SMALL AUXIN UP RNAs (SAURs), the largest family of early auxin response genes, plays crucial roles in multiple processes, including cell expansion, leaf growth and senescence, auxin transport, tropic growth and so on. Although the rice SAUR gene family was identified in 2006, it is necessary to identify the rice SAUR gene due to the imperfection of its analysis methods. In this study, a total of 60 OsSAURs (including two pseudogenes) distributed on 10 chromosomes were identified in rice (Oryza sativa). Bioinformatics tools were used to systematically analyze the physicochemical properties, subcellular localization, motif compositions, chromosomal location, gene duplication, evolutionary relationships, auxin-responsive cis-elements of the OsSAURs. In addition, the expression profiles obtained from microarray data analysis showed that OsSAUR genes had different expression patterns in different tissues and responded to auxin treatment, indicating functional differences among members of OsSAUR gene family. In a word, this study provides basic information for SAUR gene family of rice and lays a foundation for further study on the role of SAUR in rice growth and development.

BACKGROUND: Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed.
RESULTS: To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction.
CONCLUSIONS: The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.

CONCLUSIONS: Auxin (AUX) promotion of apple fruit ripening is ethylene-dependent, and AUX-MdARF17-MdERF003 plays a role in AUX-promoted ethylene synthesis in apple. Phytohormones play important roles in plant growth and fleshy fruit ripening, and the phytohormone auxin (AUX) can either promote or inhibit the ripening of fleshy fruits. Although AUX can influence ethylene (ETH) synthesis in apple (Malus domestica) fruits by affecting ETH system II, this mechanism remains to be explored. Here, we identified an ETH response factor (ERF) family transcription factor, MdERF003, whose expression could be activated by naphthalene acetic acid. The transient silencing of MdERF003 inhibited ETH synthesis in fruits, and MdERF003 could bind to the MdACS1 promoter. To explore the upstream target genes of MdERF003, we screened the MdARF family members by yeast one-hybrid assays of the MdERF003 promoter, and found that the transcription factor MdARF17, which showed AUX-promoted expression, could bind to the MdERF003 promoter and promote its expression. Finally, we silenced MdERF003 in apple fruits overexpressing MdARF17 and found that MdERF003 plays a role in MdARF17-promoted ETH synthesis in apple. Thus, AUX-MdARF17-MdERF003 promotes ETH synthesis in apple fruits.

The Caenorhabditis elegans germline is arranged spatiotemporally and is therefore a powerful model system for the interrogation of meiotic molecular dynamics. Coupling this property with the temporal control that the auxin-inducible degron (AID) system allows can unveil new/unappreciated roles for critical meiotic factors in specific germline regions. Here we describe a widely used approach for the introduction of degron tags to specific targets and provide a procedure for applying the AID system to C. elegans meiotic DSB repair dynamics in the germline.

The bilateral-to-radial symmetry transition occurring during the development of the Arabidopsis thaliana female reproductive organ (gynoecium) is a crucial biological process linked to plant fertilization and seed production. Despite its significance, the cellular mechanisms governing the establishment and breaking of radial symmetry at the gynoecium apex (style) remain unknown. To fill this gap, we employed quantitative confocal imaging coupled with MorphoGraphX analysis, in vivo and in vitro transcriptional experiments, and genetic analysis encompassing mutants in two bHLH transcription factors necessary and sufficient to promote transition to radial symmetry, SPATULA (SPT) and INDEHISCENT (IND). Here, we show that defects in style morphogenesis correlate with defects in cell-division orientation and rate. We showed that the SPT-mediated accumulation of auxin in the medial-apical cells undergoing symmetry transition is required to maintain cell-division-oriented perpendicular to the direction of organ growth (anticlinal, transversal cell division). In addition, SPT and IND promote the expression of specific core cell-cycle regulators, CYCLIN-D1;1 (CYC-D1;1) and CYC-D3;3, to support progression through the G1 phase of the cell cycle. This transcriptional regulation is repressed by auxin, thus forming an incoherent feed-forward loop mechanism. We propose that this mechanism fine-tunes cell division rate and orientation with the morphogenic signal provided by auxin, during patterning of radial symmetry at the style.

Facile synthesis and characterisation of three natural compounds and their two synthetic analogues based on onion skin content were performed. Both OSE and 2,4,6-trihydroxyphenylglyoxylic acid was induced effect on cell proliferation during barley germination with a difference of approximately %4 compared to the control group.

Trichoderma, a highly abundant soil fungus, may benefit plants, yet it remains understudied in sorghum (Sorghum bicolor). In this study, sorghum plants were cultivated for five weeks in soil pots with or without the inoculation of T. afroharzianum T22. We found that plants inoculated with T. afroharzianum T22 exhibited significant increases in growth parameters and nutrient levels, demonstrating its beneficial role in sorghum. The split-root assay demonstrated that T. afroharzianum T22 is essential in both compartments of soil pots for promoting plant growth. This suggests that local signals from this fungus drive symbiotic benefits in sorghum. The RNA-seq analysis revealed the induction of genes responsible for mineral transport (such as nitrate and aquaporin transporters), auxin response, sugar assimilation (hexokinase), and disease resistance (thaumatin) in the roots of sorghum inoculated with T. afroharzianum T22. Microbial community analysis further unveiled the positive role of T. afroharzianum T22 in enriching Penicillium (ITS) and Streptomyces (16S) while reducing disease-causing Fusarium in the roots. The microbial consortium, consisting of enriched microbiomes from bacterial and fungal communities, showed disrupted morphological features in plants inoculated with T. afroharzianum T22 in the absence of S. griseus. However, this disruption was not observed in the absence of P. chrysogenum. These results suggest that S. griseus may act as a helper microbe in close association with T. afroharzianum T22 in the sorghum endosphere. This study provides the first comprehensive explanation of how T. afroharzianum T22 modulates host molecular determinants and endophytic helper microbes, thereby collectively promoting sorghum growth. These findings may encourage the formulation of a synthetic inoculum dominated by T. afroharzianum T22 to enhance growth and stress resilience in sorghum and other similar crops.

Wheat culms, comprising four to six internodes, are critically involved in determining plant height and lodging resistance, essential factors for field performance and regional adaptability. This study revealed the regulatory function of miR319 in common wheat plant height. Repression of tae-miR319 through short tandem target mimics (STTM) caused an increased plant height, while overexpression (OE) of tae-miR319 had the opposite effect. Overexpressing a miR319-resistant target gene TaPCF8 (rTaPCF8), increased plant height. TaPCF8 acted as a transcription repressor of downstream genes TaIAAs, which interact physically with TaSPL14. The significant differences of indole-3-acetic acid (IAA) contents indicate the involvement of auxin pathway in miR319-mediated plant height regulation. Finally, we identified two TaPCF8 haplotypes in global wheat collections. TaPCF8-5A-Hap2, as per association and evolution examinations, was subjected to strong substantial selection throughout wheat breeding. This haplotype, associated with shorter plant height, aligns with global breeding requirements. Consequently, in high-yield wheat breeding, we proposed a potential molecular marker for marker-assisted selection (MAS). Our findings offer fresh perspectives into the molecular mechanisms that underlie the miR319-TaPCF8 module\'s regulation of plant height by orchestrating auxin signaling and biosynthesis in wheat.

Infection with smut fungus like Ustilago maydis decreases crop yield via inducing gall formation. However, the in vitro impact of Ustilago spp. on plant growth and stress tolerance remains elusive. This study investigated the plant growth promotion and cadmium stress mitigation mechanisms of a filamentous fungus discovered on a cultural medium containing 25 μM CdCl2. ITS sequence alignment revealed 98.7 % similarity with Ustilago bromivora, naming the strain Ustilago sp. HFJ311 (HFJ311). Co-cultivation with HFJ311 significantly enhanced the growth of various plants, including Arabidopsis, tobacco, cabbage, carrot, rice, and maize, and improved Arabidopsis tolerance to abiotic stresses like salt and metal ions. HFJ311 increased chlorophyll and Fe contents in Arabidopsis shoots and enhanced root-to-shoot Fe translocation while decreasing root Fe concentration by approximately 70 %. Concurrently, HFJ311 reduced Cd accumulation in Arabidopsis by about 60 %, indicating its potential for bioremediation in Cd-contaminated soils. Additionally, HFJ311 stimulated IAA concentration by upregulating auxin biosynthesis genes. Overexpression of the Fe transporter IRT1 negated HFJ311\'s growth-promotion effects under Cd stress. These results suggest that HFJ311 stimulates plant growth and inhibits Cd uptake by enhancing Fe translocation and auxin biosynthesis while disrupting Fe absorption. Our findings offer a promising bioremediation strategy for sustainable agriculture and food security.

Combinatorial interactions between different regulators diversify and enrich the chance of transcriptional regulation in eukaryotic cells. However, a dose-dependent functional switch of homologous transcriptional repressors has rarely been reported. Here, we show that SHY2, an Auxin/Indole-3-Acetic Acid (Aux/IAA) repressor, exhibits a dose-dependent bimodal role in auxin-sensitive root-hair growth and gene transcription in Arabidopsis, whereas other Aux/IAA homologs consistently repress the auxin responses. The corepressor (TOPLESS [TPL])-binding affinity of a bimodal Aux/IAA was lower than that of a consistently repressing Aux/IAA. The switch of a single amino-acid residue in the TPL-binding motif between the bimodal form and the consistently repressing form switched their TPL-binding affinity and transcriptional and biological roles in auxin responses. Based on these data, we propose a model whereby competition between homologous repressors with different corepressor-binding affinities could generate a bimodal output at the transcriptional and developmental levels.