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PubMed2025

Water shortage reduces PHYTOCHROME INTERACTING FACTOR 4, 5 and 3 expression and shade avoidance in Arabidopsis.

In agricultural crops, forests and grasslands, water deficit often occurs in the presence of cues from neighbouring vegetation. However, most studies have addressed separately the mechanisms of plant growth responses to these two aspects of the environment. Here we show that transferring Arabidopsis thaliana seedlings to agar containing polyethylene glycol (PEG) to restrict water availability reduces hypocotyl growth responses to shade without simultaneously affecting cotyledon expansion or its response to shade. Hypocotyl growth showed significant triple interaction among water availability, shade and the presence of PHYTOCHROME INTERACTING FACTOR 4 (PIF4), PIF5 and PIF3. Water restriction diminished auxin signalling and the activity of the PIF4, PIF5, PIF3 gene promoters and their transcript levels. The responses of PIF4 expression and hypocotyl growth to PEG were reduced in mutants of its positive morning regulators CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). The CCA1 and LHY gene promoters also reduced their activity in response to PEG. In addition to the changes in PIF4 levels, post-transcriptional processes also contributed to the PIF4 protein response to PEG. Collectively, these results unveil PIFs as a hub that interlinks shade and drought information to control growth.

Arabidopsis↗

PubMed2025

Efficient and versatile rapeseed transformation for new breeding technologies.

Many gene functions are widely studied and understood in Arabidopsis; however, the lack of efficient transformation systems often limits the application and verification of this knowledge in crop plants. Brassica napus L., a member of the Brassicaceae family, is usually transformed by Agrobacterium-mediated hypocotyl transformation, but not all growth types are equally amenable to transformation. In particular, winter rapeseed, which requires vernalization to initiate flowering, is recalcitrant to in vitro regeneration and transformation. The analysis of gene functions in rapeseed is further complicated by the allotetraploid nature of its genome and the genome triplication within the Brassica genus, which has led to the presence of a large number of gene homologs for each Arabidopsis ortholog. We have established a transformation method that facilitates the regeneration of winter rapeseed by using the WUSCHEL gene from Beta vulgaris. This allowed us to efficiently transform a winter and spring rapeseed genotype in small-scale experiments. As proof of principle, we targeted BnCLV3 and BnSPL9/15 with CRISPR/Cas9 and showed that entire gene families are effectively edited using this transformation protocol. This allowed us to simultaneously study many redundantly acting homologous genes in rapeseed. We observed mutant phenotypes for BnCLV3 and BnSPL9/15 in primary transformants, indicating that biallelic knockouts were obtained for up to eight genes. This allowed an initial phenotypic characterization to be performed already a few months after starting the experiment.

Brassica napus↗

PubMed2025

A PIF-regulated switch in cell axis growth drives cotyledon expansion through tissue-specific cell expansion and division.

Despite its crucial role during seedling deetiolation, cotyledon expansion has been largely overlooked, with hypocotyl elongation favored as the primary phenotypic readout in light signaling research. Here, we investigate how cotyledon expansion is regulated during seedling establishment and reveal that light-induced cotyledon expansion involves a rapid switch in growth direction - from longitudinal in darkness to transversal upon initial light exposure. Using PIFq- and phyA/phyB-deficient Arabidopsis mutants, we demonstrate that this switch is repressed by PIFs in the dark and promoted by phytochromes under red light. Notably, expansion is antagonistically regulated in the light by GUN1-mediated plastid retrograde signaling. Cotyledon expansion involves rapid epidermis cell expansion, transitioning from rectangular in darkness to characteristic lobed cells in light. Importantly, our findings show that mesophyll extension is driven not only by cell enlargement but also by palisade cell division, consistent with an enrichment of cell cycle-related genes that are antagonistically regulated by the PIF/phy system and retrograde signaling in the cotyledon. Finally, using mutant lines expressing PIF1 and phyB specifically in the epidermis, we establish that epidermal expansion can drive palisade cell growth, while mesophyll cell division is predominantly regulated by light at the tissue-specific level. This study provides a novel framework for investigating cotyledon expansion during seedling deetiolation, incorporating tissue-level regulation. We propose that cotyledons serve as an excellent model for studying morphogenesis and organ geometry, which in plants is governed by directional cell growth.

Cotyledon↗

PubMed2026

Long-day photoperiod promotes growth of pea (Pisum sativum L.) via auxin biosynthesis and polar transport.

Photoperiodic sensitivity is an essential factor that may affect agricultural practices under current climate scenarios. This study used pea (Pisum sativum) to examine effects of varying photoperiods on growth and photosynthetic parameters and then reveal the mechanistic basis of this process by linking them with tissue-specific distribution of auxin and regulation of related genes. This was achieved by transcriptome sequencing, genome-wide gene family identification, and expression pattern analysis. Best results in terms of growth and yield were obtained with a 20 h/4 h light/dark photoperiod and these plants had the highest content of endogenous indole-3-acetic acid (IAA) in both the shoot apex and the root. Genes consistently upregulated with prolonged light exposure were significantly enriched in pathways related to light signal transduction, photosynthetic carbon metabolism, and phytohormone signal transduction. Through genome-wide identification, we characterized the TAA/TAR and YUCCA families (key gene families involved in auxin biosynthesis) as well as the PIN family (responsible for auxin polar transport) in pea. Extending the light duration positively affected expression of several genes related to auxin biosynthesis and transport, among them members of the Elongated Hypocotyl (HY) and Phytochrome-Interacting Factor (PIF) families being key light-induced transcription factors, PsTAR2, the principal gene regulating auxin biosynthesis, as well as PsPIN4, PsPIN5, PsPIN11, and PsPIN13 which mediate polar auxin transport. By elucidating mechanisms underlying the coordinated regulation of pea growth by light and auxin, this work provides a significant reference for photoperiod research on long-day crops for both protected- and field-based horticulture.

Auxin↗

PubMed1978

Developmental restrictions on hormone modulated gene transcription. II. Hormone induced interactions of RNA polymerase with chromatin.

Chromatin-bound and soluble RNA polymerase subspecies have been isolated and fractionated by isoelectric focusing at various times (0, 6, 12 and 18 h) following auxin treatment of 4 day (responsive) and 8 day (unresponsive) soybean hypocotyls. Young 4 day seedlings displayed two well defined phases of auxin induced gene transcription. Phase I (6 h) evidenced the selective dissociation of many RNA polymerase subspecies from the chromatin complex which was accompanied by the retention of three class II enzymes. Phase II occurred after 12 h of treatment when the dissociated enzymes including some species which were soluble in the 0 h controls became re-associated with chromatin. These induced RNA polymerases may be responsible for the synthesis of auxin induced RNAs. In contrast, the unresponsive 8 day hypocotyl did not display two phases of auxin induction. Phase one, the dissociation of the chromatin bound enzymes, occurred at 12 h (compared to 6 h for the 4 day seedling) and was not followed by the later translocation of any soluble enzymes towards the chromatin complex. The results support earlier findings suggesting that the developmental "phasing out" of RNA polymerase subspecies limits the hormone induced growth response of this tissue and thus is regarded as an off switch for the transcription of such hormone controlled gene sequences.

2,4-Dichlorophenoxyacetic Acid↗