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Transcriptome alterations of an in vitro-selected, moderately-resistant, two-row malting barley in response to 3ADON, 15ADON and NIV chemotypes of Fusarium graminearium

ABSTRACT: Transcriptome alterations of an in vitro-selected, moderately-resistant, two-row malting barley in response to 3ADON, 15ADON and NIV chemotypes of Fusarium graminearium

PROVIDER: PRJNA728113 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14467100_1.fastq.gz	Fastqsanger.gz
	SRR14467100_2.fastq.gz	Fastqsanger.gz
	SRR14467101_1.fastq.gz	Fastqsanger.gz
	SRR14467101_2.fastq.gz	Fastqsanger.gz
	SRR14467102_1.fastq.gz	Fastqsanger.gz

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Transcriptome alterations of an in vitro-selected, moderately-resistant, two-row malting barley in response to 3ADON, 15ADON and NIV chemotypes of Fusarium graminearium

Project description: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.

2021-05-08 | GSE174081 | GEO

Transcriptome alterations of an in vitro-selected, moderately-resistant, two-row malting barley in response to 3ADON, 15ADON and NIV chemotypes of Fusarium graminearium

Project description:Transcriptome alterations of an in vitro-selected, moderately-resistant, two-row malting barley in response to 3ADON, 15ADON and NIV chemotypes of Fusarium graminearium

| PRJNA728113 | ENA

Transcriptome Alterations of an <i>in vitro</i>-Selected, Moderately Resistant, Two-Row Malting Barley in Response to 3ADON, 15ADON, and NIV Chemotypes of <i>Fusarium graminearum</i>.

Project description: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-h 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 multitiered, 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 for application of breeding varieties with reduced deoxynivalenol content.

| S-EPMC8385242 | biostudies-literature

Drosophila ROW RNAi gene expression profiling

2015-05-01 | GSE49103 | GEO

Transcription profiling of malting barley seeds

Project description:Malting is seed germination under strictly controlled environmental conditions. Malting quality is a complex phenotype that combines a large number of interrelated components, each of which shows complex inheritance. Currently, only a few genes involved in determining malting quality have been characterized. This study combined transcript profiling with phenotypic correlations to identify candidate genes for malting quality. We used the Barley1 GeneChipÂ® array to identify differentially expressed genes in four malting stages relative to dry seed in the barley variety Morex, and to identify differentially expressed genes among four barley varieties. Experiment Overall Design: Four malting barley cultivars were micromalted: Morex and Legacy (6-row), Merit and Harrington (2-row). Two to three batches of micromalting (biological replications) were performed. For each micromalting experiment, 20 g samples were collected for Morex at four stages: steeping, 24 h germination (day 1), 93 h germination (day 4), and finished malt after kilning was completed. Ungerminated, dry seed of Morex was used as reference sample. In another experiment, seeds of Legacy, Harrington, and Merit were micromalted and 20 g samples were collected for each variety during day 1 and day 4 germination stages. Expression profiles were compared among the four cultivars separately for day 1 and day 4.

2009-03-15 | E-GEOD-11200 | biostudies-arrayexpress

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Project description:Heterochromatin-protein 1 (HP1) is a functionally diverse family of proteins. In particular, Drosophila dHP1c forms a complex with the transcription factors WOC and ROW (dHP1EU) that localizes at euchromatin and regulates gene expression. We used microarrays to analyse the changes in gene expression after row depletion by RNAi. For expression profiling analyses, total RNAs were prepared from control S2 cells and upon RNAi-mediated depletion of ROW, converted to cDNA and hybridized to Drosophila Genome 2.0 GeneChip (Affymetrix).

2015-05-01 | E-GEOD-49103 | biostudies-arrayexpress

Henipavirus nipahense strain:NiV-BD

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The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [RNA_seq_S2]

Project description:Chromatin insulators are involved in transcription regulation and long-range chromatin contacts. In Drosophila the Boundary Element-Associated Factor Of 32kD (BEAF-32) binds to promoters of housekeeping genes and the boundaries of Topological Associated Domains (TAD) and is involved in the regulation of long-range targets by mechanisms that remain incompletely understood. Here we show that Relative-Of-WOC (ROW), which is part of the Heterochromatin Protein 1c (HP1c) complex, is essential for the long-range transcription regulation mediated by BEAF-32. We found that ROW physically interacts with the insulator complex proteins BEAF-32 and Chromator, as well as with HP1c, HP1b, and Without Children (WOC). Moreover, we found that ROW binds AT-rich sequences flanked by BEAF-32 motifs, which are located at promoters of housekeeping genes and in TAD boundaries. In agreement with these results, the genome distribution of ROW strongly correlated with BEAF-32 and WOC, but at a lower level with HP1c and HP1b. Knockdown of row resulted in downregulation of genes that are long-range targets of BEAF-32, are indirectly bound by BEAF-32 and ROW, and enriched with factors associated with RNA polymerase II pausing. These results suggest that ROW and BEAF-32 are involved in the recruitment of protein complexes required for transcription activation and long-range contacts between promoters of housekeeping and inducible genes.

2022-07-14 | GSE169413 | GEO

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