recently endangered in South Korea.

BACKGROUND: Hill pigeons (Columba rupestris) are close to local extinction (ca. less than 100 individuals) in South Korea where a variety of conservation management procedures are urgently required. OBJECTIVE: This study was aimed at determining the conservation direction of captive propagation and reintroduction of hill pigeons using genetic information based on mitochondrial DNA. We also evaluated the extent of hybridization between hill pigeons and cohabiting domestic pigeons. METHODS: We used 51 blood samples of hill pigeons from Goheung (GH), Gurye (GR), and Uiryeong (UR), and domestic pigeons cohabiting with hill pigeon populations. Genetic diversity, pairwise Fst, analysis of molecular variance, and haplotype network analysis were used to examine the genetic structure of hill pigeons. RESULTS: Hill pigeons that inhabited South Korea were not genetically distinct from Mongolian and Russian populations and showed relatively low genetic diversity compared with other endangered species in Columbidae. The GR population that exhibited the largest population size showed lower genetic diversity, compared to the other populations, although the pairwise Fst values of the three populations indicated low genetic differentiation. The GH and GR populations were confirmed to lack hybridization, relatively, whereas the UR population was found to exhibit some degrees of hybridization. CONCLUSION: To conserve hill pigeons with low genetic diversity and differentiation in South Korea, the conservation process of captive propagation and reintroduction may require artificial gene flows among genetically verified populations in captivity and wildness. The introduction of foreign individuals from surrounding countries is also considered an alternative strategy for maintaining genetic diversity.

Effects of Light Condition on Growth and Physiological Characteristics of the Endangered Species Sedirea japonica under RCP 6.0 Climate Change Scenarios.

This study was conducted to evaluate the physiological and growth responses of Sedirea japonica cultured in chambers under RCP 6.0 and different light conditions. S. japonica was grown in a soil-plant daylight system chamber under two treatments, a control (CO2 = 400 ppm) and a climate change treatment (CCT) (CO2 = 650 ppm, temperature = control + 3 °C), and three different shading treatments (60%, 90%, and no-shading). S. japonica showed the characteristics of typical Crassulacean acid metabolism (CAM) plants. As the shading rate increased, it increased chlorophyll content, leaf area, and leaf dry weight to efficiently absorb and use light. The CCT had a lower CO2 absorption rate, stomatal conductance, and growth rate and slightly higher water utilization efficiency than the control. This was because stomatal closure occurred in the CCT to reduce water loss due to a relatively higher temperature. As CO2 fixation decreased and consumption increased due to respiration, the overall growth was inhibited. The CCT without shading revealed a dynamic photoinhibition phenomenon showing a significant increase in ABS/RC, TRo/RC, ETo/RC, and DIo/RC and a decrease in PI ABS and DF ABS. In this group, leaf, root, and total dry weight, chlorophyll content, and carotenoid content were the worst growth indices.

Effects of Different Growth Media on In Vitro Seedling Development of an Endangered Orchid Species Sedirea japonica.

Sedirea japonica is becoming endangered, and even extinct, due to habitat destruction and illegal collection, and the development of an optimized artificial propagation system is necessary for its conservation and reintroduction. Thus, the effects of plant growth medium strength (Murashige and Skoog (MS) and Hyponex media) and the addition of activated charcoal (AC) and organic supplements on seedling growth of S. japonica were investigated through in vitro seed culture. The results showed that seedling growth was higher in half-strength (1/2) media than in full-strength media. After the addition of AC, the highest leaf area (2.14 cm2) was recorded in the seedlings grown in 1/2 Hyponex medium, and after the addition of organic supplements, root development increased regardless of the media type. Among the sixteen suitable media tested at later seedling growth stages, 1/2 MS medium with the addition of 0.6 g·L-1 AC, 30 g·L-1 banana homogenate and 10 g·L-1 apple homogenate was generally effective in fresh weight (6.13 g) and root length (9.59 cm). We demonstrated which organic supplements are preferred for in vitro growth of seedlings developed from S. japonica protocorms by asymbiotic seed culture, which can be used for mass production and conservation of this rare epiphytic orchid.

Overexpression of rice F-box protein OsFBX322 confers increased sensitivity to gamma irradiation in Arabidopsis.

Ionizing radiation has a substantial effect on physiological and biochemical processes in plants via induction of transcriptional changes and diverse genetic alterations. Previous microarray analysis showed that rice OsFBX322, which encodes a rice F-box protein, was downregulated in response to three types of ionizing radiation: gamma irradiation, ion beams, and cosmic rays. In order to characterize the radiation-responsive genes in rice, OsFBX322 was selected for further analysis. OsFBX322 expression patterns in response to radiation were confirmed using quantitative RT-PCR. Transient expression of a GFP-OsFBX322 fusion protein in tobacco leaf epidermis indicated that OsFBX322 is localized to the nucleus. To determine the effect of OsFBX322 expression on radiation response, OsFBX322 was overexpressed in Arabidopsis. Transgenic overexpression lines were more sensitive to gamma irradiation than control plants. These results suggest that OsFBX322 plays a negative role in the defense response to radiation in plants. In addition, we obtained four co-expression genes of OsFBX322 by specific co-expression networks using the ARANCE. Quantitative RT-PCR showed that the four genes were also downregulated after exposure to the three types of radiation. These results imply that the co-expressed genes may serve as key regulators in the radiation response pathway in plants.

Overexpression of rice jacalin-related mannose-binding lectin (OsJAC1) enhances resistance to ionizing radiation in Arabidopsis.

BACKGROUND: Jacalin-related lectins in plants are important in defense signaling and regulate growth, development, and response to abiotic stress. We characterized the function of a rice mannose-binding jacalin-related lectin (OsJAC1) in the response to DNA damage from gamma radiation. RESULTS: Time- and dose-dependent changes of OsJAC1 expression in rice were detected in response to gamma radiation. To identify OsJAC1 function, OsJAC1-overexpressing transgenic Arabidopsis plants were generated. Interestingly, OsJAC1 overexpression conferred hyper-resistance to gamma radiation in these plants. Using comparative transcriptome analysis, genes related to pathogen defense were identified among 22 differentially expressed genes in OsJAC1-overexpressing Arabidopsis lines following gamma irradiation. Furthermore, expression profiles of genes associated with the plant response to DNA damage were determined in these transgenic lines, revealing expression changes of important DNA damage checkpoint and perception regulatory components, namely MCMs, RPA, ATM, and MRE11. CONCLUSIONS: OsJAC1 overexpression may confer hyper-resistance to gamma radiation via activation of DNA damage perception and DNA damage checkpoints in Arabidopsis, implicating OsJAC1 as a key player in DNA damage response in plants. This study is the first report of a role for mannose-binding jacalin-related lectin in DNA damage.

Comparisons of item difficulty and passing scores by test equating in a basic medical education curriculum.

PURPOSE: Test equating studies in medical education have been conducted only for high-stake exams or to compare two tests given in a single course. Based on item response theory, we equated computer-based test (CBT) results from the basic medical education curriculum at the College of Medicine, the Catholic University of Korea and evaluated the validity of using fixed passing scores. METHODS: We collected 232 CBTs (28,636 items) for 40 courses administered over a study period of 9 years. The final data used for test equating included 12 pairs of tests. After test equating, Wilcoxon rank-sum tests were utilized to identify changes in item difficulty between previous tests and subsequent tests. Then, we identified gaps between equated passing scores and actual passing scores in subsequent tests through an observed-score equating method. RESULTS: The results of Wilcoxon rank-sum tests indicated that there were no significant differences in item difficulty distribution by year for seven pairs. In the other five pairs, however, the items were significantly more difficult in subsequent years than in previous years. Concerning the gaps between equated passing scores and actual passing scores, equated passing scores in 10 pairs were found to be lower than actual passing scores. In the other two pairs, equated passing scores were higher than actual passing scores. CONCLUSION: Our results suggest that the item difficulty distributions of tests taught in the same course during successive terms can differ significantly. It may therefore be problematic to use fixed passing scores without considering this possibility.

Functional Mechanisms Underlying the Antimicrobial Activity of the Oryza sativa Trx-like Protein.

Plants are constantly subjected to a variety of environmental stresses and have evolved regulatory responses to overcome unfavorable conditions that might reduce or adversely change a plant's growth or development. Among these, the regulated production of reactive oxygen species (ROS) as a signaling molecule occurs during plant development and pathogen defense. This study demonstrates the possible antifungal activity of Oryza sativa Tetratricopeptide Domain-containing thioredoxin (OsTDX) protein against various fungal pathogens. The transcription of OsTDX was induced by various environmental stresses known to elicit the generation of ROS in plant cells. OsTDX protein showed potent antifungal activity, with minimum inhibitory concentrations (MICs) against yeast and filamentous fungi ranging between 1.56 and 6.25 and 50 and 100 µg/mL, respectively. The uptake of SYTOX-Green into fungal cells and efflux of calcein from artificial fungus-like liposomes suggest that its killing mechanism involves membrane permeabilization and damage. In addition, irregular blebs and holes apparent on the surfaces of OsTDX-treated fungal cells indicate the membranolytic action of this protein. Our results suggest that the OsTDX protein represents a potentially useful lead for the development of pathogen-resistant plants.

A comprehensive analysis of the Korean fir (Abies koreana) genes expressed under heat stress using transcriptome analysis.

Korean fir (Abies koreana), a rare species endemic to South Korea, is sensitive to climate change. Here, we used next-generation massively parallel sequencing technology and de novo transcriptome assembly to gain a comprehensive overview of the Korean fir transcriptome under heat stress. Sequencing control and heat-treated samples of Korean fir, we obtained more than 194,872,650 clean reads from each sample. After de novo assembly and quantitative assessment, 42,056 unigenes were generated with an average length of 908 bp. In total, 6,401 differentially expressed genes were detected, of which 2,958 were up-regulated and 3,443 down-regulated, between the heat-treated and control samples. A gene ontology analysis of these unigenes revealed heat-stress-related terms, such as "response to stimulus". Further, in depth analysis revealed 204 transcription factors and 189 Hsps as differentially expressed. Finally, 12 regulated candidate genes associated with heat stress were examined using quantitative real-time PCR (qRT-PCR). In this study, we present the first comprehensive characterisation of Korean fir subjected to heat stress using transcriptome analysis. It provides an important resource for future studies of Korean fir with the objective of identifying heat stress tolerant lines.

Prevalence and predictors of tricyclic antidepressant use among elderly Koreans in primary-care and specialty clinics.

OBJECTIVES: Tricyclic antidepressants (TCAs) are prescribed with caution in the elderly due to diverse side effects. We analyzed the patterns of TCA use in elderly patients in primary-care and specialty clinics and investigated factors influencing TCA prescriptions. MATERIALS AND METHODS: Elderly patients (≥ 65 years old) prescribed antidepressants in primary-care clinics in 2013 were included from the Health Insurance Review and Assessment Service-Aged Patient Sample (HIRA-APS). Prevalence of TCA prescriptions was assessed by insurance coverage status, clinical specialty, and region. Multiple logistic regression analysis was performed to compute odds ratios (ORs) and 95% confidence intervals (CIs) for factors associated with TCA prescriptions. RESULTS: TCAs and selective serotonin reuptake inhibitors (SSRIs) comprised 45.2% and 15.0% of all antidepressant prescriptions, respectively. TCAs comprised 61.5% and 20.7% of antidepressant prescriptions for pain and depression, respectively. Patients aged ≥ 85 years were less likely to be treated with TCAs (OR 0.81, 95% CI 0.79 - 0.84) than those aged 65 - 69 years. The odds for being prescribed TCAs were higher for patients residing in cities (OR 1.20, 95% CI 1.18 - 1.23), treated in nonpsychiatric clinics (OR 5.64, 95% CI 5.53 - 5.76), and those covered by Veteran's Health (OR 1.62, 95% CI 1.37 - 1.90) when compared to patients residing in the Seoul metropolitan area, treated in psychiatric clinics, or covered by National Health Insurance, respectively. The prescriptions of TCAs with pain diagnoses were much higher than prescriptions for depression (OR 1.87, 95% CI 1.82 - 1.93). CONCLUSIONS: Compared with a 2005 report, the prevalence of TCA prescriptions in elderly patients in Korea has decreased substantially, but remains high. Various efforts should be considered to reduce TCA prescriptions in the elderly.
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Individual class evaluation and effective teaching characteristics in integrated curricula.

BACKGROUND: In an integrated curriculum, multiple instructors take part in a course in the form of team teaching. Accordingly, medical schools strive to manage each course run by numerous instructors. As part of the curriculum management, course evaluation is conducted, but a single, retrospective course evaluation does not comprehensively capture student perception of classes by different instructors. This study aimed to demonstrate the need for individual class evaluation, and further to identify teaching characteristics that instructors need to keep in mind when preparing classes. METHODS: From 2014 to 2015, students at one medical school left comments on evaluation forms after each class. Courses were also assessed after each course. Their comments were categorized by connotation (positive or negative) and by subject. Within each subject category, test scores were compared between positively and negatively mentioned classes. The Mann-Whitney U test was performed to test group differences in scores. The same method was applied to the course evaluation data. RESULTS: Test results for course evaluation showed group difference only in the practice/participation category. However, test results for individual class evaluation showed group differences in six categories: difficulty, main points, attitude, media/contents, interest, and materials. That is, the test scores of classes positively mentioned in six domains were significantly higher than those of negatively mentioned classes. CONCLUSIONS: It was proved that individual class evaluation is needed to manage multi-instructor courses in integrated curricula of medical schools. Based on the students' extensive feedback, we identified teaching characteristics statistically related to academic achievement. School authorities can utilize these findings to encourage instructors to develop effective teaching characteristics in class preparation.

Molecular dissection of the response of the rice Systemic Acquired Resistance Deficient 1 (SARD1) gene to different types of ionizing radiation.

PURPOSE: Exposure to ionizing radiation induces plant defenses by regulating the expression of response genes. The systemic acquired resistance deficient 1 (SARD1) is a key gene in plant defense response. In this study, the function of Oryza sativa SARD1 (OsSARD1) was investigated after exposure of seeds/plants to ionizing radiation, jasmonic acid (JA) or salicylic acid (SA). MATERIALS AND METHODS: Rice seeds exposed to two types of ionizing radiations (gamma ray [GR] and ion beam [IB]) were analyzed by quantitative reverse transcription PCR (qRT-PCR) to identify the genes that are altered in response to ionizing radiation. Then, OsSARD1-overexpressing homozygous Arabidopsis plants were generated to assess the effects of OsSARD1 in the response to irradiation. The phenotypes of these transgenic plants, as well as control plants, were monitored after GR irradiation at doses of 200 and 300 Gray (Gy). RESULTS: The OsSARD1 transcript was strongly downregulated after exposure to GR and IB irradiation. Previous phylogenetic analysis showed that the Arabidopsis SARD1 (AtSARD1) protein is closely related to Arabidopsis calmodulin-binding protein 60g (AtCBP60g), which is known to be required for activation of SA biosynthesis. In this study, phylogenetic analysis showed that OsSARD1 was grouped with AtSARD1. The OsSARD1 gene was induced after exposure to SA and JA. The biological phenotype of OsSARD1-overexpressing Arabidopsis plants was examined. OsSARD1-overexpressing plants displayed resistance to GR; in comparison with wild-type plants, the height and weight of OsSARD1-overexpressing plants were significantly greater after GR irradiation. In addition, OsSARD1 protein was abundantly accumulated in the nucleus. CONCLUSIONS: The results indicate that OsSARD1 plays an important role in the regulation of the defense responses to GR and IB irradiation and exhibits phytohormone induced expression.

Identification of gamma ray irradiation-induced mutations in membrane transport genes in a rice population by TILLING.

A high-salt environment represents environmental stress for most plants. Those that can grow and thrive in such an environment must have membrane transport systems that can respond effectively. Plant roots absorb Na+ from the soil, and the plant must maintain Na+ homeostasis to survive salt stress. A major mechanism by which salt-tolerant plants adapt to salt stress is through modulation of ion transport genes. We have subjected a population of rice plants to mutagenesis, and identified lines with both single-nucleotide polymorphisms (SNPs) in membrane transport genes and altered responses to salt stress. Primers labeled with FAM or HEX fluorescent dyes were designed for nine target genes encoding membrane transport proteins that are believed to regulate salt stress tolerance. A TILLING (Targeting Induced Local Lesions IN Genome) assay was performed on 2,961 M2 rice mutant lines using electrophoresis. After the TILLING assay, a total of 41 mutant lines containing SNPs in the target genes were identified and screened. The average number of mutations per gene was 1/492 kb in lines having SNPs, and the percentage of mutation sites per total sequence was 0.67. Among the 41 lines, nine had altered sequences in the exon region of the genes. Of these nine lines, seven were tolerant to salt stress after exposure to 170 mM NaCl for three weeks, while the other two lines were not more salt-tolerant than the control lines. Furthermore, five mutant lines containing SNPs in the coding region of OsAKT1, OsHKT6, OsNSCC2, OsHAK11 and OsSOS1 showed changed expression levels for each gene. We conclude that variation in membrane transport genes, such as expression levels and protein structures, may affect the rice plant's tolerance to salt stress. These mutations represent traits that may be selected for large rice mutant populations, permitting efficient acquisition of salt-tolerant lines.

Transcriptome analysis of reproductive-stage Arabidopsis plants exposed gamma-ray irradiation at various doses.

PURPOSE: Gamma rays (GR) induce significant changes in the structure and expression of genes involved in the regulation of diverse biochemical and physiological processes. Arabidopsis plants exhibit different growth and development patterns in response to exposure to GR. The effects on gene expression of different radiation doses of GR (100 and 800 Gy) administered to Arabidopsis plants were examined at the reproductive stage. MATERIALS AND METHODS: We irradiated 26-day-old plants with three replications [developmental stages 5.1-6.0, according to Boyes et al. ( 2001 )] using a GR irradiator (60 Co, ca. 150 TBq capacity, Atomic Energy of Canada Limited, Ontario, Canada) at the Korea Atomic Energy Research Institute. Plants were treated with 100, 200, 300, 400, 800, 1200, 1600, or 2000 Gy, and the doses were made from varying the distance to the source. RESULTS: We conducted a high-throughput screening analysis and detected 883 GR-responsive genes that showed significant changes; these were involved in several putative metabolic pathways related to biotic stress. Additionally, five overrepresented cis-regulatory elements were identified in the 1-kb upstream regions of GR-responsive genes by using motif enrichment analysis. We also detected three GR-responsive genes associated with stamen development and confirmed their co-regulation with functionally interacting genes. CONCLUSIONS: This finding suggests that a network-based analysis is a viable approach to identify significant GR-responsive genes associated with the reproductive stage of Arabidopsis. Our results provide further insights into the complex biological systems involved in the response to different doses of GR in plants.

Identification of altered metabolic pathways of γ-irradiated rice mutant via network-based transcriptome analysis.

In order to develop rice mutants for crop improvement, we applied γ-irradiation mutagenesis and selected a rice seed color mutant (MT) in the M14 targeting-induced local lesions in genome lines. This mutant exhibited differences in germination rate, plant height, and root length in seedlings compared to the wild-type plants. We found 1645 different expressed probes of MT by microarray hybridization. To identify the modified metabolic pathways, we conducted integrated genomic analysis such as weighted correlation network analysis with a module detection method of differentially expressed genes (DEGs) in MT on the basis of large-scale microarray transcriptional profiling. These modules are largely divided into three subnetworks and mainly exhibit overrepresented gene ontology functions such as oxidation-related function, ion-binding, and kinase activity (phosphorylation), and the expressional coherences of module genes mainly exhibited in vegetative and maturation stages. Through a metabolic pathway analysis, we detected the significant DEGs involved in the major carbohydrate metabolism (starch degradation), protein degradation (aspartate protease), and signaling in sugars and nutrients. Furthermore, the accumulation of amino acids (asparagine and glutamic acid), sucrose, and starch in MT were affected by gamma rays. Our results provide an effective approach for identification of metabolic pathways associated with useful agronomic traits in mutation breeding.

Selection and molecular characterization of a lipoxygenase-free soybean mutant line induced by gamma irradiation.

KEY MESSAGE: A lipoxygenase-free soybean mutant line (H70) induced by gamma ray was selected and its detailed information about the lipoxygenase was analyzed by comparison of DNA sequence. Soybean seeds contain three lipoxygenase enzymes, which induce a beany or grassy flavor. The elimination of lipoxygenases can reduce the poor stability and off-flavors of soybean oil and protein products. In this study, we selected a soybean mutant (H70) in which the three lipoxygenases had been mutated using gamma rays. To obtain detailed information about the lipoxygenase, we investigated the sequences of the Lox1, Lox2 and Lox3 genes in H70 compared to the original cultivar, Hwanggum. Comparisons of the sequences of the Lox1 and Lox2 genes in H70 with those in a line with normal lipoxygenase (HG) showed that the mutations in these genes affected a highly conserved group of six histidine residues necessary for enzymatic activity. Lox1 in H70 contained a 74 bp deletion in exon 8, creating a stop codon that prematurely terminates translation. A single point mutation (T-A) in exon 8 of Lox2 changed histidine (H532, one of the iron-binding ligands essential for Lox2 activity) to glutamine. The mutation in the Lox3 gene in H70 was a single-point mutation in exon 6 (A-G), which changed the amino acid from histidine to arginine. This amino acid alteration in Lox3 was located in the N-terminal barrel, which might play a role in molecular recognition during catalysis and/or proteolysis. These results suggest that gene analysis based on DNA sequencing could be useful for elucidating the lipoxygenase content in soybean mutant lines. Additionally, the soybean mutant line selected in this study could be used to develop soybean cultivars with improved flavor.