Ontology highlight
ABSTRACT:
PROVIDER: PRJNA512440 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Identify the change in transcriptomic and epigenetic profiles within the sorghum root system of the cultivar BTx623 in response to limiting phosphorus conditions. This data is from the 2022 publication "Sorghum root epigenetic landscape during limiting phosphorus conditions".
2023-10-04 | GSE244604 | GEO
Project description:Purpose: We investigated root foraging strategies for K of tea plants using a multi-layer split-root system by RNA-seq. Methods: One-year old tea cuttings were cultivated with the roots evenly planted on the two sides of the split root hydroponic box with a root canal. Three treatments were included to simulate the heterogeneous and homogeneous K environments. After 5d treatment, the roots on the two sides of the split root hydroponic box were collected separately and the RNA sequencing were analyzed by the Illumina Hiseq (2500, Illumina, San Diego, CA). Results: RNA-seq data had a linear relationship with qRT–PCR (r2=0.76), which confirmed the reliability of the RNA-seq data. Conclusions: Our study screened the key genes of tea root system to adapt to potassium heterogeneity.
2022-08-17 | GSE198198 | GEO
Project description:We investigated the morphological roots decisions of Arabidopsis in a NO3- heterogeneous medium. To do so, we used the Split-Root System which is an experimental set up to assess root decisions in nutrient heterogeneous medium. Split-root plants have been subjected to three different treatments. ‘Control KNO3’ plants received KNO3 on both sides of the root system (C.NO3) and ‘Control KCl’ plants received KCl on both sides (C.KCl) as a nitrogen deprivation treatment. 'Split' plants received KNO3 on one side (Sp.NO3) and KCl on the other side (Sp.KCl) of the root system to assess the root decision-making in a heterogeneous environment. We observed that the total lateral roots length in the Sp.NO3 and C.KCl compartments is induced as compared to C.NO3 and Sp.KCl compartments. This corresponds to a root proliferation response in strategic territories to compensate the nitrogen deprivation. To decipher the molecular basis of this morphological root response on day 4 after the beginning of the split-root treatment, we used a transcriptomic approach on roots at 2hours, 8 hours and 2 days after the beginning of the treatment. From our microarrays data, we have identified a global set of 150 genes for which the expression pattern match with the lateral roots responses. Among them, we selected 8 early marker genes of the root decisions, which allowed us to show that the shoots and the NO3- itself are essential for the decision. Finally, we tested the role of the cytokinins phytohormones as a NO3--derived systemic signal in the root decision. Interestingly, we have demonstrated that the systemic cytokinins are involved into the decision of inducing maker genes expression and making lateral roots in the Sp.NO3 compartment specifically.
2011-12-01 | GSE22966 | GEO
Project description:We addressed the question how the interaction between the beneficial root endophyte Serendipita vermifera (Sv) and the pathogen Bipolaris sorokiniana (Bs) affects fungal behavior and determines barley host responses using a gnotobiotic natural soil-based split-root system for phenotypic and transcriptional analyses.
2019-07-06 | GSE130517 | GEO
Project description:We investigated the morphological roots decisions of Arabidopsis in a NO3- heterogeneous medium. To do so, we used the Split-Root System which is an experimental set up to assess root decisions in nutrient heterogeneous medium. Split-root plants have been subjected to three different treatments. ‘Control KNO3’ plants received KNO3 on both sides of the root system (C.NO3) and ‘Control KCl’ plants received KCl on both sides (C.KCl) as a nitrogen deprivation treatment. 'Split' plants received KNO3 on one side (Sp.NO3) and KCl on the other side (Sp.KCl) of the root system to assess the root decision-making in a heterogeneous environment. We observed that the total lateral roots length in the Sp.NO3 and C.KCl compartments is induced as compared to C.NO3 and Sp.KCl compartments. This corresponds to a root proliferation response in strategic territories to compensate the nitrogen deprivation. To decipher the molecular basis of this morphological root response on day 4 after the beginning of the split-root treatment, we used a transcriptomic approach on roots at 2hours, 8 hours and 2 days after the beginning of the treatment. From our microarrays data, we have identified a global set of 150 genes for which the expression pattern match with the lateral roots responses. Among them, we selected 8 early marker genes of the root decisions, which allowed us to show that the shoots and the NO3- itself are essential for the decision. Finally, we tested the role of the cytokinins phytohormones as a NO3--derived systemic signal in the root decision. Interestingly, we have demonstrated that the systemic cytokinins are involved into the decision of inducing maker genes expression and making lateral roots in the Sp.NO3 compartment specifically. 36 samples were analyzed. They correspond to three biological repeats of the C.NO3, Sp.NO3, Sp.KCl and C.KCl root samples (12 samples) that we have collected at 2hours, 8 hours and 2 days (12 samples x 3 time points) after the beginning of the split-root treatment. We analyzed the normalized microarrays data by using a three way ANOVA. The three factors of the ANOVA are 1) presence/absence of NO3-, 2) split/control and 3) time. The measures of the significance of each probe were done by the Q-value method (q<0.2, panova<0.001). The genes differentially expressed between the C.NO3 and Sp.NO3 samples, and the C.KCl and Sp.KCl samples were determined by the post-hoc Tukey test (p<0.05).
2011-12-01 | E-GEOD-22966 | biostudies-arrayexpress
Project description:This study utilized next generation sequencing technology (RNA-Seq and BS-Seq) to examine the transcriptome and methylome of various tissues within sorghum plants with the ultimate goal of improving the Sorghum bicolor annotation We examined the mRNA of various Sorghum bicolor (BTx623) tissues (flowers, vegitative and floral meristems, embryos, roots and shoots) and bisulfite treated DNA from two root samples
2014-08-29 | E-GEOD-50464 | biostudies-arrayexpress
Project description:After experiencing drought, Sorghum bicolor generates substantial root pressure, which varies with genotype and re-watering amount.
2020-06-10 | GSE152143 | GEO
Project description:Sugarcane aphids (SCA; Melanaphis sacchari Zehntner) is a key piercing-sucking type pest of sorghum (Sorghum bicolor) which cause significant yield losses. While feeding on host plants, complex signaling networks are invoked from recognition of insect attack to induction of plant defenses. Consequently, these signaling networks lead to the production of insecticidal compounds or limited access to nutrients to insects. Previously, several studies are published on the transcriptomics analysis of sorghum in response to SCA infestation, but no information is available on the physiological changes of sorghum at proteome level. We used SCA resistant sorghum genotype SC265 for the global proteomics analysis after 1 and 7 days of SCA infestation using TMT-plex technique.
2022-05-11 | PXD029691 | Pride
Project description:Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk). RNAseq deep sequencing
2014-05-01 | E-GEOD-54705 | biostudies-arrayexpress
Project description:Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk).
2014-05-01 | GSE54705 | GEO