Characterization of phytochrome C functions in the control of de-etiolation and agronomic traits in rice

Clinal variation in PHY (PAS domain) and CRY (CCT domain)-Signs of local adaptation to light quality in Norway spruce

Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.

Domestication-associated PHYTOCHROME C is a flowering time repressor and a key factor determining Setaria as a short-day plant

Phytochromes play vital roles in the regulation of flowering time, but little is known in Panicoideae species, especially the C₄ model Setaria. Here, genomic variations of PHYTOCHROME C (PHYC) between wild and cultivated Setaria gene pools were analysed and three SiphyC mutants were identified. The function of SiPHYC was verified by CRISPR-Cas9 approach and transcriptome sequencing. Furthermore, efficiency of indoor cultivation of SiphyC mutants were systematically evaluated. An extreme purified selection of PHYC was detected in wild to cultivated domestication process of Setaria. SiphyC mutants and knockout transgenic plants showed an early heading date and a loss of response to short-day photoperiod. Furthermore, variable expression of SiFTa, SiMADS14 and SiMADS15 might be responsible for promoting flowering of SiphyC mutants. Moreover, SiphyC mutant was four times that of the indoor plot ratio of wild-type and produced over 200 seeds within 45 d per individual. Our results suggest that domestication-associated SiPHYC repressed flowering and determined Setaria as a short-day plant, and SiphyC mutants possess the potential for creating efficient indoor cultivation system suitable for research on Setaria as a model, and either for maize or sorghum as well.

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

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 (WT) plants. The delay in heading between WT and phy mutants was greater in LD than in SD, confirming the importance of PHYB and PHYC in accelerating heading date in LDs. Both mutants flowered earlier in SD than LD, the inverse response to that of WT plants. In both SD and LD photoperiods, PHYB regulated more genes than 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 found that photoperiod had a contrasting effect on transcript levels of the flowering promoting genes VRN-A1 and PPD-B1 in phyB and phyC mutants compared to the WT.

CONCLUSIONS

Our study confirms the major role of both PHYB and PHYC in flowering promotion in LD conditions. Transcriptome characterization revealed an unexpected reversion of the wheat LD plants into SD plants in the phyB-null and phyC-null mutants and identified flowering genes showing significant interactions between phytochromes and photoperiod that may be 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.

Regulation of Photomorphogenic Development by Plant Phytochromes

Photomorphogenesis and skotomorphogenesis are two key events that control plant development, from seed germination to flowering and senescence. A group of wavelength-specific photoreceptors, E3 ubiquitin ligases, and various transcription factors work together to regulate these two critical processes. Phytochromes are the main photoreceptors in plants for perceiving red/far-red light and transducing the light signals to downstream factors that regulate the gene expression network for photomorphogenic development. In this review, we highlight key developmental stages in the life cycle of plants and how phytochromes and other components in the phytochrome signaling pathway play roles in plant growth and development.

Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.