Search Results (9)

Dendrobium officinale is a traditional and valuable medicinal herb, with extensive research conducted on its polysaccharides, alkaloids, and other components, yet studies on anthocyanins remain limited. In this study, we analyzed the expression levels of GST family genes in green and purplish D. officinale and found that DoGSTF11 is highly expressed in the purplish variety. DoGSTF11 is localized to the nucleus and cell membrane but lacks transcriptional activation activity. Overexpression of DoGSTF11 in tomato enhances anthocyanin accumulation, suggesting a role in anthocyanin sequestration or transport. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays further revealed that DoGSTF11 interacts with DoGST31, while DoIDD12 and DoNF-YB3 are potential transcriptional regulators based on promoter-binding assays and expression correlation. In conclusion, our study demonstrates that DoGST11 positively regulates anthocyanin accumulation in D. officinale. These findings provide valuable insights into the metabolic engineering of flavonoids in D. officinale. Full article

The plant-specific IDD transcription factors (TFs) are vital for regulating plant growth and developmental processes. However, the characteristics and biological roles of the IDD gene family in tomato (Solanum lycopersicum) are still largely unexplored. In this study, 17 SlIDD genes were identified in the tomato genome and classified into seven subgroups according to the evolutionary relationships of IDD proteins. Analysis of exon–intron structures and conserved motifs reflected the evolutionary conservation of SlIDDs in tomato. Collinearity analysis revealed that segmental duplication promoted the expansion of the SlIDD family. Ka/Ks analysis indicated that SlIDD gene orthologs experienced predominantly purifying selection throughout evolution. The analysis of cis-acting elements revealed that the promoters of SlIDD genes contain numerous elements associated with light, plant hormones, and abiotic stresses. The RNA-seq data and qRT-PCR experimental results showed that the SlIDD genes exhibited tissue-specific expression. Additionally, Group A members from Arabidopsis thaliana and rice are known to play a role in regulating plant shoot gravitropism. QRT-PCR analysis confirmed that the expression level of SlIDD15 in Group A was high in the hypocotyls and stems. Subcellular localization demonstrated that the SlIDD15 protein was localized in the nucleus. Surprisingly, the loss-of-function of SlIDD15 by CRISPR/Cas9 gene editing technology did not display obvious gravitropic response defects, implying the existence of functional redundant factors within SlIDD15. Taken together, this study offers foundational insights into the tomato IDD gene family and serves as a valuable guide for exploring their molecular mechanisms in greater detail. Full article

The indeterminate domain proteins (IDD proteins) play essential roles in the growth and development of various plant tissues and organs across different developmental stages, but members of this gene family have not yet been characterized in foxtail millet (Setaria italica). To have a comprehensive understanding of the IDD gene family in foxtail millet, we performed a genome-wide characterization and haplotypic variation analysis of the IDD gene family in foxtail millet. In this study, sixteen IDD genes were identified across the reference genome of Yugu1, a foxtail millet cultivar. Phylogenetic analysis revealed that the Setaria italica IDD (SiIDD) proteins were clustered into four groups together with IDD proteins from Arabidopsis thaliana (dicot) and Oryza sativa (monocot). Conserved protein motif and gene structure analyses revealed that the closely clustered SiIDD genes were highly conserved within each subgroup. Furthermore, chromosomal location analysis showed that the SiIDD genes were unevenly distributed on nine chromosomes of foxtail millet and shared collinear relationships with IDD genes of other grass species. Transcriptional analysis revealed that the SiIDD genes differed greatly in their expression patterns, and paralogous genes shared similar expression patterns. In addition, superior haplotypes for two SiIDD genes (SiIDD8 and SiIDD14) were identified to correlate with traits of early heading date, and high thousand seed weight and molecular markers were designed for SiIDD8 and SiIDD14 to distinguish different haplotypes for breeding. Taken together, the results of this study provide useful information for further functional investigation of SiIDD genes, and the superior haplotypes of SiIDD8 and SiIDD14 will be particularly beneficial for improving heading date and yield of foxtail millet in breeding programs. Full article

Castanea mollissima is an important monoecious fruit crop with high economic and ecological value in China. However, its yield is restricted by an imbalanced ratio of male and female flowers for chestnut production. To address this issue, we examined the morphology of bisexual flower organs, measured the levels of endogenous hormones in the flowers, profiled gene expression related to plant hormone biosynthesis and signaling pathways and transcription factors, and investigated the effects of exogenous jasmonic acid (JA) and zeatin (ZT) hormone application on flower development in C. mollissima ‘Tanqiao’. Morphological studies indicated that the development of male and female flowers can be divided into nine and eight stages, respectively. Male flowers contained higher levels of gibberellic acid (GA₃) and abscisic acid (ABA) than female flowers, whereas female flowers had higher levels of JA and ZT. The analysis of the Kyoto encyclopedia of genes and genomes (KEGG) pathways revealed that the major significant enrichment pathways of differentially expressed genes (DEGs) consisted of plant hormone signal transduction and zeatin biosynthesis. Through time-series analyses, we screened 3 genes related to jasmonic acid biosynthesis and signal transduction and 21 genes related to zeatin biosynthesis and transduction. Among these genes, only the gene family LOG, related to zeatin biosynthesis, was highly expressed in female flowers. This result indicated that LOG may be the core gene hormone family involved in regulating female flower development. However, a weighted gene co-expression network analysis (WGCNA) suggested that IDD7 was the core gene involved in regulating female flower development. The results of exogenous hormone application indicated that zeatin could greatly increase the quantity of fertile female flowers, but JA was not significant. These findings demonstrated that zeatin and transcription factors were crucial regulators in the formation of female flowers in C. mollissima. Full article

Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize. Full article

INDETERMINATE DOMAIN (IDD) proteins, a family of transcription factors unique to plants, function in multiple developmental processes. Although the IDD gene family has been identified in many plants, little is known about it in moso bamboo. In this present study, we identified 32 PheIDD family genes in moso bamboo and randomly sequenced the full-length open reading frames (ORFs) of ten PheIDDs. All PheIDDs shared a highly conserved IDD domain that contained two canonical C2H2-ZFs, two C2HC-ZFs, and a nuclear localization signal. Collinearity analysis showed that segmental duplication events played an important role in expansion of the PheIDD gene family. Synteny analysis indicated that 30 PheIDD genes were orthologous to those of rice (Oryza sativa). Thirty PheIDDs were expressed at low levels, and most PheIDDs exhibited characteristic organ-specific expression patterns. Despite their diverse expression patterns in response to exogenous plant hormones, 8 and 22 PheIDDs responded rapidly to IAA and 6-BA treatments, respectively. The expression levels of 23 PheIDDs were closely related to the outgrowth of aboveground branches and 20 PheIDDs were closely related to the awakening of underground dormant buds. In addition, we found that the PheIDD21 gene generated two products by alternative splicing. Both isoforms interacted with PheDELLA and PheSCL3. Furthermore, both isoforms could bind to the cis-elements of three genes (PH02Gene17121, PH02Gene35441, PH02Gene11386). Taken together, our work provides valuable information for studying the molecular breeding mechanism of lateral organ development in moso bamboo. Full article

Intellectual development disorder (IDD) is characterized by a general deficit in intellectual and adaptive functioning. In recent years, there has been a growing interest in studying the genetic structure of IDD. Of particular difficulty are patients with non-specific IDD, for whom it is impossible to establish a clinical diagnosis without complex genetic diagnostics. We examined 198 patients with non-specific IDD from 171 families using whole-exome sequencing and chromosome microarray analysis. Hereditary forms of IDD account for at least 35.7% of non-specific IDD, of which 26.9% are monogenic forms. Variants in the genes associated with the BAF (SWI/SNF) complex were the most frequently identified. We were unable to identify phenotypic features that would allow differential diagnosis of monogenic and microstructural chromosomal rearrangements in non-specific IDD at the stage of clinical examination, but due to its higher efficiency, exome sequencing should be the diagnostic method of the highest priority study after the standard examination of patients with NIDD in Russia. Full article

INDETERMINATE DOMAIN (IDD) family proteins are plant-specific transcription factors. Some Arabidopsis IDD (AtIDD) proteins regulate the expression of SCARECROW (SCR) by interacting with GRAS family transcription factors SHORT-ROOT (SHR) and SCR, which are involved in root tissue formation. Some AtIDD proteins regulate genes involved in the synthesis (GA3ox1) or signaling (SCL3) of gibberellic acid (GA) by interacting with DELLA proteins, a subfamily of the GRAS family. We analyzed the DNA binding properties and protein–protein interactions of select AtIDD proteins. We also investigated the transcriptional activity of the combination of AtIDD and GRAS proteins (AtIDD proteins combined with SHR and SCR or with REPRESSOR of ga1-3 (RGA)) on the promoters of SCR, SCL3, and GA3ox1 by conducting a transient assay using Arabidopsis culture cells. Our results showed that the SCR promoter could be activated by the IDD and RGA complexes and that the SCL3 and GA3ox1 promoters could be activated by the IDD, SHR, and SCR complexes, indicating the possibility that these complexes regulate and consequently coordinate the expression of genes involved in GA synthesis (GA3ox1), GA signaling (SCL3), and root formation (SCR). Full article

The INDETERMINATE DOMAIN (IDD) genes comprise a conserved transcription factor family that regulates a variety of developmental and physiological processes in plants. Many recent studies have focused on the genetic characterization of IDD family members and revealed various biological functions, including modulation of sugar metabolism and floral transition, cold stress response, seed development, plant architecture, regulation of hormone signaling, and ammonium metabolism. In this review, we summarize the functions and working mechanisms of the IDD gene family in the regulatory network of metabolism and developmental processes. Full article