Eucalyptus grandisAuxinResponseFactor 10 (EgrARF10) is associated with the modulation of secondary xylem cell wall chemistry

Multi-organ single-cell transcriptomic atlas identifies QrIAA14 as a candidate negative regulator of adventitious root development in Quercus robur.

Plant organ development involves coordinated cell fate transitions across multiple tissues, yet the cellular programs underlying organ-specific differentiation in woody plants remain poorly understood, particularly the mechanisms limiting efficient root development during vegetative propagation of oak species. Here, we generated a comprehensive single-cell transcriptomic landscape of leaf, stem, and root tissues of Quercus robur to resolve developmental trajectories at cellular resolution. A total of 41,471 high-quality cells were classified into 30 distinct clusters, enabling the identification of major cell types and organ-specific transcriptional features across three vegetative organs. Pseudotime analyses exhibited the developmental programs related to guard cell differentiation in leaves, vascular formation in stems, and root tissue development. Additionally, combining scRNA-seq, bulk transcriptome profiling, and phytohormone investigations, we identified auxin signaling as an important regulator during adventitious root development process. Notably, QrIAA14-1, an IAA14 homolog, was preferential enrichment in root hair, near-root hair cells and root cap along root developmental trajectories, which was further supported by RT-qPCR and in situ hybridization assays. Furthermore, the overexpression of QrIAA14-1 significantly inhibited oak root elongation, resulting in around 64.46% reduction in adventitious root length compared with control plants, providing mechanistic insight into the limitations of root development in oak. Together, this study provides the first high-resolution single-cell atlas of cellular organization and developmental dynamics across oak vegetative organs and identifies the candidate regulator genes associated with root development, offering new insights into the regulatory mechanisms of woody plant root regeneration and clonal propagation.

Integrated scRNA-Seq and ATAC-Seq Decipher the Xylem Development Atlas and Regulatory Landscape in Rubber Tree (Hevea brasiliensis).

Rubber tree is an economically important woody plant, whereas the cellular heterogeneity and regulatory networks underlying its xylem differentiation remain poorly characterised. Here, we built a protocol to isolate differentiating xylem protoplasts and performed scRNA-seq on two rubber tree cultivars (RK525 and RY73397) with distinct rates of girth growth. The first single-cell transcriptional atlas of differentiating xylem in the rubber tree was established, providing a cellular basis for growth variations. Ten distinct cell clusters were identified, with cell types-including vessel element, libriform fibre, and ray parenchyma-determined by established marker genes. Pseudotime analysis revealed two clearly developmental trajectories, underscoring fusiform lineages (fibres and vessels) being crucial for growth differences. Specifically, the fast-growing cultivar RK525 exhibited a cluster of upregulated genes in fibre and vessel cells. Subsequently, differentially expressed genes (DEGs) in fusiform cell clusters between the two cultivars were intersected with subcluster-upregulated genes and pseudotime-core DEGs in RK525, highlighting secondary cell wall (SCW) biosynthesis genes that regulate xylem development and promote rapid growth. WGCNA further identified a specific module significantly correlated with fibre cells, which includes six key transcription factors. Moreover, ATAC-seq revealed variety-specific chromatin accessibility patterns and transcription factor binding motifs associated with xylem development. Functional validation using Arabidopsis mutants of rubber tree homologues confirmed their crucial roles in vascular development. These findings reveal intricate regulatory programmes in differentiating xylem, and provide valuable resources and targets for genetic improvement of the rubber tree.

RhSCL3 and RhSCL33 (SCARECROW-LIKE) Regulate the Adventitious Root Formation of Rosa hybrida Responding Auxin

Adventitious root (AR) formation is critical for the successful establishment and survival of rose (Rosa hybrida) cuttings. SCARECROW-LIKE (SCL) genes are known to regulate plant growth and development; however, their functions in rose AR formation remain poorly understood. In this study, the rooting rate of rose cuttings declined, whereas AR number increased with increasing concentrations of exogenous indole-3-butyric acid (IBA) and N-1-naphthylphthalamic acid (NPA). Most of the 36 identified RhSCL genes were significantly up-regulated during AR formation. Notably, the expression level of RhSCL3 and RhSCL33 was positively associated with AR formation under low concentrations of exogenous IBA and NPA. Both genes were expressed at higher levels in roots than in other organs and encoded nuclear-localized proteins with transcriptional activation activity. Heterologous expression of RhSCL3 and RhSCL33 in tobacco increased primary root length under exogenous IBA treatment, enhanced AR number and length, and promoted dry matter accumulation, accompanied by increased starch degradation and soluble sugar production. Compared with wild-type plants (WT), transgenic plants showed reduced indole-3-acetic acid (IAA) levels, more pronounced changes in gibberellic acid (GA3) content, and higher activities of superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO), catalase (CAT), and indole-3-acetic acid oxidase (IAAO). These findings suggest that overexpression of RhSCL3 and RhSCL33 facilitates rooting under low-auxin conditions, and RhSCL33 acting earlier during AR development, and RhSCL3 functioning mainly at later stages. This regulatory module may provide useful genetic targets for improving vegetative propagation efficiency in rose and other horticultural or crop species.

Genome-Wide Analysis of Triticum aestivum Root Meristem Growth Factor (RGF) Gene Family Highlights TaRGF5 as a Putative Component of Root-Associated Signaling

Wheat (Triticum aestivum), a key global crop, faces rising drought stress that limits root growth and water uptake. Root meristem growth factors (RGFs) are small peptides that regulate root stem cell maintenance, meristem activity, and lateral root formation in model plants, yet the RGF gene family remains unexplored in wheat. Here, we performed a comprehensive genome-wide analysis of the TaRGF gene family, identifying 15 genes distributed across the A, B, and D subgenomes and classified into five homeologous groups (TaRGF1–TaRGF5), predominantly located on chromosomes 2 and 6. All TaRGFs contained a characteristic RGF motif, with dibasic cleavage sites and Asp–Tyr motifs indicating conserved maturation mechanisms. Based on the phylogenetic analysis, the TaRGF5 homeologs showed the highest similarity to Arabidopsis thaliana RGF5. Tested RNA-seq data revealed predominantly root-enriched expression for all TaRGF genes, with TaRGF5 exhibiting the most root-preferential and downregulation under drought stress. Quantitative real-time PCR (qRT-PCR) confirmed that drought stress suppressed the expression of TaRGF5A, TaRGF5B, and TaRGF5D in roots of wheat cultivar Sids-13 across all time points, unlike the higher accumulation seen in controls. Promoter analysis predicted a unique BES1 transcription factor binding site exclusively in TaRGF5B, linking brassinosteroid signaling to peptide-mediated root regulation. Structural modeling and molecular docking predicted an interaction between wheat TaRGF5 homeologs and root growth factor-insensitive receptor kinase (TaRGI3), characterized by conserved sulfotyrosine-mediated binding and favorable interaction energetics. Based on this characterization of the wheat RGF gene family, particularly the potential role of TaRGF5 in root development and drought-adaptation signaling, we propose targeting this gene for functional analysis to improve wheat resilience under water-limited conditions.

SBT4.1 promotes xylem cell expansion and coordinates secondary wall deposition and PCD by modulating PME61 activity downstream of SND1/VND6/MYB46 in Arabidopsis thaliana.

Xylem development involves a series of coordinated processes, including cell differentiation, expansion, secondary cell wall (SCW) deposition, and programmed cell death (PCD). Here, we characterize a subtilisin-like serine protease gene, SBT4.1, which exhibits specific expression in stem xylem. Loss of SBT4.1 function results in reduced xylem cell number, smaller cell size, thinner secondary walls, and delayed organelle degradation during PCD. In contrast, SBT4.1 overexpression accelerates cellular clearance and increases xylem cell number, size, and wall thickness, indicating its critical roles in differentiation, SCW synthesis, and PCD. Consistent with a positive regulatory function, pectinase activity and the expression of pectin-related genes are decreased in the mutant but increased in overexpressors. Accordingly, SBT4.1 promotes cell expansion, at least partly, by modulating pectinase activity, as evidenced by enhanced pectin methylesterase (PME) activity upon co-expression with specific PME genes in Nicotiana benthamiana. Molecular analyses revealed that SBT4.1 is a direct transcriptional target of the key SCW regulators SND1, VND6, and MYB46. Furthermore, the expression of SCW synthesis-related genes and PCD-associated protease genes is downregulated in the mutant and upregulated in overexpressing plants. Taken together, our findings demonstrate that SBT4.1, transcriptionally activated by SND1/VND6/MYB46, coordinates xylem cell differentiation, SCW deposition, and PCD, while also promoting cell expansion through modulation of pectin metabolism.

LfiRAV7 antagonizes LfiGI to regulate gibberellin biosynthesis and modulate plant height of crape myrtle.