GNPS Sorghum_Root_Metabolomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Sorghum Bicolor (ncbitaxon:4558)
SUBMITTER: 
Vidya Suseela
PROVIDER: MSV000088242 | GNPS | Sun Oct 17 16:39:00 BST 2021
REPOSITORIES: GNPS
Similar Datasets
Project description:Beneficial root-associated microbes can enhance plant resilience by complementing aspects of host immunity. The fungal root endophyte Serendipita indica (Si) is known to promote plant growth and confer broad stress tolerance. To assess how natural host genetic variation influences Si-mediated protection, we screened 47 Arabidopsis thaliana accessions for susceptibility to the fungal pathogen Bipolaris sorokiniana (Bs) with and without Si colonization. All accessions benefited from Si, indicating that endophyte-mediated disease mitigation occurs broadly across diverse host genotypes. A focused comparison of two genetically and geographically proximate Swedish accessions, T510 and T530, which displayed the most divergent protection scores, revealed substantial differences in Bs susceptibility. Transcriptome profiling under bi- and tripartite colonization showed conserved defense responses in both accessions. Bs infection downregulated growth- and development-related genes, consistent with a growth–immunity trade-off, with T530 exhibiting higher Bs colonization and a stronger transcriptional response than T510. Co-colonization with Si effectively suppressed pathogen growth and disease symptoms in both accessions. Comparative genomic and transcriptomic analyses identified four immune receptor genes, including the TIR-NLR ISI, present in T510 but absent in T530. An isi T-DNA insertion mutant phenocopied the heightened Bs susceptibility of T530, confirming that ISI contributes to root immunity, while Si-mediated protection remained intact despite increased pathogen susceptibility. Together, these findings demonstrate that fungal endophytes can mitigate the functional consequences of natural immune variation and enhance the resilience of genetically diverse plant populations.
2026-04-01 | GSE307677 | GEO
Project description:We determined the transcript profile of sorghum root epiphytic H. rubrisubabicans M1 and identified putative mechanisms required for early colonization of the host plant.
2015-08-13 | E-MTAB-3538 | biostudies-arrayexpress
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:Sorghum plants (Btx623 background) were grown in a glasshouse between March and May 2014. At panicle emergence, two biological replicates of flag leaf tissue and two biological replicates of emerging panicle tissue were harvested and used for RNA extraction. Btx623 is a non-shattering Sorghum accession, thus in the future we would like to add additional samples from accessions with varying degrees of seed shattering. This dataset will be useful for future comparisons of 1) shattering individuals at these stages and 2) additional flowering developmental time points in a variety of accessions (http://www.rnaseqforthenextgeneration.org/profiles/carrie-thurber.html#research)
2015-08-19 | E-MTAB-4203 | biostudies-arrayexpress
Project description:<p>This study presents an untargeted metabolomics analysis of root exudates from sorghum (Sorghum bicolor) under control and severe drought conditions. Samples were collected from experimental sites in Shanxi, China. The study aims to investigate metabolic changes in sorghum root exudates in response to drought stress.</p>
2026-06-09 | MTBLS14131 | MetaboLights
Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression during early stages of Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on mycorrhizal root fragments enriched for early fungal infection stages. We used Medicago GeneChips to detail the global programme of gene expression in response to early stages of colonization by arbuscular mycorrhizal fungi and identified genes differentially expressed during these early stages.
2012-03-28 | GSE34617 | GEO
Project description:Plant secondary cell walls constitute the majority of plant biomass and are an important source of biomaterials. Secondary cell walls are particularly prominent in xylem cells present in the vascular tissue. Although the process of vascularization has been extensively studied in the dicot Arabidopsis thaliana, remarkably little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome data using laser capture microdissection in the developing vascular and non-vascular tissues of the sorghum root. Many sorghum genes with enriched expression in developing vasculature were orthologous to genes previously associated with vascular development in other species. However, a number of transcription factor families, including NAC domain, MYB and ARF varied in their complement of vascular expressed genes to a considerable degree in sorghum compared to Arabidopsis and/or maize. Differential expression of genes associated with DNA methylation and chromatin modification were identified between vascular and non-vascular cell types, implying that changes in DNA methylation may be a feature of sorghum root vascularization. To profile DNA methylation in these tissues, sodium bisulfite sequencing of laser capture microdissected tissue was performed. DNA methylation was enriched in genic regions of genes demonstrating higher expression in non-vascular tissues. Methylation in genic and intergenic regions varied by tissue type and gene expression level. Furthermore, genes involved in cell elongation showed differences in methylation levels concomitant with expression between non-vascular and vascular tissue types suggesting a novel mode by which root growth in distinct tissues may be modulated. Our results provide both a genetic and epigenetic framework for studying vascularization and secondary cell wall development in sorghum.
2016-12-30 | GSE70903 | GEO
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:Salinity is a major constraint on agricultural productivity worldwide. Despite the serious impacts of salinity on rice yields, particularly in Asia, mechanisms of salt tolerance in wild rice species are yet to be explored. Here we extracted and quantified root microsomal proteins of Oryza australiensis accessions contrasting in salt tolerance. Whole root systems of two-week-old seedlings were treated with 80 mM NaCl for 30 days or left untreated. Proteins were quantified by tandem mass tags (TMT) and triple-stage MS. We found >200 differentially expressed proteins (DEPs) between the salt-treated and control in the two accessions (p-value <0.05). Gene Ontology (GO) analysis showed that ‘metabolic process’, ‘transport’ and ‘transmembrane transporter’ activities were highly responsive categories following salt treatment of the O. australiensis seedlings. In particular, ATPases and SNARE proteins were up-regulated in the salt-tolerant accession and appeared to have a major role in response to salinity. ATPases are the central link between energy generation and transport, while SNARE proteins facilitate vesicle fusion and interact with voltage-gated potassium channels to regulate K+ influx. We successfully validated the putative function of two strongly upregulated proteins, a monosaccharide transporter and a VAMP-like protein, by measuring the growth under salinity of yeast mutants in which homologous genes were deleted. Our results demonstrate the potential use of wild species as a source of new mechanisms of salt tolerance for the breeding of elite cultivars of rice.
2019-09-11 | PXD013701 | Pride
Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression in Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on whole mycorrhizal roots. We used GeneChips to detail the global programme of gene expression in response to colonization by arbuscular mycorrhizal fungi and in response to a treatment with phosphate and identified genes differentially expressed during this process.
2011-10-29 | GSE32208 | GEO