Identification of root system architecture associated genes, regulatory network, and expression analysis under abiotic stress in maize.

Comparative transcriptomic analysis identifies conserved abiotic stress-responsive hub genes in Sorghum bicolor.

BACKGROUND Sorghum bicolor is a climate-resilient cereal crop capable of adapting to diverse environmental stresses. Understanding the molecular mechanisms underlying abiotic stress responses in sorghum is essential for improving crop resilience under changing climatic conditions. Integrative transcriptomic approaches using publicly available datasets provide an opportunity to identify conserved stress-responsive genes and regulatory networks associated with stress adaptation. RESULTS In this study, a comparative transcriptomic analysis was conducted by combining microarray (GSE48205) and RNA-seq (GSE140928) datasets representing different abiotic stress conditions in sorghum. Differential expression analysis identified 1,097 overlapping differentially expressed genes (DEGs) between the datasets. Protein-protein interaction network construction revealed significant gene connectivity, and network topology analysis using MCODE and CytoHubba identified several highly connected genes. Among these, four candidate hub genes-Sobic.010G233800, Sobic.001G453300, Sobic.001G191000, and Sobic.004G231800-showed strong centrality within the network. Functional enrichment analysis indicated that these genes were primarily associated with biosynthetic processes, nitrogen compound metabolism, ribosome-related functions, and organelle-associated pathways. Additional transcription factor enrichment analysis predicted putative associations with stress-responsive regulatory families, suggesting their potential involvement in abiotic stress-responsive cellular processes. CONCLUSIONS This integrative analysis identified conserved candidate hub genes associated with abiotic stress responses in sorghum. The findings provide insights into the molecular networks involved in stress adaptation and highlight potential genetic targets for improving stress tolerance in sorghum. Although the present study is computational, the identified genes provide a foundation for future experimental validation and functional studies aimed at developing climate-resilient sorghum cultivars.

Multi-Omics Integration Predicts Cell-Specific Gene Regulatory Response and Rhizosphere Dynamics in Maize Root Fertilizer Treatment

Improving nitrogen use efficiency in maize (Zea mays) requires understanding how distinct root cell types and regulatory networks process fertilizer inputs. Given the current limited understanding of fertilizer-induced, cell-type-resolved maize roots and regulatory networks, computational biology frameworks are needed to model and predict how nutrient inputs are translated into transcriptional responses. Here, we integrated fertilizer-induced maize root bulk RNA-seq with reference atlases of single-cell RNA-seq and scATAC-seq to construct and predict a cell-specific regulome of the maize root under inorganic and mixed amendments. We demonstrate that inorganic fertilization induced stress associated and management pathways. Regulome analysis identified transcription factors (TF) from the AP2/ERF, NAC, HSF, and WRKY superfamilies that were preferentially active across root tissues. Deconvolution of the regulome onto single-cell atlases predicted core TF activity to the vascular cylinder and pith across both regimes, while mature cortex regulatory programs diverged. Construction of a gene regulatory network revealed that shared TF–target edges maintained the same regulatory orientation across fertilizer regimes. However, a small number of stress related TFs, including WRKY24, DREB1A, and NAC61, underwent a directional change between fertilization treatments. In silico knockout analysis predicted the activation targets for six of the seven regulators in their resident vascular/pith tissues, indicating the network behaves as a coherent, perturbable system. Additionally, soil metagenomic analysis showed that host soil microbial functions overlap with differentially expressed genes (DEGs) in shared functional categories, linking host regulome dynamics to rhizosphere processes. These findings and predictions suggest that the maize root regulome is spatially organized and dynamically reprogrammed by master regulators, predicting high-priority candidate nodes for engineering improved nutrient use efficiency.

Genome-wide analysis of the plant-specific PLATZ gene family in Taraxacum kok-saghyz and its roles in response to drought and salt tolerance.

Abiotic stress severely limits plant growth and productivity. Taraxacum kok-saghyz Rodin (TKS), known for its environmental resilience, represents a valuable resource for identifying stress-tolerant genes to improve stress-adaptive crops. Plant AT-rich protein and zinc-binding protein (PLATZ) transcription factors serve as core regulators of plant growth, developmental processes, and adaptive responses to various stress conditions; however, they remain uncharacterized in TKS. Here, we identified 10 TksPLATZ genes through a whole-genome analysis. Phylogenetically, these genes were grouped into five distinct evolutionary branches. Promoter sequence analysis revealed multiple types of cis-acting regulatory elements that are connected with hormonal signal responses and environmental stress adaptation. Integrated analysis of transcriptome datasets and RT-qPCR validation demonstrated that TksPLATZ genes display tissue-specific expression profiles and show distinct responsive patterns to drought and salt stress treatments. Among them, TksPLATZ1, TksPLATZ2 and TksPLATZ7 were markedly induced under both stressors and were selected for further functional study. We demonstrated that TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively. Phenotypic data from overexpression experiments in plants confirm that heterologous expression of TksPLATZ1, TksPLATZ2, and TksPLATZ7 enhances the tolerance of Arabidopsis to salt and osmotic stress. These findings provide valuable genetic resources for improving plant tolerance to environmental stresses.

Evolution trajectory of auxin response factor across Triticeae species underpin candidate genes for the regulation of salt/alkali stress responsive networks

Genome-wide analysis of amino acid transporter genes reveals their potential roles in drought stress and drought-associated disease responses in peanut (Arachis hypogaea)

Amino acid transporters (AATs) are central to nitrogen allocation, amino acid distribution, and metabolic adjustment in plants, but this gene family has not been systematically characterized in cultivated peanut (Arachis hypogaea). In this study, 30 AAT genes were identified from the peanut genome and analyzed for chromosomal distribution, protein properties, gene structure, phylogenetic relationships, and expression profiles. The identified ArahyAAT genes were unevenly distributed across 18 chromosomes and showed marked variation in exon-intron organization, which indicates structural diversification within the family. Transcriptome analysis revealed different expression patterns across vegetative and reproductive tissues, with several genes showing preferential expression in roots, nodules, and reproductive organs. To assess their stress responsiveness, five root low-expression genes were selected for RT-qPCR analysis under drought stress and combined drought stress plus charcoal rot infection. ArahyAAT04, ArahyAAT09, and ArahyAAT21 were induced under drought stress, while ArahyAAT07 showed strong induction under the combined treatment. ArahyAAT23 showed limited transcriptional change across the tested conditions. These results suggest that specific ArahyAAT genes may contribute to stress-associated amino acid transport and metabolic adjustment in peanut roots. This study provides a genome-wide characterization and expression analysis of the peanut AAT gene family and identifies candidate genes for future functional studies on...

Integrated Transcriptomic and Phenotypic Analyses Reveal Tissue-Specific Nitrogen Responses and Candidate Genes for Low-Nitrogen Tolerance in Sorghum

Sorghum (Sorghum bicolor (L.) Moench) is an important crop with remarkable tolerance to adverse environments, including nitrogen deficiency. To investigate the mechanisms underlying sorghum tolerance to low-nitrogen (LN) stress, we integrated phenotypic evaluation, transcriptome profiling, weighted gene co-expression network analysis (WGCNA), and haplotype analysis. Two accessions, the LN-tolerant ‘Liaonian B-1’ and the LN-sensitive ‘Yikeerli’, were examined under hydroponic and field conditions. Under LN conditions, Liaonian B-1 showed increases of 32% in root length, 4.3-fold in root fresh weight, and 91% in root dry weight, whereas the LN-sensitive accession showed severe reductions in shoot biomass and a decrease in root fresh weight, with root dry weight remaining relatively stable. Transcriptomic analysis revealed more shared differentially expressed genes and stronger enrichment of N metabolism pathways in shoots, whereas roots showed enrichment of ATP-binding cassette (ABC) transporter and fatty acid elongation pathways. WGCNA identified 500 hub genes in roots and shoots. Five genes in the glutamine synthetase/glutamate synthase (GS-GOGAT) pathway were significantly associated with nitrogen-related traits. SORBI_3001G116400, which encodes glutamate synthase, showed the strongest haplotype effect in 232 sorghum accessions. The A allele (Hap1) was significantly associated with increased plant height, SPAD value, grain number, nitrogen accumulation, and biomass under LN stress, suggesting that SORBI_3001G116400 as a candidate gene requiring functional validation and testing in additional genetic backgrounds.