Comprehensive transcriptomic analysis of three varieties with different brown planthopper-resistance identifies leaf sheath lncRNAs in rice.

BACKGROUND: Long non-coding RNAs (lncRNAs) have been brought great attention for their crucial roles in diverse biological processes. However, systematic identification of lncRNAs associated with specialized rice pest, brown planthopper (BPH), defense in rice remains unexplored. RESULTS: In this study, a genome-wide high throughput sequencing analysis was performed using leaf sheaths of susceptible rice Taichung Native 1 (TN1) and resistant rice IR36 and R476 with and without BPH feeding. A total of 2283 lncRNAs were identified, of which 649 lncRNAs were differentially expressed. During BPH infestation, 84 (120 in total), 52 (70 in total) and 63 (94 in total) of differentially expressed lncRNAs were found only in TN1, IR36 and R476, respectively. Through analyzing their cis-, trans-, and target mimic-activities, not only the lncRNAs targeting resistance genes (NBS-LRR and RLKs) and transcription factors, but also the lncRNAs acting as the targets of the well-studied stress-related miRNAs (miR2118, miR528, and miR1320) in each variety were identified. Before the BPH feeding, 238 and 312 lncRNAs were found to be differentially expressed in TN1 vs. IR36 and TN1 vs. R476, respectively. Among their putative targets, the plant-pathogen interaction pathway was significantly enriched. It is speculated that the resistant rice was in a priming state by the regulation of lncRNAs. Furthermore, the lncRNAs extensively involved in response to BPH feeding were identified by Weighted Gene Co-expression Network Analysis (WGCNA), and the possible regulation networks of the key lncRNAs were constructed. These lncRNAs regulate different pathways that contribute to the basal defense and specific resistance of rice to the BPH. CONCLUSION: In summary, we identified the specific lncRNAs targeting the well-studied stress-related miRNAs, resistance genes, and transcription factors in each variety during BPH infestation. Additionally, the possible regulating network of the lncRNAs extensively responding to BPH feeding revealed by WGCNA were constructed. These findings will provide further understanding of the regulatory roles of lncRNAs in BPH defense, and lay a foundation for functional research on the candidate lncRNAs.

Bulk segregant analysis coupled with transcriptomics and metabolomics revealed key regulators of bacterial leaf blight resistance in rice.

BACKGROUND: Bacterial leaf blight (BLB) is a highly destructive disease, causing significant yield losses in rice (Oryza sativa). Genetic variation is contemplated as the most effective measure for inducing resistance in plants. The mutant line T1247 derived from R3550 (BLB susceptible) was highly resistant to BLB. Therefore, by utilizing this valuable source, we employed bulk segregant analysis (BSA) and transcriptome profiling to identify the genetic basis of BLB resistance in T1247. RESULTS: The differential subtraction method in BSA identified a quantitative trait locus (QTL) on chromosome 11 spanning a 27-27.45 Mb region with 33 genes and 4 differentially expressed genes (DEGs). Four DEGs (P < 0.01) with three putative candidate genes, OsR498G1120557200, OsR498G1120555700, and OsR498G1120563600,0.01 in the QTL region were identified with specific regulation as a response to BLB inoculation. Moreover, transcriptome profiling identified 37 resistance analogs genes displaying differential regulation. CONCLUSIONS: Our study provides a substantial addition to the available information regarding QTLs associated with BLB, and further functional verification of identified candidate genes can broaden the scope of understanding the BLB resistance mechanism in rice.

Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice.

Heterosis has been widely used in multiple crops. However, the molecular mechanism and prediction of heterosis remains elusive. We generated five F1 hybrids [four showing better-parent heterosis (BPH) and one showing mid-parent heterosis], and performed the transcriptomic and methylomic analyses to identify the candidate genes for BPH and explore the molecular mechanism of heterosis and the potential predictors for heterosis. Transcriptomic results showed that most of the differentially expressed genes shared in the four better-parent hybrids were significantly enriched into the terms of molecular function, and the additive and dominant effects played crucial roles for BPH. DNA methylation level, especially in CG context, significantly and positively correlated with grain yield per plant. The ratios of differentially methylated regions in CG context in exons to transcription start sites between the parents exhibited significantly negative correlation with the heterosis levels of their hybrids, as was further confirmed in 24 pairwise comparisons of other rice lines, implying that this ratio could be a feasible predictor for heterosis level, and this ratio of less than 5 between parents in early growth stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better-parent hybrids as the candidate genes for BPH. Our findings helped shed more light on the molecular mechanism and heterosis prediction.

The grain yield regulator NOG1 plays a dual role in latitudinal adaptation and cold tolerance during rice domestication.

Rice originated in tropical and subtropical regions and is distributed worldwide. Low temperature is one of the most critical abiotic stresses affecting grain yield and geographical distribution of rice. It is vital to elucidate the molecular mechanism of chilling tolerance in rice for ensuring cereals production. Previously we isolated the domestication-related gene NOG1 which affects rice grain number and yield. In this study, we specified that rice varieties harboring high-yielding NOG1 allele are more distributed in low-latitude regions. Additionally, we observed NOG1 influences the chilling tolerance of rice. Through genome-wide transcriptional analysis after cold treatment at 10°C, there were 717 differentially expressed genes (DEGs) in nog1 near-isogenic lines compared with the control Guichao 2, including 432 up-regulated DEGs and 284 down-regulated DEGs. Gene ontology annotations and KEGG enrichment analysis of DEGs showed that various biological processes and signaling pathways were related to cold stress, such as lipid metabolism and genetic information processing. These results provide new insights into the mechanism of chilling tolerance in rice and the molecular basis of environmental adaptation during rice domestication.

Blockchain technology-based sustainable management research: the status quo and a general framework for future application.

The problems of data leakage and unreliable information transfer in the management process make sustainability management an inevitable need for future development. Globally, there is increasing attention paid to blockchain technology and particularly its application in addressing sustainable management issues, both from academia and industry. Aiming to deepen the understanding of how blockchain technology could deal with sustainable management issues across different disciplines, this paper investigates the latest research on the application of blockchain technology in sustainable management published from 2017 to 2021. It is found that there is a drastic surge of publications in the recent 2 years. The analysis focuses on authors' origins, the collaboration network of the keywords, countries, and research topics covered. The application of blockchain technology in five key sectors of sustainable management, encompassing energy management, construction management, supply chain management, environmental management, and e-government management, is selected for further analysis detail. Also, a general framework for applying blockchain technology is proposed for broadening its use and dealing with sustainable management issues. The findings show that the identified 108 publications are distributed in 75 different journals, and scholars from China, the UK, and the USA have been working closely in BT-based sustainable management research. Blockchain technology is just emerging in sustainable management, and there is a great potential for applying blockchain technology to improve sustainable management performance and, more importantly, to provide solutions to quite a few long-lasting problems in these sectors. Opportunities for future research are also presented and discussed.

Rice Brittle Culm19 Encoding Cellulose Synthase Subunit CESA4 Causes Dominant Brittle Phenotype But has No Distinct Influence on Growth and Grain Yield.

BACKGROUND: Mechanical strength is a crucial agronomic trait in rice (Oryza sativa), and brittle mutants are thought suitable materials to investigate the mechanism of cell wall formation. So far, almost all brittle mutants are recessive, and most of them are defected in multiple morphologies and/or grain yield, limiting their application in hybrid breeding and in rice straw recycling. RESULTS: We identified a semi-dominant brittle mutant Brittle culm19 (Bc19) isolated from the japonica variety Nipponbare through chemical mutagenesis. The mutant showed the same apparent morphologies and grain yield to the wild type plant except for its weak mechanical strength. Its development of secondary cell wall in sclerenchyma cells was affected, along with reduced contents of cellulose, hemicellulose, lignin and sugars in culms and leaves. Positional cloning suggested that the Bc19 gene was allelic to OsCESA4, encoding one of the cellulose synthase A (CESA) catalytic subunits. In this mutant, a C-to-T substitution occurred in the coding sequence of BC19, causing the P507S missense mutation in its encoded product, which was located in the second cytoplasmic region of the OsCESA4 protein. Furthermore, introducing mutant gene Bc19 into the wild-type plant resulted in brittle plants, confirming that the P507S point mutation in OsCESA4 protein was responsible for the semi-dominant brittle phenotype of Bc19 mutant. Reverse correlation was revealed between cellulose contents and expression levels of mutant gene Bc19 among the homozygous mutant, the hybrid F1 plant, and the Bc19 overexpression transgenic plants, implying that gene Bc19 might affect cellulose synthesis in a dosage-dependent manner. CONCLUSIONS: Bc19, a semi-dominant brittle mutant allele of gene OsCESA4, was identified using map-based cloning approach. The mutated protein of Bc19 possessing the P507S missense mutation behaved in a dosage-dependent semi-dominant manner. Unique brittle effect on phenotype and semi-dominant genetic quality of gene Bc19 indicated its potential application in grain-straw dual-purpose hybrid rice breeding.

A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems.

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

The prevalence of posttraumatic stress in adolescents eight years after the Wenchuan earthquake.

In 2008, an 8.0 Richter scale earthquake devastated Wenchuan in China, which resulted in heavy casualties, and had wide-reaching psychological effects on survivors. To examine its impact on the survivors, this study aims to investigate the prevalence of posttraumatic stress disorder (PTSD) and posttraumatic growth (PTG) in adolescents eight years after the earthquake. The cross-section survey was conducted in two different earthquake-affected areas, and data were collected from 4118 respondents. Instruments included the questionnaire on demographic information, the questionnaire on seismic exposure, PTSD Checklist-Civilian Version (PCL-C) questionnaire, Posttraumatic Growth Inventory (PTGI), Perceived Social Support Scale (PSSS) and Simple Coping Style Questionnaire (SCSQ). During the survey, there were 1998 valid questionnaires from the generally affected area and 2120 questionnaires from the severely affected area. The rate of PTSD is 1.9% in the generally affected area and 2.7% in the severely affected disaster area; there is no significant difference between the two differently affected areas. Occurrences of PTSD and PTG are significantly positively correlated in the generally affected area, nevertheless, there is a significant negative correlation between PTSD and PTG in most systems of the severely affected area. The results of this study help to expand our knowledge regarding posttraumatic stress in adolescents 8 years after the Wenchuan earthquake, and it provides suggestions for specific long-term health interventions in such populations. To prevent earthquake-related psychological issues among adolescent survivors, social support, psychological aid, and improvement of the living environment are necessary to buffer negative posttraumatic stress.

QTL mapping using an ultra-high-density SNP map reveals a major locus for grain yield in an elite rice restorer R998.

To dissect the genetic basis of yield formation in restorer line of hybrid rice, we conducted QTL analysis for 6 yield traits including panicles per plant (PPP), grains per panicle (GPP), grain yield per plant (GY), thousand-grain weight (TGW), above-ground biomass (AGB), and harvest index (HI) using SNP markers in a recombinant inbred lines (RILs) population derived from a cross between a tropical japonica inbred Francis and an elite indica restorer Guanghui 998 (R998). A total of 26 QTLs were detected using a high density genetic map consisting of 3016 bin markers. Nineteen out of the 26 QTL alleles from R998 had a beneficial effect on yield traits. Most of the QTLs were co-located with previously reported rice QTLs. qAGB6 and qHI9, controlling AGB and HI respectively, were detected as novel QTLs. Four QTLs for GY were repeatedly detected across two years, with all the beneficial alleles from R998. Notably, qGY8 explained over 20% of the yield variance in both years. Moreover, qGY8 together with qTGW8 and qHI8 formed a QTL cluster. Markers tightly linked with qGY8 were developed. Cloning of qGY8 will facilitate its further exploitation in high-yield breeding.

Transcriptomic Analysis Reveals New Insights into High-Temperature-Dependent Glume-Unclosing in an Elite Rice Male Sterile Line.

Glume-unclosing after anthesis is a widespread phenomenon in hybrid rice and also a maternal hereditary trait. The character of Glume-unclosing in rice male sterile lines also seriously influences germination rate and the commercial quality of hybrid rice seeds. We validated that the type of glume-unclosing after anthesis in the elite rice thermo-sensitive genic male sterile (TGMS) line RGD-7S was caused by high temperature. Transcriptomic sequencing of rice panicles was performed to explore the change of transcript profiles under four conditions: pre- and post-anthesis under high temperature (HRGD0 and HRGD1), and pre- and post-anthesis under low temperature (LRGD0 and LRGD1). We identified a total of 14,540 differentially expressed genes (DEGs) including some heat shock factors (HSFs) across the four samples. We found that more genes were up-regulated than down-regulated in the sample pair HRGD1vsHRGD0. These up-regulated genes were significantly enriched in the three biological processes of carbohydrate metabolism, response to water and cell wall macromolecular metabolism. Simultaneously, we also found that the HSF gene OsHsfB1 was specially up-regulated in HRGD1vsHRGD0. However, the down-regulated DEGs in LRGD1vsLRGD0 were remarkably clustered in the biological process of carbohydrate metabolism. This suggests that carbohydrate metabolism may play a key role in regulation of glume-unclosing under high temperature in RGD-7S. We also analyzed the expression pattern of genes enriched in carbohydrate metabolism and several HSF genes under different conditions and provide new insights into the cause of rice glume-unclosing.

Map-based cloning and characterization of the novel yellow-green leaf gene ys83 in rice (Oryza sativa).

Leaf-color mutants have been extensively studied in rice, and many corresponding genes have been identified up to now. However, leaf-color mutation mechanisms are diverse and still need further research through identification of novel genes. In the present paper, we isolated a leaf-color mutant, ys83, in rice (Oryza sativa). The mutant displayed a yellow-green leaf phenotype at seedling stage, and then slowly turned into light-green leaf from late tillering stage. In its yellow leaves, photosynthetic pigment contents significantly decreased and the chloroplast development was retarded. The mutant phenotype was controlled by a recessive mutation in a nuclear gene on the short arm of rice chromosome 2. Map-based cloning and sequencing analysis suggested that the candidate gene was YS83 (LOC_Os02g05890) encoding a protein containing 165 amino acid residues. Gene YS83 was expressed in a wide range of tissues, and its encoded protein was targeted to the chloroplast. In the mutant, a T-to-A substitution occurred in coding sequence of gene YS83, which caused a premature translation of its encoded product. By introduction of the wild-type gene, the ys83 mutant recovered to normal green-leaf phenotype. Taken together, we successfully identified a novel yellow-green leaf gene YS83. In addition, number of productive panicles per plant and number of spikelets per panicle only reduced by 6.7% and 7.6%, respectively, meanwhile its seed setting rate and 1000-grain weight (seed size) were not significantly affected in the mutant, so leaf-color mutant gene ys83 could be used as a trait marker gene in commercial hybrid rice production.

[A USB-Based Digital ECG Sensor].

Based on the ECG-specific BMD 101 integrated circun chip, this study designed a digital ECG sensor. In practical application, users just need to connect the ECG sensor 'o upper computer (such as PC or mobile phone) through USB interface, to realize the functions including display, alarm, saving, transfer etc. After tests, They demonstrate that the sensor can be applied to the detection of arrhythmia, such as bigeminy coupled rhythm, proiosystole etc. Besides, the sensor has various advantages in monitoring an managing the heart health of people out of hospital, including low cost, small volume, usableness, simplicity of operation etc.

Mutation of FdC2 gene encoding a ferredoxin-like protein with C-terminal extension causes yellow-green leaf phenotype in rice.

Ferredoxins (Fds) are small iron-sulfur proteins that mediate electron transfer in a wide range of metabolic reactions. Besides Fds, there is a type of Fd-like proteins designated as FdC, which have conserved elements of Fds, but contain a significant C-terminal extension. So far, only two FdC genes of Arabidopsis (Arabidopsis thaliana) have been identified in higher plants and thus the functions of FdC proteins remain largely unknown. In this study, we isolated a yellow-green leaf mutant, 501ys, in rice (Oryza sativa). The mutant exhibited yellow-green leaf phenotype and reduced chlorophyll level. The phenotype of 501ys was caused by mutation of a gene on rice chromosome 3. Map-based cloning of this mutant resulted in identification of OsFdC2 gene (LOC_Os03g48040) showing high identity with Arabidopsis FdC2 gene (AT1G32550). OsFdC2 was expressed most abundantly in leaves and its encoded protein was targeted to the chloroplast. In 501ys mutant, a missense mutation was detected in DNA sequence of the gene, resulting in an amino acid change in the encoded protein. The mutant phenotype was rescued by introduction of the wild-type gene. Therefore, we successfully identified FdC2 gene via map-based cloning approach, and demonstrated that mutation of this gene caused yellow-green leaf phenotype in rice.

GRY79 encoding a putative metallo-ß-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice.

KEY MESSAGE: The green - revertible yellow79 mutant resulting from a single-base mutation suggested that the GRY79 gene encoding a putative metallo-ß-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice. Functional studies of metallo-ß-lactamases and trihelix transcription factors in higher plants remain very sparse. In this study, we isolated the green-revertible yellow79 (gry79) mutant in rice. The mutant developed yellow-green leaves before the three-leaf stage but recovered to normal green at the sixth-leaf stage. Meanwhile, the mutant exhibited reduced level of chlorophylls and arrested development of chloroplasts in the yellow leaves. Genetic analysis suggested that the mutant phenotype was controlled by a single recessive nuclear gene on rice chromosome 2. Map-based cloning revealed that the candidate gene was Os02g33610 encoding a putative metallo-ß-lactamase-trihelix chimera. In the gry79 mutant, a single-base mutation occurred in coding region of the gene, resulting in an amino acid change in the encoded protein. Furthermore, the mutant phenotype was rescued by transformation with the wild-type gene. Therefore, we have confirmed that the gry79 mutant phenotype resulted from a single-base mutation in GRY79 (Os02g33610) gene, suggesting that the gene encoding a putative metallo-ß-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice. In addition, we considered that the gry79 mutant gene could be applicable as a leaf-color marker gene for efficient identification and elimination of false hybrids in commercial hybrid rice production.

Effects of cigarette smoke on aerobic capacity and serum MDA content and SOD activity of animal.

OBJECTIVE: Study the effects of cigarette smoke on aerobic capacity, serum MDA content and SOD activity of animal. METHODS: 60 male mice are randomly divided into mild smoking group, heavy smoking group, and control group, and the exhausted swimming time, serum SOD activity and MDA content of the three groups of mice are respectively measured before and after the experiment. RESULTS: After the experiment, the exhausted swimming time for the control group, mild smoking and heavy smoking groups is respectively 276.57 min, 215.57 min and 176.54 min, and the serum SOD activities for the three objects are 216.46 U/mL, 169.16 U/mL and 154.91 U/mL, and the MDA contents are respectively 16.41 mol/mL, 22.31 mol/mL and 23.55 mol/mL. According to the comparison, it is found that compared with the control group and pre-intervention, the exhausted swimming time and serum SOD activity of the smoking group decreases obviously, and its MDA content rises sharply, and the difference has significance (P < 0.05), moreover, the heavy smoking group has more obvious changes than the mild group. CONCLUSION: Cigarette smoke can significantly weaken the aerobic capacity and fatigue resistance of mice, and the more the smoking time is longer, the more the harmful effect is more serious, this is related to the SOD activity drops and MDA content rises due to smoking.

One divinyl reductase reduces the 8-vinyl groups in various intermediates of chlorophyll biosynthesis in a given higher plant species, but the isozyme differs between species.

Divinyl reductase (DVR) converts 8-vinyl groups on various chlorophyll intermediates to ethyl groups, which is indispensable for chlorophyll biosynthesis. To date, five DVR activities have been detected, but adequate evidence of enzymatic assays using purified or recombinant DVR proteins has not been demonstrated, and it is unclear whether one or multiple enzymes catalyze these activities. In this study, we systematically carried out enzymatic assays using four recombinant DVR proteins and five divinyl substrates and then investigated the in vivo accumulation of various chlorophyll intermediates in rice (Oryza sativa), maize (Zea mays), and cucumber (Cucumis sativus). The results demonstrated that both rice and maize DVR proteins can convert all of the five divinyl substrates to corresponding monovinyl compounds, while both cucumber and Arabidopsis (Arabidopsis thaliana) DVR proteins can convert three of them. Meanwhile, the OsDVR (Os03g22780)-inactivated 824ys mutant of rice exclusively accumulated divinyl chlorophylls in its various organs during different developmental stages. Collectively, we conclude that a single DVR with broad substrate specificity is responsible for reducing the 8-vinyl groups of various chlorophyll intermediates in higher plants, but DVR proteins from different species have diverse and differing substrate preferences, although they are homologous.