Genome-wide analysis of maize OSCA family members and their involvement in drought stress

Background Worldwide cultivation of maize is often impacted negatively by drought stress. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis. However, the involvement of members of the maize OSCA (ZmOSCA) gene family in response to drought stress is unknown. It is furthermore unclear which ZmOSCA gene plays a major role in genetic improvement of drought tolerance in Maize. Methods We predicted the protein domain structure and transmembrane regions by using the NCBI Conserved Domain Database database and TMHMM server separately. The phylogeny tree was built by Mega7. We used the mixed linear model in TASSEL to perform the family-based association analysis. Results In this report, 12 ZmOSCA genes were uncovered in the maize genome by a genome-wide survey and analyzed systematically to reveal their synteny and phylogenetic relationship with the genomes of rice, maize, and sorghum. These analyses indicated a relatively conserved evolutionary history of the ZmOSCA gene family. Protein domain and transmembrane analysis indicated that most of the 12 ZmOSCAs shared similar structures with their homologs. The result of differential expression analysis under drought at various stages, as well as the expression profiles in 15 tissues, revealed a functional divergence of ZmOSCA genes. Notably, the expression level of ZmOSCA4.1 being up-regulated in both seedlings and adult leaves. Notably, the association analysis between genetic variations in these genes and drought tolerance was detected. Significant associations between genetic variation in ZmOSCA4.1 and drought tolerance were found at the seedling stage. Our report provides a detailed analysis of the ZmOSCAs in the maize genome. These findings will contribute to future studies on the functional characterization of ZmOSCA proteins in response to water deficit stress, as well as understanding the mechanism of genetic variation in drought tolerance in maize

Discovering genetic linkage between periodontitis and type 1 diabetes: A bioinformatics study

Background: Relationship between periodontitis (PD) and type 1 diabetes (T1D) has been reported, but the detailed pathogenesis requires further elucidation. This study aimed to reveal the genetic linkage between PD and T1D through bioinformatics analysis, thereby providing novel insights into scientific research and clinical treatment of the two diseases.Methods: PD-related datasets (GSE10334, GSE16134, GSE23586) and T1D-related datasets(GSE162689)were downloaded from NCBI Gene Expression Omnibus (GEO). Following batch correction and merging of PD-related datasets as one cohort, differential expression analysis was performed (adjusted p-value <0.05 and ∣log2  fold change| > 0.5), and common differentially expressed genes (DEGs) between PD and T1D were extracted. Functional enrichment analysis was conducted via Metascape website. The protein-protein interaction (PPI) network of common DEGs was generated in The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Hub genes were selected by Cytoscape software and validated by receiver operating characteristic (ROC) curve analysis.Results: 59 common DEGs of PD and T1D were identified. Among these DEGs, 23 genes were commonly upregulated, and 36 genes were commonly downregulated in both PD- and T1D-related cohorts. Functional enrichment analysis indicated that common DEGs were mainly enriched in tube morphogenesis, supramolecular fiber organization, 9 + 0 non-motile cilium, plasma membrane bounded cell projection assembly, glomerulus development, enzyme-linked receptor protein signaling pathway, endochondral bone morphogenesis, positive regulation of kinase activity, cell projection membrane and regulation of lipid metabolic process. After PPI construction and modules selection, 6 hub genes (CD34, EGR1, BBS7, FMOD, IGF2, TXN) were screened out and expected to be critical in linking PD and T1D. ROC analysis showed that the AUC values of hub genes were all greater than 70% in PD-related cohort and greater than 60% in T1D-related datasets.Conclusion: Shared molecular mechanisms between PD and T1D were revealed in this study, and 6 hub genes were identified as potential targets in treating PD and T1D

Micrometeorological monitoring reveals that canopy temperature is a reliable trait for the screening of heat tolerance in rice

Micrometeorological monitoring is not just an effective method of determining the impact of heat stress on rice, but also a reliable way of understanding how to screen for heat tolerance in rice. The aim of this study was to use micrometeorological monitoring to determine varietal differences in rice plants grown under two weather scenarios−Long-term Heat Scenario (LHS) and Normal Weather Scenario (NWS)− so as to establish reliable methods for heat tolerance screening. Experiments were conducted with two heat susceptible varieties−Mianhui 101 and IR64−and two heat tolerant varieties, Quanliangyou 681 and SDWG005. We used staggered sowing method to ensure that all varieties flower at the same time. Our results showed that heat tolerant varieties maintained lower canopy temperature compared to heat susceptible varieties, not just during the crucial flowering period of 10 am to 12 pm, but throughout the entire day and night. The higher stomatal conductance rate observed in heat tolerant varieties possibly decreased their canopy temperatures through the process of evaporative cooling during transpiration. Conversely, we found that panicle temperature cannot be used to screen for heat tolerance at night, as we observed no significant difference in the panicle temperature of heat tolerant and heat susceptible varieties at night. However, we also reported that higher panicle temperature in heat susceptible varieties decreased spikelet fertility rate, while low panicle temperature in heat tolerant varieties increased spikelet fertility rate. In conclusion, the results of this study showed that canopy temperature is probably the most reliable trait to screen for heat tolerance in rice

Identification of Genome-Wide Variations among Three Elite Restorer Lines for Hybrid-Rice

Rice restorer lines play an important role in three-line hybrid rice production. Previous research based on molecular tagging has suggested that the restorer lines used widely today have narrow genetic backgrounds. However, patterns of genetic variation at a genome-wide scale in these restorer lines remain largely unknown. The present study performed re-sequencing and genome-wide variation analysis of three important representative restorer lines, namely, IR24, MH63, and SH527, using the Solexa sequencing technology. With the genomic sequence of the Indica cultivar 9311 as the reference, the following genetic features were identified: 267,383 single-nucleotide polymorphisms (SNPs), 52,847 insertion/deletion polymorphisms (InDels), and 3,286 structural variations (SVs) in the genome of IR24; 288,764 SNPs, 59,658 InDels, and 3,226 SVs in MH63; and 259,862 SNPs, 55,500 InDels, and 3,127 SVs in SH527. Variations between samples were also determined by comparative analysis of authentic collections of SNPs, InDels, and SVs, and were functionally annotated. Furthermore, variations in several important genes were also surveyed by alignment analysis in these lines. Our results suggest that genetic variations among these lines, although far lower than those reported in the landrace population, are greater than expected, indicating a complicated genetic basis for the phenotypic diversity of the restorer lines. Identification of genome-wide variation and pattern analysis among the restorer lines will facilitate future genetic studies and the molecular improvement of hybrid rice

miR396-OsGRFs Module Balances Growth and Rice Blast Disease-Resistance

Fitness cost is a common phenomenon in rice blast disease-resistance breeding. MiR396 is a highly conserved microRNA (miRNA) family targeting Growth Regulating Factor (OsGRF) genes. Mutation at the target site of miR396 in certain OsGRF gene or blocking miR396 expression leads to increased grain yield. Here we demonstrated that fitness cost can be trade-off in miR396-OsGRFs module via balancing growth and immunity against the blast fungus. The accumulation of miR396 isoforms was significantly increased in a susceptible accession, but fluctuated in a resistant accession upon infection of Magnaporthe oryzae. The transgenic lines over-expressing different miR396 isoforms were highly susceptible to M. oryzae. In contrast, overexpressing target mimicry of miR396 to block its function led to enhanced resistance to M. oryzae in addition to improved yield traits. Moreover, transgenic plants overexpressing OsGRF6, OsGRF7, OsGRF8, and OsGRF9 exhibited enhanced resistance to M. oryzae, but showed different alteration of growth. While overexpression of OsGRF7 led to defects in growth, overexpression of OsGRF6, OsGRF8, and OsGRF9 resulted in better or no significant change of yield traits. Collectively, our results indicate that miR396 negatively regulates rice blast disease- resistance via suppressing multiple OsGRFs, which in turn differentially control growth and yield. Therefore, miR396-OsGRFs could be a potential module to demolish fitness cost in rice blast disease-resistance breeding

Climate adaptation, institutional change, and sustainable livelihoods of herder communities in northern Tibet

The Tibetan grassland social-ecological systems are widely held to be highly vulnerable to climate change. We aim to investigate livelihood adaptation strategies of herder households and the types of local institutions that shaped those adaptation strategies. We examined the barriers and opportunities for strengthening adaptive capacity of local herder communities. We designed and implemented a household survey in the herder communities of northern Tibet. The survey results showed that migratory grazing has become less feasible. Storage, diversification, and market exchange have become the dominant adaptation strategies. The adaptation strategies of local herders have been reshaped by local institutional change. Local governmental and market institutions played the dominant roles in reshaping climate adaptation strategies. Although the present livelihood adaption strategies related to sedentary grazing have improved productivity and profitability of the herding livelihood, they have led to continuous deterioration of pastures. The local grazing system has become more and more dependent on artificial feeding and inputs from outside the grazing system. Purchasing forage has become one of the dominant adaptation strategies of local herder households. Multilevel regression modeling of this adaptation behavior showed that explanatory variables related to climate variability, household capital, and local institutional arrangements had statistically significant relationships with the adoption of this adaptation strategy. The results implies that building household capital and promoting the coordination among local governmental, market, and communal institutions are critical for strengthening adaptive capacity of the Tibetan herder communities

Urban Metabolism of Three Cities in Jing-Jin-Ji Urban Agglomeration, China: Using the MuSIASEM Approach

Urban problems—such as resources depletion, environment pollution and waste generation—usually occur during rapid urbanisation processes, especially in mega-urban agglomerations. Finding solutions to sustainable urban development is a global research interest, and urban metabolism is an effective approach to analysing the socio-economic system and ecosystem. In this study, three cities in the Jing-Jin-Ji urban agglomeration in China—Beijing, Tianjin and Tangshan—were selected as study cases. Multiscale integrated analysis of the societal and ecosystem metabolism (MuSIASEM) method and complete decomposition model were applied to reveal the metabolic characteristics and evolutionary trajectories of the three cities from multiple levels and dimensions. Results showed that the metabolic patterns of Beijing, Tianjin and Tangshan were service-dominated, technology and capital aggregation-dominated and traditional industry-dominated, respectively. The evolution of economic efficiency, ecological pressure and social welfare in the three cities were different because of the stage of urban development where they were located. Tianjin and Tangshan showed positive correlations between economic growth and energy consumption, whereas Beijing demonstrated a more neutral correlation. In the future, issues—such as overpopulation, labour shortage and low efficiency of energy and labour—are likely to be the key factors that impede sustainable development in the three cities, respectively. Several policy implications were raised, including the combination of population dispersal and competitive industry relocation policies for Beijing, attracting young labour in the short term and transforming the economic growth patterns in the long term for Tianjin, and industrial upgrades and technical innovation for Tangshan