Salt stress is a major cause of crop loss. Soybean (Glycine max), a globally vital legume crop, faces mounting yield constraints due to soil salinization. It is known that the flavonoid biosynthesis pathway involving flavonoid 3'-hydroxylase (F3'H) plays an important role in salt tolerance. However, the precise molecular basis of F3'H-mediated salt tolerance remains inadequately characterized. This study aimed to elucidate the function and explore the pleiotropic molecular basis of F3'H protein in soybean salt tolerance. Innovation on elite new crop varieties facilitates breeding and production applications on salt tolerance. We employed CRISPR/Cas9-mediated knockout and Agrobacterium-based overexpression to generate GmF3'H allelic variants and ectopic expression in soybeans. Sanger sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to confirm the specificity of gene editing and quantify expression levels in overexpression transgenic plants, respectively. As well as Subcellular localization analysis, Yeast two-hybrid (Y2H) assay, LUC activity assay and plant physiological measurements were carried out to elucidate the F3'H-mediated salt tolerance molecular basis in plants. In this study, we identified the flavonoid 3' hydroxylase gene (GmF3'H) in soybeans, which as a master regulator of salt stress adaptation during seed germination and seedling stages in both soybean and Arabidopsis thaliana. Furthermore, our study revealed that the evolutionarily conserved F3'H protein competitively binds to photomorphogenic factor COP9 signalosome subunit 5B (CSN5B) and disrupts its interaction with GDP-mannose pyrophosphorylase 1 (VTC1), a key enzyme in ascorbate biosynthesis. This competitive inhibition redirects metabolic flux toward the L-galactose pathway, leading to an increase in ascorbic acid (AsA) biosynthesis. The enhanced AsA production subsequently improves seedling salt stress tolerance in plants by maintaining redox homeostasis through ROS scavenging. The discovery and characterization of F3'H-mediated salt tolerance provide a crucial framework for the genetic improvement of crops. This work provides new insights into plant salt stress tolerance and develops innovative strategies to enhance broad-spectrum salt tolerance, a crucial aspect for ensuring food security in crops.

Understanding somatic cell totipotency remains a challenge facing scientific inquiry today. Plants display remarkable cell totipotency expression, illustrated by single-cell differentiation during somatic embryogenesis (SE) for plant regeneration. Determining cell identity and exploring gene regulation in such complex heterogeneous somatic cell differentiation have been major challenges. Here, we performed high-throughput single-cell sequencing assays to define the precise cellular landscape and revealed the modulation mode of marker genes during embryogenic differentiation in cotton (Gossypium hirsutum L.) as the crop for biotechnology application. We demonstrated that nonembryogenic calli (NEC) and primary embryogenic calli (PEC) tissues were composed of heterogeneous cells that could be partitioned into 4 broad populations with 6 distinct cell clusters. Enriched cell clusters and cell states were identified in NEC and PEC samples, respectively. Moreover, a broad repertoire of new cluster-specific genes and associated expression modules were identified. The energy metabolism, signal transduction, environmental adaptation, membrane transport pathways, and a series of transcription factors were preferentially enriched in cell embryogenic totipotency expression. Notably, the SE-ASSOCIATED LIPID TRANSFER PROTEIN (SELTP) gene dose-dependently marked cell types with distinct embryogenic states and exhibited a parabolic curve pattern along the somatic cell embryogenic differentiation trajectory, suggesting that SELTP could serve as a favorable quantitative cellular marker for detecting embryogenic expression at the single-cell level. In addition, RNA velocity and Scissor analysis confirmed the pseudo-temporal model and validated the accuracy of the scRNA-seq data, respectively. This work provides valuable marker-genes resources and defines precise cellular taxonomy and trajectory atlases for somatic cell embryogenic differentiation in plant regeneration.

Intercellular material transport and information transmission in plants are carried out through the plasmodesmata (PD). The amount of callose around the PD controls channel permeability. In plants, β-1,3-glucanase can degrade callose and affect plant growth and development. In this study, the gene producing PD-localized β-1,3-glucanase and regulating the leaf trichomes is identified and named PdBG4. Based on functional analysis through a series of genetic manipulation assays, we found that the high expression of PdBG4 was associated with strong PD permeability and short Arabidopsis thaliana leaf trichomes. Conversely, the low expression of PdBG4 correlated with weak PD permeability and long Arabidopsis thaliana leaf trichomes. This study revealed that the PdBG4 gene negatively modulates leaf trichome growth and development by regulating PD permeability.

Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information.

Green fiber (GF) is a naturally colored fiber. A limited understanding of its color formation mechanism restricts the improvement of colored cotton quality. This experiment used upland cotton green fiber germplasm 1-4560 and genetic inbred line TM-1; the lipid profiles of green fibers at 30 (white stage) and 35 days post-anthesis (DPA) (early greening stage), as well as those of TM-1 at the same stages, were revealed. Among the 109 differential types of lipids (DTLs) unique to GF, the content of phosphatidylserine PS (16:0_18:3) was significantly different at 30 and 35 DPA. It is speculated that this lipid is crucial for the pigment accumulation and color formation process of green fibers. The 197 DTLs unique to TM-1 may be involved in white fiber (WF) development. Among the shared DTLs in GF35 vs. GF30 and WF35 vs. WF30, sulfoquinovosyldiacyl-glycerol SQDG (18:1_18:1) displays a significant difference in the content change between green fibers and white fibers, potentially affecting color formation through changes in content. The enriched metabolic pathways in both comparison groups are relatively conserved. In the most significantly enriched glycerophospholipid metabolic pathway, 1-acyl-sn-glycero-3-phosphocholine (C04230) only appears in white cotton. This indicates differences in the metabolic pathways between white and green fibers, potentially related to different mechanisms of color formation and fiber development. These findings provide a new theoretical basis for studying cotton fiber development and offer important insights into the specific mechanism of green fiber color formation.

TGA transcription factors are key regulators within the plant bZIP superfamily, coordinating stress adaptation as well as plant growth and development. Rapid-cycling Brassica rapa (RCBr) is a valuable genetic resource for investigating gene functions in Brassica rapa; however, systematic investigations of its TGA gene family remain limited. In this study, we performed a genome-wide identification of the TGA gene family and identified 19 BrTGA genes in RCBr. Subsequent bioinformatic analyses revealed that the BrTGA family exhibited conserved protein sequences but divergent gene structures. Quantitative expression profiling across multiple tissues revealed that most BrTGA genes were predominantly expressed in roots, with several members exhibiting distinct tissue-preferential expression patterns. These findings provide valuable insights and genetic resources for further investigating the regulatory functions of TGA transcription factors in B. rapa.