Abstract
Background Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-of-function mutations in either PHYB or PHYC result in large delays in heading time and in the differential regulation of a large number of genes in wheat plants grown in an inductive long day (LD) photoperiod.
Results We found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed later than wild-type plants. Unexpectedly, both mutants flowered earlier in SD than LD, the inverse response to that of wild-type plants. We observed a larger number of differentially expressed genes between mutants and wild-type under SD than under LD, and in both cases, the number was larger for phyB than for phyC. We identified subsets of differentially expressed and alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We observed significantly higher transcript levels of the flowering promoting genes VRN-A1, PPD-B1 and GIGANTEA in the phy-null mutants in SD than in LD, which suggests that they could contribute to the earlier flowering of the phy-null mutants in SD than in LD.
Conclusions Our study revealed an unexpected reversion of the wheat LD plants into SD plants in the phyB-null and phyC-null mutants and identified candidate genes potentially involved in this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive and non-inductive photoperiods and a set of candidate genes to dissect the underlying developmental regulatory networks in wheat.
List of abbreviations
- AS
- Alternative Splicing
- BAM
- Binary Alignment Map
- bHLH
- basic Helix Loop Helix
- COR
- Cold Responsive
- DE
- Differentially Expressed
- EMS
- Ethyl-Methane Sulfonate
- FDR
- False Discovery Rate
- FR
- Far Red
- GO
- Gene Ontology
- IWGSC
- International Wheat Genome Sequencing Consortium
- LD
- Long Day
- MDS
- Multi-Dimensional Scaling
- PEBP
- Phosphatidylethanolamine-Binding Proteins
- PHY
- Phytochrome
- PIF
- Phytochrome Interacting Factor
- PRG
- Photoperiod Regulated Gene
- PRR
- Pseudo-Response Regulator
- PI
- Photoperiod Insensitive
- PS
- Photoperiod Sensitive
- qRT-PCR
- quantitative Reverse Transcriptase Polymerase Chain Reaction
- R
- Red
- rMATS
- replicate Multivariate Analysis of Transcript Splicing
- SAM
- Sequence Alignment Map
- SEM
- Standard Error of the Mean
- TILLING
- Targeted Induced Local Lesions IN Genomes
- TPM
- Transcripts per Million
- WT
- Wild-type