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

It is demonstrated that inorganic fertilization induced stress associated and management pathways and 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.

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

It is demonstrated that heterologous expression of TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively, which enhances the tolerance of Arabidopsis to salt and osmotic stress.

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)

A genome-wide characterization and expression analysis of the peanut AAT gene family and identifies candidate genes for future functional studies on stress-associated amino acid transport and metabolic adjustment in peanut roots are provided.

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

The A allele (Hap1) was significantly associated with increased plant height, SPAD value, grain number, nitrogen accumulation, nitrogen accumulation, and biomass under LN stress, suggesting that SORBI_3001G116400 as a candidate gene requiring functional validation and testing in additional genetic backgrounds.