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SRX10816602: GSM5285896: Sample39_NIV, Norman, 96 hr, Replicate 1 [NIV-N-96-1]; Hordeum vulgare; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 72.7M spots, 14.5G bases, 5.8Gb downloads

Submitted by: NCBI (GEO)
Study: Transcriptome alterations of an in vitro-selected, moderately-resistant, two-row malting barley in response to 3ADON, 15ADON and NIV chemotypes of Fusarium graminearium
show Abstracthide Abstract
Fusarium head blight caused by Fusarium graminearum is a devastating disease of malting barley. Mycotoxins associated with contaminated grain can be transferred from malt to beer and pose a health risk to consumers. In western Canada, F. graminearum has undergone an adaptive shift from 15ADON constituency to dominance by virulent 3ADON-producers, likewise NIV-producers have established in regions of southern United States. Lack of adapted resistance sources with adequate malting quality has promoted the use of alternative breeding methodologies such as in vitro selection. We studied the low-deoxynivalenol characteristic of in vitro selected, two-row malting barley variety 'Norman' by RNAseq in contrast to its parental line 'CDC Kendall', when infected by 15ADON-, 3ADON- and NIV-producing isolates of F. graminearum. The current study documents higher mycotoxin accumulation by 3ADON isolates, thereby representing increased threat to barley production. At 72-96 hours post infection, significant alterations in transcription patterns were observed in both varieties with pronounced upregulation of the phenylpropanoid pathway and detoxification gene categories (UGT, GST, CyP450 and ABC) particularly in 3ADON treatment. Defense response was multi-tiered, where differential expression in 'Norman' associated with antimicrobial peptides (thionin 2.1, defensing, non-specific lipid-transfer protein) and stress-related proteins such as late embryogenesis abundant proteins, heat-shock, desiccation-related and a peroxidase (HvPrx5). Several gene targets identified in 'Norman' would be useful in application of breeding varieties with reduced deoxynivalenol content. Overall design: Adult plants of Norman and CDC Kendall were sprayed with macroconidia (5 x 10^4 spores ml-1) of Fusarium graminearum (3ADON, 15ADON and NIV chemotypes + mock control). Seed tissue samples were collected at the time-points 72 h and 96h post-inoculation for Norman and CDC Kendall from all Fusarium treated and control plants. Total RNA was prepared and used for the RNA-seq analysis. Three independent biological replicates were sampled.
Sample: Sample39_NIV, Norman, 96 hr, Replicate 1 [NIV-N-96-1]
SAMN19068995 • SRS8901541 • All experiments • All runs
Organism: Hordeum vulgare
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: Seeds were pulverized in liquid nitrogen using a mortar and pestle, and total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen, Canada) following the manufacturer's protocol. Three biological replicates of Norman and CDC Kendall at 72 h and 96 h time-points, were subjected to RNA-seq analysis. The RNA quality and concentration were verified using a NanoDrop 1000 spectrophotometer (ThermoFisher Scientific, Canada) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Canada) prior to sequencing. Sequencing libraries were generated using Illumina first-strand TruSeq® mRNA Prep Kit following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using oligo (dT)-attached magnetic beads. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.
Experiment attributes:
GEO Accession: GSM5285896
Runs: 1 run, 72.7M spots, 14.5G bases, 5.8Gb
Run# of Spots# of BasesSizePublished


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