Project description:Transcriptome sequencing (RNA-seq) was used to profile genome-wide transcript abundance in the primary root growth zone (PRGZ) of maize seedlings grown in different water deficit treatments: well-watered (-0.02 MPa), mild water deficit stress (-0.3 MPa), or severe water deficit stress (-1.6 MPa). For each water deficit treatment, the PRGZ transcriptome was profiled at 26 hours after initiation of the water deficit treatment. By comparing the abundance of each transcript under mild or severe water deficit stress relative to its abundance under well-watered conditions, we identified transcripts that are differentially regulated in the PRGZ in response to the two levels of water deficit stress.
Project description:Nitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation. Root is the organ that plants transport nitrate. we used the microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in maize.
Project description:Maintenance of root growth is critical to plant adaptation to drought conditions. Previous work on the maize (Zea mays L.) primary root under water stress showed that cell elongation is maintained in the apical region of the growth zone but progressively inhibited further from the apex. These responses involve spatially differential and coordinated regulation of cellular growth processes, including modifications of both cell production rate and cell wall extensibility. As the interface between the cytoplasm and the apoplast (including the cell wall), the plasma membrane is likely to play major functions in the coordination of cell production and expansion. In addition, plasma membrane proteins may be involved in solute uptake for osmotic adjustment, pH regulation, ion homeostasis and other critical processes in roots growing under water-stressed conditions. Due to technical limitations, however, plasma membrane proteomic studies have not been reported for water-stressed tissues. Using a simplified method for enrichment of plasma membrane proteins, we compared the developmental distribution of plasma membrane proteins that are differentially regulated in the growth zone of well-watered and water-stressed roots.
Project description:The genomic distribution of trait-associated SNPs (TASs) discovered in genome-wide association studies (GWAS) can provide insight into the genetic architecture of complex traits and the design of future studies. Here we report on a maize GWAS that identified TASs underlying five quantitative traits measured across a large panel of samples and examine the characteristics of these TASs. A set of SNPs obtained via RNA sequencing (RNA-seq), most of which are located within annotated genes (~87%) were complemented with additional SNPs from the maize HapMap Project that contains approximately equal proportions of intragenic and intergenic SNPs. TASs were identified via a genome scan while controlling for polygenic background effects. The diverse functions of TAS-containing candidate genes indicate that complex genetic networks shape these traits. The vast majority of the TAS-containing candidate genes have dynamic expression levels among developmental stages. Overall, TASs explain 44~54% of the total phenotypic variation for these traits, with equal contributions from intra- and inter-genic TASs. Association of ligueless2 with upper leaf angle was implicated by two intragenic TASs; rough sheath1 was associated with leaf width by an upstream intergenic TAS; and Zea agamous5 was associated with days to silking by both intra- and inter-genic TASs. A large proportion (82%) of these TASs comes from noncoding regions, similar to findings from human diseases and traits. However, TASs were enriched in both intergenic (53%) and promoter 5kb (24%) regions, but under-represented in a set of nonsynonymous SNPs.
Project description:Nitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation. We used the microarray systems to detect miRNAs responding to the chronic nitrate limiting conditions in maize leaves and roots.
Project description:To increase crop yield without polluting the environment, improving crop nutrient efficiency is of great importance. The RSA of plants is centrally involved in nutrient use efficiency. Therefore, to uncover the molecular mechanisms that regulate RSA of maize under nutrient-deficiency conditions and to improve maize nutrient use efficiency based on this knowledge, we investigated the morphological changes and ribonucleic acid sequencing (RNA-seq) profiles of maize roots during growth under normal and N-, P-, and K-deficiency conditions. We analyzed the data in different aspects and verified the reliability of the RNA-seq data by real-time quantitative polymerase chain reaction (RT-qPCR). These results will provide theoretical support for improving plant nutrient use efficiency. The maize (Z. mays) inbred line DengHai 605 was used in this study. Provided for four treatment conditions: normal N, P, and K level (CK); potassium deficiency (K-DEF); nitrogen deficiency (N-DEF); and phosphorus deficiency (P-DEF). The experiments were carried out by combining sand culture with water culture. The standard for evaluating differential gene expression is fold change (FC) > 2 or FC < -2 and p value < 0.05.The numbers of DEGs under N-, P-, and K-deficiency conditions were 3494 (1801 up-regulated and 1693 down-regulated), 3424 (1761 up-regulated and 1663 down-regulated), and 1830 (827 up-regulated and 1003 down-regulated), respectively. A total of 1483, 1470, and 519 genes were specifically expressed under the N-, P-, and K-deficiency conditions, respectively.
Project description:Ustilago maydis is a basidiomycete fungus that causes smut disease in maize. Most prominent symptoms of the disease are plant tumors, which can be induced by U. maydis on all aerial parts of the plant. We identified two linked genes, pit1 and pit2, which are specifically expressed during plant colonization. Deletion mutants for either pit1 or pit2 are unable to induce tumor development and elicit plant defense responses. We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to deletion pit1 and pit2 mutants and found plant responses to both mutants being not significantly distinguishable. U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200Dpit1 and SG200Dpit2, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023, 4d mock and 4d SG200 Samples, equivalent record in Arrayexpress: E-GEOD-10023). These data served as controls for this experiment.
Project description:Nitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation. Root is the organ that plants transport nitrate. we used the microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in maize. MicroRNAs (miRNAs) are small, endogenous RNAs that are regulators of gene expression in plants and animals. And, miRNAs have been known for years to be important for phosphate, sulphate and copper deprivation responses in plants. In Arabidopsis, small RNA deep sequencing associated with nitrate response had been analyzed. However, information about the way by which miRNA are regulated by abiotic stresses in general and by low nitrate in particular is unavailable for maize. In this study, we used GeneChip® microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in roots in maize.
Project description:ngs2021_19_rhizophagus-responses of maize to the arbuscular fungus rhizophagus irregularis mitigate n deficiency stress-What is the impact of Rhizophagus irregularis on maize transcriptome under different N nutrition conditions, what is the impact of N on R. irregularis transcriptome in maize roots.-After 4 days of germination, maize seeds were sown in pots filled with sterile mix 1:1 clay beads:unfertilized peat. Inoculation performed in 3 times with Rhizohphagus irregularis spores purchased at Agronutrition. First inoculation perfomed with 500 spores/plant at sowing. Two other incoulations performed the following week and 2 weeks later with 100 spore per plant each.
Project description:Sucrose synthase (SUS), a key enzyme of sugar metabolism, plays an important role in the regulation of carbon partitioning in plant, and affects important agronomic traits and abiotic responses to adversity. However, the function of ZmSUS1 in plant drought tolerance is still unknown. In this study, the expression patterns of ZmSUS1 in different tissues and under drought stress were analyzed in maize (Zea mays L.). It was found that ZmSUS1 was highly expressed during kernel development but also in leaves and roots of maize, and ZmSUS1 was induced by drought stress. Homozygous transgenic maize lines of ZmSUS1 overexpressing increased the content and activity of SUS under drought stress and exhibited higher relative water content, proline and abscisic acid content in leaves. Specifically, the net photosynthetic rate and the soluble sugar contents including sucrose、glucose、fructose、UDP-glucose and ADP-glucose in transgenic plants was significantly improved after drought stress. RNA-seq analysis showed that overexpressing of ZmSUS1 mainly affected the expression level of carbon metabolism-related genes, especially the expression level of sucrose metabolism-related genes including ZmSUS、ZmSPS and ZmINV were significantly up-regulated in transgenic maize. Overall, these results suggested that ZmSUS1 improved drought tolerance by regulating sucrose metabolism and increasing soluble sugar content, and endowing transgenic maize with higher relative water content and photosynthesis levels, which can be served as a new gene candidate for cultivating drought resistant maize varieties.