Identification of specific transcripts for plant heat stress tolerance through genome-wide analysis of SIZ1-dependent alternative polyadenylation

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.

Investigation of the maize (Zea mays L.) JAZ pan-gene family and expression pattern under drought stress conditions

The hormone jasmonic acid (JA) regulates plant growth and development, acts as a stress-tolerant signaling molecule, and ensures tolerance to drought stressors. The jasmonate zim-domain (JAZ) functions as a transcriptional repressor by directly interacting with transcription factors, regulating the activity of JA pathway transcription factors when JA signaling is absent. We systematically identified JAZ gene family members using a maize pangenome comprising 26 high-quality genomes. We analyzed evolutionary pressure and structural variation (SV), and reanalyzed public RNA-seq data under drought stress. Sequential expression patterns were further validated using qRT-PCR. In this study, 112 JAZ genes were identified by pan-genomic analysis of 26 high-quality maize genomes, including 12 core genes (present in all 26 lines), 33 non-core genes (in 2–22 lines), 5 near-core genes (in 23–25 lines), and 62 endemic genes (in 1 line). Analysis of Ka/Ks values showed that some varieties were under positive selection for the JAZ19 gene. Among these, 15 ZmJAZ genes had Ka/Ks values < 1, indicating they were subject to purifying selection. There were significant differences in the expression of ZmJAZ19 between genes affected by structural variation (SV) and those not affected by SV. SV altered the conserved structural domains in some varieties, resulting in a significant number of atypical genes. RNA-seq analysis of drought treatment data revealed seven differentially expressed ZmJAZ genes, four of which were core genes. However, atypical genes were identified in numerous response genes across multiple genomes. This study advances our understanding of how ZmJAZ genes contribute to drought adaptation in maize, offering a conceptual framework that links molecular responses to climate-resilient traits essential for sustainable crop production under water-limited conditions in the face of climate change.

Genome-Wide Characterization and Expression Analysis of Heat Shock Transcription Factors in Two Cultivars of Rice (Oryza sativa L.) Under Heat Stress

Rising temperatures pose daunting challenges for sustainable yield and nutritional quality of rice (Oryza sativa L.), thus putting food security at risk. Limited information exists regarding cis-acting regulatory elements and candidate genes controlling the heat shock transcription factor (HSF) gene family in rice. Therefore, the present study identified HSF genes in the japonica (Nipponbare) and indica (9311) rice cultivars through in silico repositories. Three candidate genes (HSFC2B, HSFB1, and HSFC2A) were selected for qRT-PCR analysis to validate their expression patterns under heat stress (HS). The present findings reported a total of 25 OsHSF genes through in silico genome-wide identification. Comparative analysis illustrated that the OsHSF genes had structural similarities but different expression and transcriptional regulation between the two cultivars. HSF genes were unevenly distributed across the 12 rice chromosomes, suggesting that tandem duplication and gene repetition may have contributed to the evolution of novel genes. Phylogenetic analysis revealed that all OsHSF gene family members have shared common ancestry, but several genes lack introns, potentially facilitating swift stress responses as indicated by gene structure analysis. Expression analysis revealed that candidate genes were active, with HSFC2A exhibiting the highest level of expression in the japonica cultivar compared to indica under heat-stressed conditions. HSFC2B gene showed a higher statistical difference in its response between cultivars, time points, and cultivar vs. time points interactions compared to HSFC2A and HSFB1. These findings offer valuable insights into the function of OsHSF genes that will contribute to the development of climate-resilient rice cultivars.

GENOME-WIDE ANALYSIS AND IDENTIFICATION OF HSF (HEAT SHOCK TRANSCRIPTION FACTOR) GENES IN COFFEE (COFFEE ARABICA L.) UNDER ABIOTIC STRESS

Coffee is a livelihood source for millions of farmers and plays a significant role in the economy of many coffee-producing countries. Abiotic stresses, such as drought and high temperature, however, negatively impact coffee growth, productivity, and bean quality. Heat shock factors (HSFs) play a crucial role in the plant response to heat and other abiotic stresses. However, there is still not a lot of detailed knowledge about the HSF gene family in Coffea arabica. In this study, a genome-wide search was performed to find and characterize the genes of HSF from C.arabica. A total of 59 putative CaHSF genes have been identified and characterized according to their physicochemical properties, chromosomal distribution, gene structure, conserved motifs, phylogenetic relationship, duplication event, synteny, cis-regulatory elements, and protein–protein interactions. The genes identified for CaHSF were assigned to different scaffolds of the genome, and they had different sizes, molecular mass, isoelectric point, GRAVY value, and aliphatic index of their protein. Through the relationships induced by the phylogenetic and conserved-domain analyses, and by their conservation, it was possible to get insight into the evolution of the proteins of the CaHSF family. Abiotic stress response, hormone signaling, and light regulation were noted to have several cis-regulatory elements associated with them in the promoter analysis and hence the possible role of the CaHSF genes in stress adaptation. Duplication and synteny analyses also showed that gene duplication played a role in the diversification and expansion of the CaHSF gene family in C. arabica. Overall, this study is a thorough genomic analysis of the CaHSF gene family, which can serve as a basis for future functional studies for understanding the molecular mechanism of abiotic stress tolerance in coffee.

Comprehensive genome-wide analysis of DUF668 gene family in potato reveals roles in growth and stress responses.

Genomic characterization, expression and functional analysis of the plant homeodomain (PHD) family in tomato (Solanum lycopersicum L.) under abiotic stresses