With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.

Maize, a vital cereal in global agriculture, faces significant yield challenges due to drought exacerbated by climate change. This study explores the genetic and molecular bases of drought resilience in maize, focusing on the EPF/EPFL gene family known for its role in stomatal regulation. Through a genome-wide analysis across seven grass species, we identified and characterized 16 ZmEPF/EPFL genes in maize. Focusing on their gene structure, expression patterns, and evolutionary relationships. The study integrated genome-wide searches, phylogenetic analysis, gene expression profiling under drought and other abiotic stresses, and qRT-PCR validation to elucidate the functional roles of these genes in drought response. Our results demonstrate that specific ZmEPF/EPFL genes are differentially expressed under varying drought conditions, suggesting their involvement in the plant’s adaptive response to water scarcity. Furthermore, interaction analyses reveal that these genes are linked to key processes such as stomatal development and oxidative stress management. This study provides a comprehensive overview of the ZmEPF/EPFL gene family’s contribution to stomatal development and drought tolerance, offering insights that could guide future breeding strategies for drought-resistant maize varieties.

The TALE gene family plays a crucial role in regulating growth, development, and abiotic stress responses in plants. However, limited studies have been conducted on the functions of the ZmTALE gene family in maize under drought stress. This study identified 40 members of the ZmTALE family within the maize genome through Blast comparisons, distributed unevenly across the first nine chromosomes. Intraspecific collinearity analysis revealed 13 linked pairs. By constructing a phylogenetic tree with Arabidopsis AtTALE members as references, maize members were divided into two subfamilies, KNOX and BEL1-Like, with KNOX further divided into three branches (KNOX Class I, KNOX Class II, and KNOX Class III). The gene structure and motifs of ZmTALE genes within the same subfamily or branch showed similarities, as did their encoded proteins, which possess similar motifs and conserved domains. Analysis of the physicochemical properties of the ZmTALE proteins revealed that the proteins encoded by this family are stable. Expression analysis of ZmTALE genes in maize demonstrated their varied roles in development and drought stress regulation, confirmed through qRT-PCR. The identification, characterization, and expression analysis of ZmTALE genes provide a reference for future gene function research and aid in the genetic enhancement of maize to withstand drought stress.

Cold stress severely impacts crop production, making it crucial to dissect the metabolic and transcriptional regulatory mechanisms of cold-resistant plants for breeding cold-tolerant varieties. This study systematically explored the response mechanism of Zizania latifolia to cold stress by integrating widely targeted metabolomics and genome-wide analysis for the first time. Metabolomics analysis revealed that 690 out of 810 metabolites showed significant differences after cold treatment at 4°C, with significant enrichment of flavonoids, amino acid derivatives, and alkaloids, involving key pathways such as antioxidant defense, osmotic adjustment, and signal transduction. This indicates that Z. latifolia copes with cold stress through the coordination of secondary and primary metabolism. A total of 115 bZIP transcription factors (ZlbZIPs) were identified from the Z. latifolia genome, with 18 genes located in known cold-resistant quantitative trait locus (QTL) intervals. Four cold-tolerant candidate genes were screened through collinearity analysis with the rice genome. Expression analysis showed that ZlbZIP005, ZlbZIP075, and ZlbZIP084 were significantly upregulated (29.17-4.10 fold) at 24 hours of cold treatment, and their promoter regions with high-density G-box elements implied strong cold response potential. Phylogenetic and evolutionary analyses showed that the bZIP family of Z. latifolia is highly homologous to that of rice but exhibits subfamily-specific expansion (such as subfamily Ⅶ) and conserved motif variations related to functional differentiation. This study first elucidated the metabolic reprogramming and bZIP transcription factor regulatory network of Z. latifolia under cold stress. The screened key cold-tolerant genes provide important genetic resources for cold-resistant breeding of gramineous crops and lay a foundation for analyzing the molecular mechanism of plant cold resistance and genetic improvement.

Low-temperature stress is a critical abiotic constraint that severely impairs rice yield and quality, posing a substantial threat to global food security-especially as rice, a staple food for more than half of the world's population, is inherently susceptible to cold stress. This review systematically summarizes the typical phenotypic and physiological impairments induced by cold stress across key rice growth stages, and elaborates on the multi-layered molecular regulatory networks underpinning rice cold tolerance, which integrate the entire process of cold signal perception, intracellular transduction and nuclear transcriptional regulation. We also synthesize the major practical strategies for enhancing rice cold tolerance, including the optimization of agricultural cultivation management measures and the application of modern molecular breeding technologies. Furthermore, we discuss the core challenges in the genetic improvement of rice cold tolerance such as genotype-environment interaction and efficient multi-gene pyramiding, and outline the promising future research trends involving mechanism integration and intelligent breeding. This review provides a concise and comprehensive theoretical framework for deciphering the physiological and molecular mechanisms of rice cold stress response, and offers important insights to accelerate the development of cold-tolerant rice varieties, thereby laying a solid foundation for safeguarding global food security under the context of climate change.