A lateral organ boundaries domain transcription factor acts downstream of the auxin response factor 2 to control nodulation and root architecture in Medicago truncatula

Noncoding RNAs as tools for advancing translational biology in plants

Noncoding RNAs (ncRNAs), once considered the "dark matter" of the genome, have emerged as critical regulators of gene expression in plants. Research initially focused on model organisms has laid the groundwork for harnessing the potential of ncRNAs in agriculture, particularly for crop protection, improvement, and modulation. This review explores the role of long and small ncRNAs in plant biology, highlighting their application as powerful tools in agricultural biotechnology. We examine the latest strategies for ncRNA expression and delivery in crops, including transgenic and nontransgenic approaches, as well as emerging technologies that enable precise and efficient modulation of gene activity in plants and pathogens. Additionally, we provide a comprehensive overview of the current state-of-the-art in the regulation of RNA-based products, addressing the challenges and opportunities for integrating these innovations into sustainable agricultural practices. As the regulatory landscape evolves, understanding the safety, efficacy, and environmental impact of ncRNA-based technologies will be crucial for their successful deployment. By leveraging the advances in plant science research, long and small ncRNAs hold promise for designing highly specific tools to boost crop productivity while preserving genetic diversity, contributing to global food security and sustainable agriculture.

Identification and characterization of the auxin-response factor family in moso bamboo reveals that PeARF41 negatively regulates second cell wall formation

Auxin response factors (ARFs) are key transcriptional factors mediating the transcriptional of auxin-related genes that play crucial roles in a range of plant metabolic activities. The characteristics of 47 PeARFs, identified in moso bamboo and divided into three classes, were evaluated. Structural feature analysis showed that intron numbers ranged from 3 to 14, while Motif 1, 2, 7 and 10 were highly conserved, altogether forming DNA-binding and ARF domains. Analysis of RNA-seq from different tissues revealed that PeARFs showed tissue-specificity. Additionally, abundant hormone-response and stress-related elements were enriched in promoters of PeARFs, supporting the hypothesis that the expression of PeARFs was significantly activated or inhibited by ABA and cold treatments. Further, PeARF41 overexpression inhibited SCW formation by reducing hemicellulose, cellulose and lignin contents. Moreover, a co-expression network, containing 28 genes with PeARF41 at its core was predicted, and the results of yeast one hybridization (Y1H), electrophoretic mobility shift assay (EMSA) and dual-luciferase (Dul-LUC) assays showed that PeARF41 bound the PeSME1 promoter to inhibit its expression. We conclude that a 'PeARF41-PeSME1' regulatory cascade mediates SCW formation. Our findings provided a solid theoretical foundation for further research on the role of PeARFs.

Effect of exogenous IBA on root morphology and endogenous hormone Metabolic pathways in castor seedlings under Pb/Zn stress

Ricinus communis, a plant of significant industrial value for its oil, is renowned for its robust root system and vigorous growth, qualities that render it an exemplary candidate for the ecological remediation of soils contaminated with heavy metals. The impact of heavy metal stress on root development is characterized by inhibition, a phenomenon whose underlying mechanisms are not fully elucidated. To shed light on this, a study was conducted wherein varying concentrations of the exogenous auxin, IBA, were applied to the roots of Ricinus communis to scrutinize its influence on the endogenous indole-3-acetic acid (IAA) metabolism in seedlings and to delineate the molecular underpinnings of its effects on root morphology. It was observed that IBA significantly amplified the total root surface area by a factor of 1.29 and increased the number of root tips by 40.11% under lead (Pb) stress, and by 32.29% and 91.19%, respectively, under zinc (Zn) stress. These findings underscore the efficacy of IBA in promoting the proliferation of lateral roots in seedlings subjected to stress induced by either Pb or Zn. Further analysis of auxin signaling pathways revealed that the presence of Pb or Zn impedes root growth and lateral root formation by perturbing auxin transporters and signaling molecules. Notably, IBA was found to foster the development of lateral roots by modulating the expression of specific transporters. Post-application of IBA, the endogenous levels of IAA in roots exhibited a 2.80-fold elevation under Pb stress, IBA stimulated the activity of key biosynthetic enzymes, such as RcNIT and RcTAR, culminating in elevated IAA levels. Conversely, under Zn stress, IBA was observed to diminish the levels of RcTAR, which in turn led to reduced IAA levels. These outcomes contribute to a deeper comprehension of the modulatory role of IBA in the context of heavy metal stress.

Unlocking the small RNAs: local and systemic modulators for advancing agronomic enhancement

Small regulatory RNAs (sRNAs) are essential regulators of gene expression across a wide range of organisms to precisely modulate gene activity based on sequence-specific recognition. In model plants like Arabidopsis thaliana, extensive research has primarily concentrated on 21 to 24-nucleotide (nt) sRNAs, particularly microRNAs (miRNAs). Recent advancements in cell and tissue isolation techniques, coupled with advanced sequencing technologies, are revealing a diverse array of preciously uncharacterized sRNA species. These include previously novel structural RNA fragments as well as numerous cell- and tissue-specific sRNAs that are active during distinct developmental stages, thereby enhancing our understanding of the precise and dynamic regulatory roles of sRNAs in plant development regulation. Additionally, a notable feature of sRNAs is their capacity for amplification and movement between cells and tissues, which facilitates long-distance communication-an adaptation critical to plants due to their sessile nature. In this review, we will discuss the classification and mechanisms of action of sRNAs, using legumes as a primary example due to their essential engagement for the unique organ establishment of root nodules and long-distance signaling, and further illustrating the potential applications of sRNAs in modern agricultural breeding and environmentally sustainable plant protection strategies.

Nitrate Starvation Induces Lateral Root Organogenesis in Triticum aestivum via Auxin Signaling

The lateral root (LR) is an essential component of the plant root system, performing important functions for nutrient and water uptake in plants and playing a pivotal role in cereal crop productivity. Nitrate (NO3-) is an essential nutrient for plants. In this study, wheat plants were grown in 1/2 strength Hoagland's solution containing 5 mM NO3- (check; CK), 0.1 mM NO3- (low NO3-; LN), or 0.1 mM NO3- plus 60 mg/L 2,3,5-triiodobenzoic acid (TIBA) (LNT). The results showed that LN increased the LR number significantly at 48 h after treatment compared with CK, while not increasing the root biomass, and LNT significantly decreased the LR number and root biomass. The transcriptomic analysis showed that LN induced the expression of genes related to root IAA synthesis and transport and cell wall remodeling, and it was suppressed in the LNT conditions. A physiological assay revealed that the LN conditions increased the activity of IAA biosynthesis-related enzymes, the concentrations of tryptophan and IAA, and the activity of cell wall remodeling enzymes in the roots, whereas the content of polysaccharides in the LRP cell wall was significantly decreased compared with the control. Fourier-transform infrared spectroscopy and atomic microscopy revealed that the content of cell wall polysaccharides decreased and the cell wall elasticity of LR primordia (LRP) increased under the LN conditions. The effects of LN on IAA synthesis and polar transport, cell wall remodeling, and LR development were abolished when TIBA was applied. Our findings indicate that NO3- starvation may improve auxin homeostasis and the biological properties of the LRP cell wall and thus promote LR initiation, while TIBA addition dampens the effects of LN on auxin signaling, gene expression, physiological processes, and the root architecture.

Genome-Wide Identification, Expression, and Interaction Analysis of the Auxin Response Factor and AUX/IAA Gene Families in Vaccinium bracteatum

BACKGROUND

Auxin, a plant hormone, plays diverse roles in the modulation of plant growth and development. The transport and signal transduction of auxin are regulated by various factors involved in shaping plant morphology and responding to external environmental conditions. The auxin signal transduction is primarily governed by the following two gene families: the auxin response factor (ARF) and auxin/indole-3-acetic acid (AUX/IAA). However, a comprehensive genomic analysis involving the expression profiles, structures, and functional features of the ARF and AUX/IAA gene families in Vaccinium bracteatum has not been carried out to date.

RESULTS

Through the acquisition of genomic and expression data, coupled with an analysis using online tools, two gene family members were identified. This groundwork provides a distinguishing characterization of the chosen gene families in terms of expression, interaction, and response in the growth and development of plant fruits. In our genome-wide search of the VaARF and VaIAA genes in Vaccinium bracteatum, we identified 26 VaARF and 17 VaIAA genes. We analyzed the sequence and structural characteristics of these VaARF and VaIAA genes. We found that 26 VaARF and 17 VaIAA genes were divided into six subfamilies. Based on protein interaction predictions, VaIAA1 and VaIAA20 were designated core members of VaIAA gene families. Moreover, an analysis of expression patterns showed that 14 ARF genes and 12 IAA genes exhibited significantly varied expressions during fruit development.

CONCLUSION

Two key genes, namely, VaIAA1 and VaIAA20, belonging to a gene family, play a potentially crucial role in fruit development through 26 VaARF-IAAs. This study provides a valuable reference for investigating the molecular mechanism of fruit development and lays the foundation for further research on Vaccinium bracteatum.