Genome-Wide Characterization of the WIP Transcription Factor Gene Family in Soybean and Physiological Responses to Salt Stress

Genome-Wide Identification of the GmATG Gene Family and Its Response to Multiple Biotic and Abiotic Stresses in Soybean (Glycine max)

Background: Autophagy plays a central role in maintaining cellular homeostasis, regulating growth and development, and responding to multiple stresses. Autophagy-related genes (ATGs) play critical roles in autophagy, yet their functional diversity in soybean (Glycine max) remains underexplored. Methods: Genome-wide identification of GmATG genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, three-dimensional structural, and promoter cis-acting elements. Tissue-specific expression and multiple stresses response were examined using transcriptome data and profiled by RT-qPCR. Results: A total of 60 GmATG genes belonging to 20 subfamilies were identified in soybean. Gene family expansion was predominantly driven by fragment duplication (33 gene pairs), with the ATG8 family expanding to 12 members, and pan-genomic analysis uncovered prominent copy number variation (6–9 copies) in the ATG18 family. GmATG genes showed distinct expression patterns in response to multiple abiotic and biotic stresses. Specifically, GmATG18f was significantly induced by phosphorus deficiency in the low-phosphorus-tolerant soybean variety Nannong 94-156. GmATG8g, GmATG9d and GmATG13d showed a typical expression trend of initial increase followed by decrease, with expression levels peaking at 6–12 h after salt stress treatment. GmATG8g and GmATG9d were rapidly upregulated at the early drought stress stage, while GmATG13a maintained sustained upregulation. In response to Phomopsis stem rot, GmATG7a/8h/8i/11/13d/18e/18f displayed differential expression in resistant and susceptible soybean materials. Conclusions: This study systematically characterizes the composition, expansion and stress response patterns of the GmATG gene family, revealing functional differentiation among family members. The identified key candidate genes, including abiotic-stress-regulated GmATG8g/9d/13d/18f and biotic-stress-regulated GmATG7a/8h/8i/11/13d/18e/18f, provide valuable genetic resources for the molecular breeding of stress-tolerant soybean.

Genome-Wide Dissection of the TCP Gene Family in Peach and Expression Analysis Under Drought Stress

The TCP (Teosinte branched 1/Cycloidea/Proliferating) gene family comprises plant-specific transcription factors essential for regulating growth, development, and environmental adaptation. Utilizing the high-quality ‘Rui Youpan 1’ (‘RYP1’) reference genome, we conducted a comprehensive genome-wide identification and characterization of the TCP family in peach (Prunus persica). We identified 20 PpTCP genes and systematically evaluated their physicochemical properties, chromosomal distribution, phylogeny, gene architecture, and promoter cis-regulatory elements. Notably, the enrichment of abscisic acid-responsive elements (ABREs) in their promoters suggests a significant role in abiotic stress signaling. Integrated RNA-seq and RT-qPCR analyses identified six putative candidates (PpTCP3, 5, 6, 11, 14, and 15) with pronounced differential expression under drought conditions. Subcellular localization confirmed that all tested PpTCPs function within the nucleus. Moreover, the results of STRING-based computer simulations predicting protein–protein interactions indicate that PpTCP3 and PpTCP5 interact with key hormone pathways and stress-related transcription factors (TFs), including auxin signaling and strigolactone signaling.

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.

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

Genome-Wide Characterization of the PLATZ Gene Family in Medicago truncatula and Their Expression Profiles in Response to Abiotic Stress

Simple Summary PLATZ transcription factors are a plant-specific family of zinc finger proteins that play important roles in regulating plant growth, development, and abiotic stress responses. In the legume model plant Medicago truncatula, the PLATZ gene family has not been systematically characterized. In this study, a total of 16 MtPLATZ genes were identified in the M. truncatula genome and classified into four distinct subgroups based on phylogenetic analysis. This family includes five segmental duplication pairs and one tandem duplication pair, all of which have Ka/Ks ratios less than 1, indicating that MtPLATZ genes have experienced strong purifying selection during evolution. Cis-acting element analysis revealed that the promoter regions of MtPLATZ genes contain multiple stress-responsive and hormone-responsive elements, suggesting their potential extensive involvement in environmental adaptation. Preliminary expression profiling under various abiotic stresses, including PEG-induced osmotic stress, acute NaCl shock, acute heat shock, and acute cold shock, demonstrated that MtPLATZ genes exhibit treatment-specific and time-dependent expression patterns, indicating that they may have functional divergence. This study provides a systematic analysis of the MtPLATZ gene family in M. truncatula, offering a valuable reference for functional studies and genetic improvement of stress tolerance in legumes.

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