Rice is highly sensitive to chilling stress during the seedling stage. However, the adaptable photo-thermo sensitive genic male sterile (PTGMS) rice line, Yu17S, exhibits tolerance to low temperatures. Currently, the molecular characteristics of Yu17S are unclear. To evaluate the molecular mechanisms behind cold responses in rice seedlings, a comparative transcriptome analysis was performed in Yu17S during seedling development under normal temperature and low temperature conditions. In total, 9317 differentially expressed genes were detected. Gene ontology and pathway analyses revealed that these genes were involved mostly in photosynthesis, carotenoid biosynthesis, carbohydrate metabolism and plant hormone signal transduction. An integrated analysis of specific pathways combined with physiological data indicated that rice seedlings improved the performance of photosystem II when exposed to cold conditions. Genes involved in starch degradation and sucrose metabolism were activated in rice plants exposed to cold stress treatments, which was accompanied by the accumulation of soluble sugar, trehalose, raffinose and galactinol. Furthermore, chilling stress induced the expression of phytoene desaturase, 15-cis-ζ-carotene isomerase, ζ-carotene desaturase, carotenoid isomerase and β-carotene hydroxylase; this was coupled with the activation of carotenoid synthase activity and increases in abscisic acid (ABA) levels in rice seedlings. Our results suggest that Yu17S exhibited better tolerance to cold stress with the activation of carotenoid synthase activity and increasing of ABA levels, and as well as the expression of photosynthesis-related genes under cold condition in rice seedlings.

In plants, hexokinase (HXK) is a kind of bifunctional enzyme involved in sugar metabolism and sugar signal transduction that plays important roles in plant growth and development and stress response. Some HXK genes without a phosphorylation function have been found in Arabidopsis, tobacco, etc., but these genes have not been identified in tomato. Therefore, further genome-wide systematic identification and characterization is necessary for tomato HXK genes. In this study, six HXK genes were identified from the tomato genome distributed across six different chromosomes, named SlHXK1-6. Gene structure analysis showed that the SlHXK genes contain the same number of introns and exons. Gene duplication and collinearity analysis revealed two pairs of tandem repeats among SlHXKs, and a higher collinearity between tomatoes and potatoes were found. Response elements associated with phytohormones, abiotic stresses, and growth and development were identified in the promoter sequences of SlHXKs. Quantitative real-time PCR (qRT-PCR) results further indicated the potential role of SlHXKs in tomato development and stress responses. The expression levels of most SlHXKs were significantly induced by abiotic stress, hormone, and sugar solution treatments. In particular, the expression of SlHXK1 was significantly induced by various treatments. Functional complementation experiments were performed using HXK-deficient yeast strain YSH7.4-3C (hxk1, hxk2, and glk1), and the results showed that SlHXK5 and SlHXK6 were unable to phosphorylate glucose and fructose in yeast. In conclusion, these results provide valuable foundations for further exploring the sugar metabolism and sugar signal transduction mechanisms of HXK and the functions of SlHXK genes in various abiotic stresses, and some SlHXKs may be key genes for enhancing plants’ tolerance to abiotic stresses.

Fructose-1,6-bphosphate aldolases (FBAs) are key enzymes in glycolysis, gluconeogenesis, and the Calvin cycle, which are fundamental metabolic pathways in plants and they are crucial plant growth and development. While isfor FBA genes have been characterized in several plants, a thorough and comprehensive analysis of rice (Oryza sativa), has not yet been conducted. In this study, the genome-wide identification, characterization and expression analysis of FBAs were performed in Oryza sativa, and a total number of eight OsFBA genes were identified. Based on the analysis of functional domains, phylogenetic relationships, and gene structures, all OsFBAs were classified as Class I. Notably, OsFBA2, OsFBA3, OsFBA5, and OsFBA6 belonged to the same subclass and were predicted to be localized in the cytoplasm, suggesting that they might have similar functions. Furthermore, gene duplication analysis indicated that segmental duplication events promoted the expansion of the OsFBA gene family. Additionally, promoter predictions revealed the existence of various cis-acting elements related to abiotic stress and phytohormones in the 2000 bp upstream region of OsFBAs, which might influence gene expression under different environmental conditions. The expression profiles of selected OsFBA genes were differentially and markedly induced by abscisic acid (ABA) and cold stress treatments, indicating that these genes play important roles in abiotic stress. In addition, a potential interaction between OsFBA1 and OsGSK2, a protein related to seed size, was identified using the yeast two-hybrid system, suggesting that OsFBA1 might be involved in regulating seed size, an important agronomic trait. These results provide valuable foundations for further exploring the stress resistance mechanism of rice and functional characterizations of OsFBAs, and numerous OsFBAs may function as the key regulators to enhance plant tolerance to abiotic stress and in plant development. The online version contains supplementary material available at 10.1186/s12870-026-08464-3.