Dataset Information

Transcription profiling by high throughput sequencing of seed, spikelet and stem tissues of Sorghum bicolor Btx623

ABSTRACT: This study used with RNA-Seq to examine the tissue specific expression data within sorghum plants for improving the Sorghum bicolor gene annotation. We examined the RNA from tissues (spikelet, seed and stem) in Sorghum bicolor (BTx623).Total RNAs form each tissues were extracted using SDS/phenol method followed by LiCl purification

REANALYSED by: E-MTAB-4273

OTHER RELATED OMICS DATASETS IN: PRJDB3281PRJDB3280

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Sorghum Bicolor

TISSUE(S): Seed, Spikelet, Stem

SUBMITTER: Minami Matsui

PROVIDER: E-MTAB-4273 | ArrayExpress | 2015-03-11

REPOSITORIES: ArrayExpress

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Publications

MOROKOSHI: transcriptome database in Sorghum bicolor.

Makita Yuko Y Shimada Setsuko S Kawashima Mika M Kondou-Kuriyama Tomoko T Toyoda Tetsuro T Matsui Minami M

Plant & cell physiology 20141209 1

In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection facilitates the refinement of transcriptional annotation, and accurate transcription start sites help to unravel transcriptional regulation. We constructed a normalized FL-cDNA library from eight growth stages of aerial tissues in Sorghum bicolor and isolated 37,607 clones. These clones were Sanger sequenced from the 5' and/or 3' ends and in ...[more]

PMID: 25505007

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Project description:<h4>Main conclusion</h4>A novel inducible secretion system mutation in Sorghum named Red root has been identified. The mutant plant root exudes pigmented compounds that enriches Actinobacteria in its rhizosphere compared to BTx623. Favorable plant-microbe interactions in the rhizosphere positively influence plant growth and stress tolerance. Sorghum bicolor, a staple biomass and food crop, has been shown to selectively recruit Gram-positive bacteria (Actinobacteria) in its rhizosphere under drought conditions to enhance stress tolerance. However, the genetic/biochemical mechanism underlying the selective enrichment of specific microbial phyla in the sorghum rhizosphere is poorly known due to the lack of available mutants with altered root secretion systems. Using a subset of sorghum ethyl methanesulfonate (EMS) mutant lines, we have isolated a novel Red root (RR) mutant with an increased accumulation and secretion of phenolic compounds in roots. Genetic analysis showed that RR is a single dominant mutation. We further investigated the effect of root-specific phenolic compounds on rhizosphere microbiome composition under well-watered and water-deficit conditions. The microbiome diversity analysis of the RR rhizosphere showed that Actinobacteria were enriched significantly under the well-watered condition but showed no significant change under the water-deficit condition. BTx623 rhizosphere showed a significant increase in Actinobacteria under the water-deficit condition. Overall, the rhizosphere of RR genotype retained a higher bacterial diversity and richness relative to the rhizosphere of BTx623, especially under water-deficit condition. Therefore, the RR mutant provides an excellent genetic resource for rhizosphere-microbiome interaction studies as well as to develop drought-tolerant lines. Identification of the RR gene and the molecular mechanism through which the mutant selectively enriches microbial populations in the rhizosphere will be useful in designing strategies for improving sorghum productivity and stress tolerance.

Dataset Information

Transcription profiling by high throughput sequencing of seed, spikelet and stem tissues of Sorghum bicolor Btx623

Publications

MOROKOSHI: transcriptome database in Sorghum bicolor.

Similar Datasets

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