Transcription profiling by high throughput sequencing of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting nitrogen conditions
ABSTRACT: Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation.
BACKGROUND: Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been condu ...[more]
Project description:Among the mineral elements necessary for plant growth, nitrogen (N) is the macronutrient required in larger amounts. The optimization of N use efficiency (NUE) in maize could be obtained through both genetic improvement and agronomic practices in order to enhance production and reduce the negative impact of the N fertilizer use on the environment. Physiological characterizations of inbred lines with different NUE are available in maize. Maize (Zea mays L.) seeds of two inbred lines (T250, Lo5) previously soaked in running water for 24 h, were allowed to germinate in the dark at 28°C for 72 h over an aerated solution of 0.5 mM CaSO4. Half part of two-d-old seedlings was grown in a nutrient solution with 200 μM of KNO3 (treated samples, +NO3-) and the other half with appropriate amounts of the corresponding chloride salt (KCl) (control samples, -NO3-). Three biological replicates were obtained by three independent experiments and collecting roots of treated (200 μM NO3-) and not treated plants after 0, 1, 2 e 4 h for Lo5 inbred line and after 0, 5, 11 and 12 h for T250.
Project description:Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range. These findings indicate that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. Experiment Overall Design: Affymetrix expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for nine different genotypes; B37, B73, B84, Mo17, Oh43, B37xB73, B84xB73, Oh43xB73 and Oh43xMo17.
Project description:To investigate whether small RNAs (sRNAs) participate in the regulation of heterosis, we profiled the sRNA expression patterns in the germ seeds of five inbred lines and theirs three F1 hybrids using high-throughput sequencing technology. Overall design: In this study, three hybrid varieties of maize, which were elite hybrids and widely cultivated in China that exhibited high heterosis for grain yield, and theirs five parental inbred lines were utilized. The relationship of these varieties is as followed: Chang 7-2 (Paternal, P), Zheng 58 (Maternal, M), and Zhengdan 958 (Hybrid, H); Chang 7-2 (P), 9058 (M), and Lingdan 20 (H); 87-1 (P), Zong 3 (M), and Yuyu22 (H). Small RNA profile of eight maize varieties are generated by deep sequencing.
Project description:This SuperSeries is composed of the following subset Series:; GSE8174: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Seedling data; GSE8176: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data; GSE8179: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Embryo data Experiment Overall Design: Refer to individual Series
Project description:Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation. Many genes exhibit presence-absence variation among the inbred lines. Experiment Overall Design: Affymetrix expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for eight different inbred lines; B37, B73, B84, Mo17, Oh43, B14a, Wf9 and W22.
Project description:Anthracnose caused by the ascomycete Colletotrichum graminicola is one of the most severe fungal diseases of Zea maize. Cultivars with different levels of resistance have been described. However, which genes contribute to cultivar-specific constitutive and/or induced defense in this economically important pathosystem is still elusive. Transcriptome analyses of infected maize leaves of varieties Golden Jubilee (GJ) and B73 by RNA-Seq was performed for the penetration, biotrophic and necrotrophic phases.
Project description:Background: Heavy metal cadmium (Cd) is a common environmental pollutant in soils, which has an negative impacts on crop growth and development. At present, cadmium has become a major soil and water heavy metal pollutant, which not only causes permanent and irreversible health problems for humans, but also causes a significant reduction in crop yields. Results: This study examined the chemical forms of Cd in the roots of two wheat varieties (M1019 and Xinong20) by continuous extraction and analyzed differences in distribution characteristics of Cd in the root cell wall, cytoplasm, and organelles by elemental content determination and subcellular separation. Furthermore, we conducted proteomics analysis of the roots of the two varieties under Cd pollution using mass spectrometry quantitative proteomics techniques. A total of 11,651 proteins were identified, of which 10,532 proteins contained quantitative information. In addition, the differentially expressed proteins in the two varieties were related to DNA replication and repair, protein metabolism, and the glutathione metabolism pathway. Conclusion: The results of this study improve our understanding of the mechanism of plant responses to Cd stress.
Project description:Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. B73 X Mo17 is a model maize hybrid. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology. B73 X Mo17 hybrid_developing earshoot microarray data: Technical replicates, no biological replicates
Project description:Genome-wide transcriptomics experiment (RNA-seq) on proliferative tissue of eight maize inbred lines (A632, B73, B96, F7, H99, HP301, Mo17, W153R). These inbreds are used as parents in a funnel breeding design to generate an advanced recombinant maize population.