1 Introduction

Flowering time is an important factor for rice yield and adaptability. It will directly affect the yield and also influence the growth performance of the plants in different environments. The appropriate flowering time can make the reproductive development of rice match the local climatic conditions. If the flowering time is not appropriate, it may lead to a decrease in yield and also reduce its adaptability to the local agricultural environment (Wang et al., 2018). As climate change becomes increasingly evident, understanding and regulating the flowering time is of great significance for ensuring rice yields and food security.

The molecular regulation of rice flowering time involves many genes, transcription factors and epigenetic mechanisms. Key genes such as OsMADS56, Hd3a and RFT1 integrate environmental signals to control the transition of plants from vegetative growth to reproductive growth (Shin et al., 2022). Recent studies have found that long non-coding Rnas (lncrnas) also play an important role in these regulatory pathways. lncRNA is over 200 nucleotides in length and does not encode proteins. They can act as molecular scaffolds, lures or guides to influence gene expression through chromatin modification, transcriptional interference and interaction with micrornas (Gao et al., 2020; Zhou et al., 2021). For instance, the intron lncRNA RIFLA inhibits OsMADS56, thereby promoting early flowering; Some lncrnas bind to histone modification proteins or act as endogenous target mimics to regulate gene expression during development (Wang et al., 2021). These findings indicate that lncRNA is becoming increasingly important in the regulation of plant development, including flowering timing.

This study will summarize the research progress of lncRNA in regulating the flowering time of rice, explain the molecular interaction mechanisms between them and known flowering pathways, explore their potential applications in rice breeding, and also analyze future research directions and challenges. This study combines the achievements of molecular genetics and functional genomics, emphasizing the significance of lncRNA as a potential target for crop improvement and sustainable agriculture, with the hope of providing references for increasing yields and enhancing the climate adaptability of rice.

2 Overview of Molecular Mechanisms Regulating Rice Flowering Time

2.1 Photoperiod pathway and its key genes

The photoperiodic pathway is the main way to regulate the flowering time of rice, enabling it to flower in the appropriate season. Rice is a facultative short-day plant. Under short-day (SD) conditions, it flowers earlier, while under long-day (LD) conditions, it flowers later. There are several important genes in this pathway, such as the heading stage 1 gene (Hd1) and the early heading stage 1 gene (Ehd1). Hd1 is a homologous gene of the CONSTANS gene in Arabidopsis thaliana and has dual functions: under short-day conditions, it can activate the heading period 3a gene (Hd3a) to promote flowering; Under long-day conditions, it inhibits flowering, and this effect is achieved through interaction with the heading 8 gene (DTH8). The DTH8-Hd1 complex increases the H3K27me3 modification on the Hd3a gene, thereby reducing its expression and delaying flowering under long-day conditions (Figure 1) (Lee and An, 2015; Du et al., 2017; Sohail, 2023; Yin et al., 2023). Ehd1 is a positive regulatory gene specific to rice. It can induce the expression of Hd3a and rice flowering locus T1 (RFT1), and promote flowering independently of Hd1, especially under long-day conditions (Hori et al., 2016; Nunez and Yamada, 2017). Other regulatory factors, such as Ghd7 and OsCOL16, can further regulate the photopedic network by inhibiting Ehd1 and Hd3a to ensure precise control of flowering (Wu et al., 2017; Sun et al., 2022).

Figure 1 93-11 Contains an Hd1 allele with a mutation in the CCT domain-encoding region (Adopted from Du et al., 2017)

2.2 Vernalization pathway and temperature signal sensing mechanisms

Vernalization (long-term low-temperature induction of flowering) is common in temperate grains and Arabidopsis thaliana, but rice, which grows in tropical and subtropical regions, is not sensitive to vernalization. However, temperature still affects the flowering time of rice. Temperature signals act in conjunction with photoperiodic pathways to regulate the expression of key genes such as Ehd1 and Hd3a. Temperature changes can alter the activity of these genes, thereby affecting flowering time and environmental adaptability (Shrestha et al., 2014; Shim and Jang, 2020; Wei et al., 2020). The combination of temperature and photoperiodic signals enables rice to flexibly adjust its flowering according to the season and climate.

2.3 Interaction between hormone signaling pathways and flowering regulation

Hormone signals such as jasmonic acid (JA), gibberellin (GA), and abscisic acid (ABA) also interact with the flowering regulatory network, affecting the flowering time. For instance, the OsMYC2-JA feedback loop can regulate the remodeling of the flower tissue cell wall, thereby affecting the circadian flowering rhythm, which is important for propagation and hybrid seed production (Zhu et al., 2024). Hormones can affect the expression or activity of key flowering genes, combining developmental signals with environmental signals to ensure that flowering occurs at the most appropriate time and under the most suitable conditions, thereby helping to increase yield and adaptability (Cho et al., 2017; Vicentini et al., 2023; Li, 2024).

3 Characteristics and Functional Classification of lncRNAs

3.1 Definition, structure, and main characteristics of lncRNAs

Long non-coding RNA (lncRNA) is a type of RNA molecule that exceeds 200 nucleotides in length and has no obvious protein-coding function. They can be transcribed by RNA polymerase II or III, and some can be capped, spliced and polyadenylate added, but not all lncrnas have these characteristics (Quinn and Chang, 2015). The sequences and structures of lncrnas vary greatly and are usually expressed only at specific tissue or developmental stages. They are different from mRNA and function more through their own secondary or tertiary structures. They can bind to DNA, RNA and proteins and regulate gene expression at multiple levels (Wang et al., 2017). This regulation includes chromatin modification, transcription and post-transcriptional regulation, as well as influencing processes such as cell differentiation and development (Dahariya et al., 2019).

3.2 Classification by mode of action

lncRNA can be classified into several types based on its genomic location, mechanism of action and function:

Cis-acting lncrnas: Regulating genes near them by recruiting chromatin modification factors or altering the transcriptional activity of adjacent genes (Ma et al., 2013; Kopp and Mendell, 2018).

Transacting lncrnas: They act on genes located far from themselves, including those on other chromosomes, often serving as molecular scaffolds or guide protein complexes.

Competitive endogenous RNA (ceRNA) : Binding to microRNA like a sponge, preventing them from inhibiting target mRNA (Benchi et al., 2023; Chodurska and Kunej, 2025).

Other functional types: Some act as "baits", isolating proteins or RNA; Some act as "scaffolds", bringing together multiple proteins. Some act as "guides", bringing regulatory complexes to specific gene locations (Dahariya et al., 2019).

According to genomic distribution, lncrnas can also be classified into intergenic type, antisense type, intron type, overlapping type and divergent type, etc., which reflect their different origins and regulatory capabilities (St Laurent et al., 2015).

3.3 Technical approaches and advances in studying plant lncRNA functions

The development of high-throughput RNA sequencing and bioinformatics enables scientists to identify and annotate tens of thousands of lncrnas in the genomes of animals and plants (Choi et al., 2019; Klapproth et al., 2021). Experimental methods for studying their functions include: conducting loss-of-function or loss-of-function experiments, analyzing their locations within cells, and mapping their interactions with other molecules (Delas and Hannon, 2017; Wu and Du, 2017). Nowadays, computational models and databases can also predict the functions and similarities of lncrnas on a large scale, accelerating the discovery of novel regulatory lncrnas (Chen et al., 2018). In addition, ribosome analysis and mass spectrometry techniques have revealed that some lncrnas can also encode short peptides, which enriches their functions (Choi et al., 2019; Tian et al., 2024; Zhang, 2024). However, distinguishing functional lncrnas from transcriptional noise and clarifying their mechanisms of action remains a challenge.

4 Mechanisms of lncRNAs in Regulating Rice Flowering Time

4.1 Regulation of flowering time through controlling transcription factor gene expression

lncRNA can directly affect the expression of key transcription factors, thereby regulating the flowering time of rice. For instance, the intron lncRNA RICE FLOWERING ASSOCIATED (RIFLA) inhibits the flowering suppressor gene OsMADS56. Overexpression of RIFLA can lead to a decrease in OsMADS56 levels and an increase in the expression of flower-inducing factors Hd3a and RFT1, resulting in earlier flowering of rice. This indicates that lncRNA can act as an upstream regulatory factor of key transcription factors during flowering transition (Gao et al., 2020; Shin et al., 2022).

4.2 Interaction with mRNAs and miRNAs to form regulatory networks

lncRNA can also participate in regulatory networks by interacting with mRNA and miRNA. Some lncrnas act as endogenous targeting mimics (ETMs), binding mirnas to prevent them from inhibiting target mrnas. For instance, in rice, some lncrnas act as ETMs of osa-miR156 and osa-miR396, regulating the expression of SPL and GRF genes, which are crucial in terms of developmental timing and fertility. In addition, there are some lncrnas that may be precursors of mirnas, so they can also participate in post-transcriptional regulation (Wang et al., 2021; Li et al., 2024).

4.3 Participation in chromatin modification and epigenetic regulation

lncRNA can also affect the flowering time through epigenetic mechanisms. For instance, RIFLA can bind to the histone methyltransferase OsiEZ1 (a homolog of Arabidopsis H3K27-specific methyltransferase) to form a complex. This will cause epigenetic suppression of OsMADS56, indicating that lncrnas can direct chromatin modification proteins to specific gene loci. Similarly, lncRNA LAIR binds to histone modification proteins OsMOF and OsWDR5, promoting the increase of two active chromatin markers, H3K4me3 and H4K16ac, in the LRK1 gene region, which is related to the improvement of gene expression and yield (Wang et al., 2018; Gao et al., 2020).

5 Case Studies of Representative lncRNAs

5.1 Key lncRNAs involved in photoperiod pathway regulation

There is a flower-related gene called RIFLA in rice, which is an lncRNA transcribed from the intron of the OsMADS56 gene. It can inhibit the flowering inhibitory factor OsMADS56, thereby increasing the expression of flowering inducible factors Hd3a and RFT1. Overexpression of RIFLA can cause rice to flower earlier, which indicates its significance in the photoperiodic pathway. Mechanically, RIFLA binds to histone methyltransferase OsiEZ1 and participates in the epigenetic regulation of OsMADS56, adjusting the flowering time according to the length of daylight (Figure 2 ) (Shin et al., 2022).

Figure 2 Heading date and phenotypes of RIFLA-overexpressing plants (Adopted from Shin et al., 2022) Image caption: (A) Expression of RIFLA in RIFLA-overexpressing plants. Total RNA was isolated from the second leaf blade (from the top) of WT and RIFLA-overexpressing plants grown under NLD photoperiod. Transcript levels of RIFLA were examined by real-time quantitative PCR (RT-qPCR) using gene-specific primers. (B) Heading date of WT and RIFLA-overexpressing plants under NLD conditions. Error bars indicate standard deviation. Asterisks ( *** ) indicate statistically significant differences in heading date (P < 0.001; Student’s t-test) between WT and RIFLA-overexpressing plants. DAG, days after germination. (C) Phenotypes of WT and RIFLA-overexpressing plants after heading under NLD conditions. Red arrows indicate panicles (Adopted from Shin et al., 2022)

5.2 lncRNAs affecting hormone signaling pathways

Whole-genome analysis revealed that some lncrnas can serve as endogenous targeted mimics (ETMs) of mirnas such as osa-miR156 and osa-miR396. These mirnas regulate the SPL and GRF genes, which are related to development time, hormone regulation processes, and may also affect flowering time. The dual-luciferase reporter gene assay demonstrated that some lncrnas could regulate hormone-related pathways by binding to mirnas, thereby affecting gene expression related to reproductive development (Wang et al., 2021).

5.3 lncRNAs associated with environmental adaptation in flowering time regulation

lncRNA also plays a role in the environmental adaptation of plants, especially under abiotic stress. For instance, in the research of deep rice, scientists have discovered that some lncrnas act as ETMs of stress-responsive mirnas, forming regulatory modules that control gene expression during stem elongation in flood environments. These lncRNA-miRNA-mRNA networks are related to the ability of plants to adjust flowering and growth in difficult environments, and also illustrate the role of lncrnas in combining environmental signals with developmental timing (Panda et al., 2022).

6 Application Potential of lncRNA Research in Rice Molecular Breeding

6.1 Novel strategies for flowering time regulation based on lncRNAs

Recent studies have shown that lncRNA can serve as a tool for precisely regulating the flowering time of rice and increasing yield. For instance, overexpression of lncRNA LAIR can not only increase rice yield, but also enhance the activity of nearby LRK gene clusters through epigenetic modifications. At the LRK1 gene locus, the levels of H3K4me3 and H4K16ac have both significantly increased. This indicates that regulating lncRNA can directly affect important agronomic traits, providing a new idea for optimizing flowering time and yield in molecular breeding (Wang et al., 2018; 2024).

6.2 Prospects for combining lncRNAs with marker-assisted breeding

lncRNA has multiple functions and precise regulation, and thus is a potential candidate for marker-assisted selection (MAS). The development of high-throughput sequencing and bioinformatics enables us to identify lncRNA variants and isomers related to yield, stress resistance and growth rhythm. For instance, alternative splicing of LAIR can produce various isomers, which can fine-tune the expression and yield traits of LRK1 and are relatively sensitive to abiotic stress. If combined with traditional genetic markers, such lncRNA markers can improve the accuracy and efficiency of breeding for complex traits, including flowering time (Gao et al., 2020).

6.3 Utilization of lncRNA regulation under changing environmental conditions

lncRNA can also help rice cope with environmental stresses such as drought and pests by regulating hormone signals, stress response gene expression and ceRNA networks. For instance, some lncrnas act as competitive endogenous Rnas (cernas), regulating drought resistance and pest resistance, which provides new resources for breeding stress-resistant varieties (Yang et al., 2022; Wu et al., 2023). Lncrnas like LAIR undergo alternative splicing under adverse conditions, thereby dynamically regulating gene expression. This characteristic contributes to phenotypic plasticity and environmental adaptability in breeding projects (Singh et al., 2017; Wang et al., 2024).

7 Conclusions and Perspectives

In the study of the regulation of rice flowering time, scientists have made many new discoveries about the role of lncRNA. Key lncrnas like RIFLA and LAIR have been demonstrated to influence flowering by interacting with transcription factors, chromatin modification factors, and other regulatory Rnas. These changes will be directly related to agronomic traits such as yield and stress resistance. Whole-genome studies have also identified tens of thousands of lncrnas, which change dynamically at different developmental stages and under different environmental conditions. However, compared with animal research, the study of plant lncrnas is not yet in-depth enough, and the speed of functional analysis lags behind the speed of discovery. The variety of lncrnas, their low expression levels, and their obvious tissue specificity all make functional annotation very difficult.

There are still many technical challenges in the functional research of rice lncRNA. They often undergo alternative splicing, which can produce multiple different subtypes, making it complicated to determine their specific functions. The low sequence conservation and the lack of reliable prediction models make the localization of functional components more difficult. To verify their effectiveness, genetic modification, RNA interference and some advanced molecular detection techniques are usually employed, all of which are time-consuming and labor-intensive. There is still an old problem, which is how to distinguish truly functional lncrnas from transcriptional noise.

Future research can focus on high-resolution lncRNA functional analysis, such as studying the roles of different subtypes, their interaction networks, and their epigenetic regulation. Combining multi-omics methods with advanced gene editing technologies will enable the faster identification of lncrnas that are valuable for agronomic traits. The regulation of flowering time, yield and stress resistance by lncRNA has great application potential in molecular breeding. If lncRNA labeling can be combined with traditional label-assisted selection and its regulatory ability under environmental changes can be utilized, crops can be better improved. Continuing to explore the regulatory network of lncRNA will also provide new genetic resources and innovative tools for sustainable rice breeding.

Acknowledgments

We are grateful to Dr. H. Zhou for his assistance with the serious reading and helpful discussions during the course of this work.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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