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:Leaf venation density has significantly increased during plant evolution. For example, higher vein density is observed in angiosperms compared to early land plants, and among angiosperms, recently diverged C4 species typically have the highest values. This adaptation has allowed plant leaves to increase water conductance, transpiration and possibly photosynthesis, although the relationship between vein density and photosynthetic efficiency has not been clearly established. The genetic architecture of vein density is still not well characterized. Using diverse native varieties of maize, a C4 plant adapted to a wide range of environmental conditions, we show that vein density is variable and plastic. We leverage this plasticity to show that higher densities are correlated with higher photosynthetic rates, but only for small intermediate veins. Moreover, we find that varieties adapted to drier environments can substantially increase vein density in response to heat, suggesting a role in water use efficiency in hot environments. Finally, using a MAGIC population, we mapped 12 QTLs associated with vein architecture traits and identified a short list of candidate genes associated with small intermediate vein development. These findings have implications for understanding vein architecture evolution, particularly that of C4 plants, which have significantly higher photosynthetic efficiency and productivity under warm and dry conditions.
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 subsistence of terrestrial plants depends upon the ability of roots to absorb water and nutrients from the soil. Directed growth of the primary root from a layer of the soil with low water content towards a zone with high water content is known as hydrotropism. This tropic response enables the root to reach soil with the proper humidity for plant growth, and therefore avoid drought conditions. Although the shortage of sufficient water is the single-most critical factor affecting world agriculture, there are very few studies on hydrotropism in crop plants. The strength of the hydrotropic response (angle of curvature) of the maize primary root in maize varies enormously. After phenotyping root hydrotropism in 231 Drought Tolerant Maize for Africa hybrids, we performed a Genome Wide Association Study and found two candidate genes that regulate the ubiquitin/26 proteasome system. We also compared the root transcriptomes between maize accessions with contrasting hydrotropic response after 6 h of hydro stimulation: (CML376<2/NVOL46)-74-1-1-B) (robust response) and (CML376<2/SNL17)-28-1-1-B) (weak response). This analysis revealed that hydrotropism in maize seems to be regulated by chaperones, heat shock proteins, late embryogenesis abundant proteins, and ubiquitin ligases. Furthermore, we biochemically examined the role of protein ubiquitination and protein degradation during hydrotropism. Our results suggest that the signal transduction pathways induced by hydro stimulation in maize are like those triggered by heat, water stress, and protein ubiquitination.
Project description:Nitrogen (N) is a key macronutrient required for plant growth, development, and yield. Improving nitrogen use efficiency (NUE) in maize is important for sustainable crop production and reducing fertilizer-associated environmental impacts. To investigate transcriptional responses to nitrate availability, we examined genome-wide gene expression dynamics in maize under nitrate-limiting, and nitrate-recovery conditions. This dataset captures rapid transcriptional shifts in both roots and leaves during nitrate deprivation and subsequent nitrate resupply.
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: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: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: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.