Abstract
BACKGROUND: Increasing the nutrient concentration of wheat grains is important to ameliorate nutritional deficiencies in many parts of the world. Proteins and nutrients in the wheat grain are largely derived from the remobilization of degraded leaf molecules during monocarpic senescence. The down-regulation of the NAC transcription factor Grain Protein Content (GPC) in transgenic wheat plants delays senescence (>3 weeks) and reduces the concentration of protein, Zn and Fe in the grain (>30%), linking senescence and nutrient remobilization.Based on the early and rapid up-regulation of GPC in wheat flag leaves after anthesis, we hypothesized that this transcription factor is an early regulator of monocarpic senescence. To test this hypothesis, we used high-throughput mRNA-seq technologies to characterize the effect of the GPC down-regulation on the wheat flag-leaf transcriptome 12 days after anthesis. At this early stage of senescence GPC transcript levels are significantly lower in transgenic GPC-RNAi plants than in the wild type, but there are still no visible phenotypic differences between genotypes. RESULTS: We generated 1.4 million 454 reads from early senescing flag leaves (average ~350 nt) and assembled 1.2 million into 30,497 contigs that were used as a reference to map 145 million Illumina reads from three wild type and four GPC-RNAi plants. Following normalization and statistical testing, we identified a set of 691 genes differentially regulated by GPC (431 ≥ 2-fold change). Transcript level ratios between transgenic and wild type plants showed a high correlation (R = 0.83) between qRT-PCR and Illumina results, providing independent validation of the mRNA-seq approach. A set of differentially expressed genes were analyzed across an early senescence time-course. CONCLUSIONS: Monocarpic senescence is an active process characterized by large-scale changes in gene expression which begins considerably before the appearance of visual symptoms of senescence. The mRNA-seq approach used here was able to detect small differences in transcript levels during the early stages of senescence. This resulted in an extensive list of GPC-regulated genes, which includes transporters, hormone regulated genes, and transcription factors. These GPC-regulated genes, particularly those up-regulated during senescence, provide valuable entry points to dissect the early stages of monocarpic senescence and nutrient remobilization in wheat.
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Claims 11
Claim · model-written summary
GPC down-regulation delayed wheat senescence by more than three weeks.
- Taxon
- wheat
Triticum aestivume0 - Treatment
- down-regulation of the NAC transcription factor Grain Protein Content (GPC)e0
- Gene
- Grain Protein Content (GPC)e0
- Outcome
- senescencee0
- Direction
- delayse0
- Value
- >3 weekse0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The down-regulation of the NAC transcription factor Grain Protein Content (GPC) in transgenic wheat plants delays senescence (>3 weeks)”
Claim · model-written summary
GPC down-regulation reduced wheat grain protein, Zn, and Fe concentrations by more than 30%.
- Taxon
- wheatTriticum aestivume0
- Treatment
- down-regulation of the NAC transcription factor Grain Protein Content (GPC)e0
- Gene
- Grain Protein Content (GPC)e0
- Outcome
- concentration of protein, Zn and Fe in the graine0
- Direction
- reducese0
- Value
- >30%e0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The down-regulation of the NAC transcription factor Grain Protein Content (GPC) in transgenic wheat plants delays senescence (>3 weeks) and reduces the concentration of protein, Zn and Fe in the grain (>30%)”
Claim · model-written summary
GPC transcript levels were significantly lower in RNAi plants than wild type at 12 days after anthesis.
Verbatim
e0“At this early stage of senescence GPC transcript levels are significantly lower in transgenic GPC-RNAi plants than in the wild type”
Claim · model-written summary
No visible phenotype differences were present between RNAi and wild-type plants at the early stage.
- Taxon
- wheatTriticum aestivumt0
- Outcome
- visible phenotypic differencese0
- Direction
- no visible phenotypic differencese0
- Comparator
- wild typee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“there are still no visible phenotypic differences between genotypes.”
e1“transgenic GPC-RNAi plants than in the wild type”
t0“wheat”
Claim · model-written summary
The study assembled 1.2 million of 1.4 million 454 reads into 30,497 contigs as a reference.
- Taxon
- wheatTriticum aestivumt0
- Organ / stage
- flag leavese0
- Outcome
- contigs that were used as a referencee0
- Value
- 30,497 contigse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“wheat”
e0“We generated 1.4 million 454 reads from early senescing flag leaves (average ~350 nt) and assembled 1.2 million into 30,497 contigs that were used as a reference to map 145 million Illumina reads”
Claim · model-written summary
The reference mapped 145 million Illumina reads.
- Taxon
- wheatTriticum aestivumt0
- Outcome
- Illumina readse0
- Value
- 145 million Illumina readse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“wheat”
e0“30,497 contigs that were used as a reference to map 145 million Illumina reads”
Claim · model-written summary
The study identified 691 GPC-regulated genes, including 431 with at least twofold changes.
- Taxon
- wheatTriticum aestivumt0
- Gene
- GPCe0
- Outcome
- genes differentially regulated by GPCe0
- Value
- 691 genese0
- Qualifier
- 431 ≥ 2-fold changee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“wheat”
e0“we identified a set of 691 genes differentially regulated by GPC (431 ≥ 2-fold change)”
Claim · model-written summary
qRT-PCR and Illumina transcript ratios had high correlation, validating the mRNA-seq approach.
- Taxon
- wheatTriticum aestivumt0
- Outcome
- high correlatione0
- Direction
- highe0
- Value
- R = 0.83e0
- Comparator
- qRT-PCR and Illumina resultse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“wheat”
e0“Transcript level ratios between transgenic and wild type plants showed a high correlation (R = 0.83) between qRT-PCR and Illumina results, providing independent validation of the mRNA-seq approach.”
Claim · model-written summary
The authors interpret monocarpic senescence as involving large gene-expression changes before visible symptoms.
- Taxon
- wheatTriticum aestivumt0
- Outcome
- large-scale changes in gene expressione0
- Qualifier
- before the appearance of visual symptoms of senescencee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“wheat”
e0“Monocarpic senescence is an active process characterized by large-scale changes in gene expression which begins considerably before the appearance of visual symptoms of senescence.”
Claim · model-written summary
mRNA-seq detected small transcript-level differences during early senescence.
- Taxon
- wheatTriticum aestivumt0
- Outcome
- detect small differences in transcript levelse0
- Value
- small differencese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“wheat”
e0“The mRNA-seq approach used here was able to detect small differences in transcript levels during the early stages of senescence.”
Claim · model-written summary
The GPC-regulated gene list includes transporters, hormone-regulated genes, and transcription factors.
- Taxon
- wheatTriticum aestivumt0
- Gene
- GPCe0
- Outcome
- transporters, hormone regulated genes, and transcription factorse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“wheat”
e0“This resulted in an extensive list of GPC-regulated genes, which includes transporters, hormone regulated genes, and transcription factors.”
The same questions in other papers
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See all 11 papers →Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.