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Barley microbiota

ABSTRACT: Structure and functions of the bacterial root microbiota in wild and domesticated barley and signatures of positive selection in the rhizosphere metagenome

PROVIDER: PRJEB5860 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR638339.fastq.gz	Fastqsanger.gz
	ERR638340.fastq.gz	Fastqsanger.gz
	ERR646488_1.fastq.gz	Fastqsanger.gz
	ERR646488_2.fastq.gz	Fastqsanger.gz

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Project description:The effects of mercury (HgCl2) on barley (Hordeum vulgare L.) growth, physiological traits and gene expression profiles were studied. The shoot to root ratio was decreased in the two levels of HgCl2 (500 and 1000 μM) assayed, which was related primarily with decreases in shoot dry weight. Moreover stomatal conductance was limited and leaf carbon isotope discrimination decreased. Therefore water uptake limitations seem to be an important component of barley responses to HgCl2. Evidences for decreased stomatal conductance and water uptake limitations were further confirmed by the over expression of ABA related transcripts and down regulation of an aquaporin in roots. Root dry weight was only affected at 1000 μM HgCl2 and root browning was observed, while several transcripts for lignin biosynthesis were up regulated in HgCl2. Microarray analysis further revealed that growth inhibition in HgCl2 was related to increased expression of genes participating in ethylene biosynthesis and down regulation of several genes participating in DNA synthesis, chromatin structure and cell division, cell wall degradation and modification, oxidative pentose phosphate cycle and nitrogen metabolism pathway. Genes involved in detoxification and defence mechanisms were up regulated including several cytochrome P450s, glucosyltransferases and glutathione-s-transferases and amino acid metabolism participatory genes. It is concluded that barley plants survive in the presence of HgCl2 through several mechanisms that include water uptake limitations, shoot and root growth regulation, increased expression of genes involved in the biosynthesis of several plant protection secondary metabolites and finally through detoxification.

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Shoot and root of barley seeds: Aluminum treatment

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Project description:Transcriptional profiling of barley shoot and root with 0.2M NaCl

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Shoot and root of barley seeds: Cold treatment

Project description:Transcriptional profiling of barley shoot and root with incubating at 4˚C

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Shoot and root of barley seeds: Non-treatment (control)

Project description:Transcriptional profiling of barley shoot and root with no-treatment

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Shoot and root of barley seeds: Methyl Jasmonate (MeJA) treatment

Project description:Transcriptional profiling of barley shoot and root with MeJA

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Shoot and root of barley seeds: Abscisic acid (ABA) treatment

Project description:Transcriptional profiling of barley shoot and root with ABA

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Distribution, functional impact and origin mechanisms of copy number variation in the barley genome

Project description:There is growing evidence for the prevalence of DNA copy number variation (CNV) and its role in phenotypic variation in recent years. Comparative genomic hybridization (CGH) was used to explore the extent of this type of structural variation in the barley genome. In a panel of 14 genotypes including domesticated cultivars and wild barleys, we found that 14.9% of all the sequences on the array are affected by CNV. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. A substantial portion (37%) of the CNV events are present in both wild and domesticated barley. CNVs are enriched in telomeric regions for all chromosomes except 4H, which is also the barley chromosome with the lowest proportion of CNVs. CNV affected 9.5% of the coding sequences represented on the array. The genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases, suggesting the potential for CNV to influence variation for responses to biotic and abiotic stress. The analysis of CNV breakpoints indicated that DNA repair mechanisms of double-strand breaks (DSBs) via single-stranded annealing (SSA) and synthesis-dependent strand annealing (SDSA) play an important role in the origin of many structural changes in barley. Here we present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance.

2013-05-09 | GSE44293 | GEO

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