Regulatory network of rice in response to heat stress and its potential application in breeding strategy

Abstract

The rapid development of global industrialization has led to serious environmental problems, among which global warming has become one of the major concerns. The gradual rise in global temperature resulted in the loss of food production, and hence a serious threat to world food security. Rice is the main crop for approximately half of the world’s population, and its geographic distribution, yield, and quality are frequently reduced due to elevated temperature stress, and breeding rice varieties with tolerance to heat stress is of immense significance. Therefore, it is critical to study the molecular mechanism of rice in response to heat stress. In the last decades, large amounts of studies have been conducted focusing on rice heat stress response. Valuable information has been obtained, which not only sheds light on the regulatory network underlying this physiological process but also provides some candidate genes for improved heat tolerance breeding in rice. In this review, we summarized the studies in this field. Hopefully, it will provide some new insights into the mechanisms of rice under high temperature stress and clues for future engineering breeding of improved heat tolerance rice.

Introduction

Response to challenges of extreme habitat conditions is remarkably complex among different organisms but shows unique features in plants. Plants cannot move to favorable environments; for survival, they have developed sophisticated mechanisms and strategies to mitigate environmental impacts. With the acceleration of global industrial processes and the intensification of the greenhouse effect, global warming has become a serious problem. Sensing changes in ambient temperature and making adjustments are critical to the survival of all organisms. Specifically, the seasonal growth and geographical distribution of plants, including crops, are controlled by ambient temperature (Li et al. 2018; Sharma et al. 2021). Heat stress is the ambient temperature increases beyond the optimal growth temperature resulting in adverse effects on the plant. The adverse effect of heat stress varies in plant species, and cultivars and the developmental stages within a species. Elevated temperature negatively affects the growth and development of crops, resulting in declines in their yield and quality (Quint et al. 2016). For example in rice, the optimal growth temperature at the seedling stage is 28°C/day and 22°C/night (Das et al. 2014); temperature above 32°C negatively affects growth and development at all stages (Aghamolki et al. 2014); temperature above 33°C is critical for pollen development and viability (Jagadish et al. 2007; Zhao et al. 2017); temperature above 35°C limits grain setting and yield (Zhao et al. 2017). Plant heat stress response has been explained by a multiple-layer system, which includes heat stress sensing, signaling transduction, transcriptional reprogramming, and protein and RNA homeostasis maintenance.

Rice, the main food crop for more than half of the world’s population, is a heat-sensitive plant and temperature has become one of the main environmental factors constraining its yield and quality (Jagadish et al. 2021). It is estimated that every rise of 1 °C in global temperature could lead to about a 3.2 % reduction in rice grain production (Zhao et al. 2017). Various mechanisms have been deployed by rice to alleviate heat stress caused damage, and rice have adapted to differential ambient temperatures during natural selection and domestication. Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are the two species of cultivated rice. Asian rice consists of two distinct subspecies, indica and japonica. Indica rice and African rice have developed delicate mechanisms for adapting to high temperatures (Li et al. 2015; Lv et al. 2016; Xu et al. 2020).

In view of the role of rice in world food security and the negative impact of global warming on rice productivity, it is urgent to develop heat-tolerant rice. Therefore, elucidation of the mechanisms underlying the heat stress response of rice at physiological and biochemical, gene expression regulation levels are all necessary, and studies in this field have been widely conducted. In this review, various responsive symptoms of rice under heat stress, as well as the genes involved in the responses (Table 1), were summarized, based on which the molecular mechanism and regulatory network of physiological changes and responses under heat stress were expounded. At the same time, the breeding strategy of heat-tolerant rice varieties is proposed as well.

Table 1.

Genes involved in heat stress response in rice

Gene name	Transgenic species	Temperature	Gene function	Reference
CNGC14, CNGC16	Rice	48°C	Positive	Cui et al. (2020)
TT2	Rice	42°C	Negative	Kan et al. (2022)
TT3.1	Rice	42°C	Positive	Zhang et al. (2022)
TT3.2	Rice	42°C	Negative	Zhang et al. (2022)
RBOHA/Nox2	Rice	38°C	Negative	Baxter et al. (2014); Wang et al. (2013)
SRL10	Rice	42°C	Positive	Wang et al. (2023)
CATB	Rice	42°C	Positive	Wang et al. (2023)
WR2	Rice	42°C	Positive	Kan et al. (2022)
SCT1	Rice	42°C	Negative	Kan et al. (2022)
ANN1	Rice	50°C	Positive	Qiao et al. (2015)
HSFA2d	Rice	42°C	Positively regulate HSP gene expression	Cheng et al. (2019) Singh et al. (2012)
HSFA2c
HSFB4b
AtDPB3-1	Arabidopsis to rice	42°C 55°C	Positive	Sato et al. (2014, 2016)
DPB3-2 DREB2B2	Rice	37°C	Positively regulates heat stress-inducible genes expression	Sato et al. (2016)
NTL3	Rice	42°C	Positive	Liu et al. (2020)
NAC127, NAC129	Rice	35°C	Dual function	Ren et al. (2021)
WRKY11	Rice	38°C	Positive	Wu et al. (2009)
HSP18.0	Rice	42°C/47°C	Positive	Kuang et al. (2017)
HSP17.4, HSP17.9A	Rice to tobacco and Arabidopsis	45°C	Positive	Sarkar et al. (2019)
HIRP1	Rice to Arabidopsis	45°C	Positive	Kim et al. (2019)
HTAS	Rice	45°C	Positive	Liu et al. (2016)
HCI1	Rice to Arabidopsis	45°C	Positive	Lim et al. (2013)
DHSRP1	Rice to Arabidopsis	45°C	Negative	Kim et al. (2020)
TT1	rice	45°C	Positive	Li et al. (2015)
EIF4A1	rice	42°C	Positive	Singha et al. (2021)
TOGR1	Rice	45°C	Positive	Wang et al. (2016)
AET1	Rice	35°C	Positive	Chen et al. (2019)
SLG1	Rice	45°C	Positive	Xu et al. (2020)

Developmental impacts of heat stress

During the entire growth, rice is highly sensitive to heat stress. When the seedling is subjected to heat stress, it will lead to serious imbalances of water, nutrient, and phytohormone, resulting in retarded seedling growth, yellowing, stunting, withering, drying, and ultimately death (Liu et al. 2016, 2018; Kilasi et al. 2018). Rice plant tolerance to heat stress at the seedling stage varies with genetic background. In general, indica rice and African rice are more tolerant to heat stress than japonica rice (Li et al. 2015; Xu et al. 2020).

Rice plants at the reproductive stage, including the processes from panicle initiation to fertilization, are hyper-sensitive to heat stress. Heat stress inhibits panicle initiation and differentiation, and spikelet development, hence forming abnormal floral organs and reducing spikelet number and size (Prasad et al. 2017). Heat stress impedes anther development and pollen viability in various aspects reviewed by Xu et al. (2021), which severely impairs the pollination and fertilization processes, thus eventually reduces male fertility (Zhang et al. 2018a, 2018b). On the contrary, the ovule is less sensitive to heat stress (Soda et al. 2018). The impact of heat stress on ovule development and viability is unclear.

In addition, elevated temperature stress after pollination can also lead to drops in rice yield and quality. Grain filling involves the redistribution and synthesis of carbohydrates, proteins, and lipids in seeds, and the development of embryos (Enrique Gomez et al. 2017; Ren et al. 2021). During this stage, heat stress causes impaired photosynthesis and carbohydrates biosynthesis, uneven filling, and leads to the deposition of irregular and smaller starch particles and loosely packed starch particles, thereby increasing the formation of immature fine grains and cracked grains, resulting in the decline of the appearance and taste quality of rice (Hurkman et al. 2003; Kotak et al. 2007; Prasad et al. 2006; Raza et al. 2020; Ren et al. 2021). It was also found that rice seeds subjected to elevated temperature stress during grain-filling had a later germination time than rice seeds under normal growth conditions (Liu et al. 2019).

Genes function in rice responses to heat stress

Genes involved in heat sensing

Sensing changes in habitats is the first event for all organisms before they can make quick responses. The cell wall is the outermost protective barrier of plant cells affecting the release of Ca²⁺ from extracellular into the cytoplasm to activate calmodulin (CaM)-dependent signal transduction pathways. Pectin methylesterase (PME) is a cell wall remodeling protein. PME-mediated demethylation of pectin which contributes to cell wall remodeling and hydrogen peroxide (H₂O₂) accumulation is required for plant heat stress response (Fig. 1) (Wu and Jinn 2010; Wu et al. 2018; Xiong et al. 2015). There are 43 PME genes and heat-induced PME activity increasing is accompanied by upregulation of PME gene expression in rice (Jeong et al. 2015). PME genes may contribute to heat sensing, even though the experimental evidence is not many.

Fig. 1.

Gene regulatory networks in plant heat stress response. When plants are subjected to heat stress, cell wall structure and properties are reshaped, promoting extracellular Ca²⁺ release. High temperature changes membrane fluidity and permeability, affects membrane protein activity, and may activate Ca²⁺ channels, leading to Ca²⁺ inflow and ROS accumulation. Ca²⁺ signals are transduced by CaM (calmodulin) and CDPK (calcium-dependent protein kinase) to activate heat stress signal transduction pathways in plants. TT3.1 translocates from the plasma membrane to the endosomes and ubiquitinates TT3.2 for vacuolar degradation to protect cell from damage. TT2-CaM/SCT-WR2 is the only known integral signal pathway from heat perception to transcriptional reprogramming conferring thermotolerance

Due to its extremely ordered structure, the membrane, acting as the main barrier inferior to the cell wall, is the most heat-sensitive component in plant cells (Niu and Xiang 2018; Shen et al. 2015). Plasma membranes can directly connect thermal signals to intracellular signaling molecules. Elevated temperature-induced changes in membrane structure and properties can affect the function of membrane proteins, thus triggering the intracellular heat stress-responsive signaling cascade (Narayanan et al. 2016).

A rapid increase of Ca²⁺ levels in a short time was found during heat stress treatment, indicating the presence of heat-sensitive Ca²⁺ channels in the plasma membrane that rapidly open or close in response to environmental signals (Gong et al. 1998; Saidi et al. 2009; Zhang et al. 2009). Membrane-located cyclic nucleotide-gated ion channels (CNGCs) are known as Ca²⁺ channels and their function in thermal sensing has been thoroughly documented (Ohama et al. 2017). In rice, 16 full-length CNGC genes have been identified to date, 13 CNGC proteins are expected to be located in the plasma membrane, and most of them are responsive to ambient temperature (Nawaz et al. 2014). CNGC14 and CNGC16 are positive regulators of thermotolerance and heat-induced cytoplasmic Ca²⁺ accumulation (Cui et al. 2020). Both CNGC14 and CNGC16 loss-of-function mutants exhibit interference with Ca²⁺ flow into the cytoplasm, and reduce or eliminate cytoplasmic Ca²⁺-mediated signal transduction in response to heat stress (Fig. 1).

Most recently, a quantitative trait locus (QTL) THERMOTOLERANCE2 (TT2) isolated from African rice encodes a Gγ subunit protein facilitating Ca²⁺ influx in response to heat treatment (Kan et al. 2022). A natural allele with loss of TT2 function increases heat tolerance associated with greater wax retention at elevated temperatures (Fig. 1). Furthermore, a thermosensor TT3.1 is isolated from the TT3 locus in African rice by the same group (Zhang et al. 2022). TT3 consists of two genes, TT3.1 encoding a plasma membrane-localized E3 ligase functioning as a thermosensor and TT3.2 encoding a chloroplast precursor protein functioning as a chloroplast protector. Encountered with heat stress, TT3.1 translocates from the plasma membrane to the endosomes and ubiquitinates TT3.2 for vacuolar degradation which is essential for protecting chloroplasts from being destroyed.

Reactive oxygen species (ROS), including superoxide anion radical (O₂-), H₂O₂, hydroxyl radical (HO•), and their derivatives, produced in plants are decoded by various ROS sensors to activate stress-specific signals that induce gene expression and protein synthesis (Fichman and Mittler 2020; Mittler et al. 2012). Heat triggers ROS burst which is considered to be an early event related to heat stress, possibly owing to activating respiratory burst oxidase homolog (RBOH), also known as NADPH oxidase, at the transcriptional and protein levels (Begcy et al. 2018; Fu et al. 2016; Sailaja et al. 2015; Zhang et al. 2018a). In rice, nine RBOH genes have been identified, which are induced by elevated temperature, and Ca²⁺ has a direct promotional effect on the activity of RBOH. The plasma membrane-located RBOHA/Nox2 coding gene is induced by high temperature, indicating its negative function in heat stress response (Baxter et al. 2014; Wang et al. 2013). Thus, cell wall and membrane dynamic regulations not only help cells to perceive temperature changes but also participate in intracellular reactions and determine cell fate.

Genes involved in signaling transduction

The earliest heat stress response event is the transient influx of the second messengers, such as Ca²⁺ and ROS, from the extracellular matrix into the cytoplasm (de Pinto et al. 2015; Gong et al. 1998). Components, functioning in signaling transduction, sense the second messenger and subsequently transmit the signals into cells in the response to heat stress (Suri and Dhindsa 2008). Heat-triggered ROS accumulation should be cleared quickly to prevent oxidation-induced cell damage. Of the ROS-scavenging enzymes, catalase is a highly conserved enzyme and plays a key role in removing excessive amounts of H₂O₂ (Mhamdi et al. 2010). There are three catalase genes CATA, CATB, and CATC in the rice genome, and CATB has been proven to play a positive role in rice thermotolerance via scavenging over-accumulated H₂O₂ (Wang et al. 2023). Another positive regulator is characterized in the same research. SEMI-ROLLED LEAF 10 (SRL) confers thermotolerance by promoting CATB stability via physical association (Fig. 1).

The calmodulin (CaM) protein plays an essential role in the transduction of elevated temperature signals. The CaM decodes Ca²⁺ through Ca²⁺-mediated interaction with its partners. After sensing Ca²⁺, the CaM and Sensing Ca²⁺ Transcription factor 1 (SCT1) interaction is strengthened and thus represses their target gene Wax Synthesis Regulatory 2 (WR2) expression to reduce wax deposition in response to heat stress (Kan et al. 2022). The CaM/SCT1-WR2 module couples TT2 regulated the heat-induced Ca²⁺ signaling. The natural allelic TT2 with loss-of-function attenuates Ca²⁺ influx, thereby weakening Ca²⁺-dependent CaM-SCT1 interaction, releasing heat-induced downregulation of WR2 transcription and increasing wax content, resulting in heat tolerance (Fig. 1). TT2-CaM/SCT-WR2 is the only known integral signal pathway from heat perception to transcriptional reprogramming conferring thermotolerance.

Rice annexin ANN1 positively regulates thermotolerance (Qiao et al. 2015). ANN1 binds to Ca²⁺ and shows Ca²⁺-dependent ATPase activity, and interacts with a Ca²⁺ sensor calcium-dependent protein kinase 24 (CDPK24). Overexpression of ANN1 can maintain redox homeostasis under heat stress conditions by promoting superoxide dismutase (SOD) and catalase (CAT) activities, thereby increasing the heat tolerance of rice. This process may be mediated by the ANN1-CDPK24 interaction. High temperature induces the over-accumulation of ROS, resulting in increased ANN1 expression, suggesting a feedback mechanism between ANN1 and ROS production in heat stress (Fig. 1).

Genes involved in transcriptional reprogramming

Heat shock transcription factors (HSFs) are the most essential components in the complex transcriptional regulatory network of the heat stress response, triggering a transcriptional cascade to activate the expression of downstream genes (Scharf et al. 1990). HSFs and heat shock proteins (HSPs) can help to maintain the cellular physiology and metabolism status under heat stress conditions (Fig. 2B). HSFs are able to identify heat shock elements in promoter regions of HSP genes involved in heat stress response and upregulate their transcription. After the first plant HSF was cloned from tomato (Solanum lycopersicum), relevant HSFs have been reported in other species subsequently (Scharf et al. 2012). According to the characteristics of gene structural regions, plant HSFs can be divided into HSFA, HSFB, and HSFC (Huang et al. 2012). Under heat stress, HSFA of the known HSF in most plants is thought to play a leading role in the transcriptional network (Gai et al. 2020). There are 25 HSF genes in rice, and 22 are transcriptionally induced by high temperature (Mittal et al. 2009). The transcriptional activity of HSFA2d is induced by alternative splicing under high temperatures, which increases the expression of HSP17.7, HSP18.2, HSP21, HSP83.1, and HSP101 genes (Cheng et al. 2019). HSFA2c interacts with HSFB4b and is involved in the transcriptional regulation of HSP100 by binding specifically to the promoter of HSP100 (Singh et al. 2012).

Fig. 2.

Protein homeostasis maintenance system are activated by heat stress. A In response to heat stress, SLG1 and AET1 are required for tRNA modification at posttranscriptional level which is essential for protein translation. In addition, functioning cooperatively with RACK1A and eIF3h, AET1 directly binds to uORF to regulate the translational efficiency uORF-containing mRNAs in response to high temperature. B Heat stress transcriptionally activates HSF to trigger a transcriptional cascade to activate the expression of downstream genes including HSP, HSF, and HSP which can help to maintain the normal physiological metabolism by stabilizing unfolded proteins and promoting the renaturation of aggregated proteins induced under heat stress. C Heat activating HIRP1 ubiquitinates ARK4 and HRK1 for degradation via Ub/26S thereby triggering response

In addition to HSFs, other types of transcription factors, such as AP2/ERF, NAC, and WRKY, have also been found to cope with heat stress. The Arabidopsis AP2/ERF family transcription factor dehydration-responsive element binding protein 2A (AtDREB2A) is a heat tolerance regulator, which functions cooperatively with a trimer comprising nuclear factor y-subunit A2 (AtNF-YA2), AtNF-YB3, and AtNF-YC10 (also known as DNA polymerase II subunit B3-1, AtDPB3-1) to activate heat stress-inducible gene expression (Sato et al. 2014). Overexpression of AtDPB3-1 enhances rice thermotolerance (Sato et al. 2014, 2016). AtDPB3-1 and its rice homolog DPB3-2 function as positive regulators of AtDREB2A and its rice homolog DREB2B2 to induce heat stress-inducible gene expression in rice cells (Sato et al. 2016), indicating their conserved functions.

Rice NTL3 encodes a NAC transcription factor with a predicted C-terminal transmembrane domain which binds to the bZIP74 promoter and regulates its expression in response to heat stress (Liu et al. 2020). NTL3 relocates from the plasma membrane to the nucleus in response to heat stress and ER stress. Loss-of-function mutation of NTL3 increases heat sensitivity while expression of the truncated form of NTL3 without the transmembrane domain enhances heat tolerance in rice.

NAC domain transcription factors NAC127 and NAC129 are responsive to heat stress and involved in the grain-filling process of rice under heat stress (Ren et al. 2021). They regulate grain filling might through affecting nutrient and sugar transportation. Paradoxically, their loss-of-function mutants and overexpression plants showed incomplete grain filling and shrunken grains. WRKY11 which encodes a WRKY domain-containing transcription factor is induced by heat stress. Its overexpressing rice shows enhanced thermotolerance, revealing its positive role in regulating heat stress response (Wu et al. 2009).

Genes involved in RNA metabolism

In addition to protein, RNAs, as indispensable participants in protein synthesis, were also adversely affected by heat stress on their metabolism, including stability, splicing, and post-transcriptional modification (El Yacoubi et al. 2012). RNA helicase plays an essential role in RNA metabolism (Jarmoskaite and Russell 2014). It is mainly involved in RNA structure formation, ribosome formation, regulation of RNA processing, and protein translation. Eukaryotic initiation factor 4A1 (EIF4A1) is a DEAD-box RNA helicase known to mediate interactions between proteins with ATP and RNA. Under heat stress, the expression of eIF4A1 is induced in rice seedlings (Singha et al. 2021). Strong ATP/Mg²⁺ binding during heat stress indicates that EIF4A1 plays a role in the heat stress response. Required Heat-resistant Growth 1 (TOGR1) is another DEAD-box RNA helicase that acts as an inherent pre-rRNA chaperone (Wang et al. 2016). Its gene expression and activity increase with increasing temperature. Heat stress disrupts the interaction between rRNA precursors and their interacting proteins. At this point, the expression of TOGR1 is enhanced in the nucleolus, which helps the rRNA precursor efficiently fold and interact with the corresponding protein to ensure normal rRNA production. Overexpression of TOGR1 significantly improved the growth of rice under heat stress.

Adaptation to Environmental Temperature 1 (AET1), encoding a dual-function tRNA^His guanylyltransferase, is crucial for rice in response to high temperature (Chen et al. 2019). As a tRNA^His guanylyltransferase, AET1 adds guanine to pre-tRNA^His to activate tRNA^His aminoacylation and is required for tRNA^His maturation and tRNA homeostasis. AET1 also interacts with receptor for activated C-kinase 1A (RACK1A) and eukaryote initiation factor 3 (eIF3h) and regulates the translational efficiency of the upstream open reading frame (uORF)-containing mRNAs by binding to the uORF, such as binding to the uORFs of auxin response factor 19 (ARF19) and ARF23 in response to high temperatures (Fig. 2A). Another tRNA-modifying enzyme gene Slender Guy 1 (SLG1) which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) plays a key role in the response to high temperature (Fig. 2A) (Xu et al. 2020). SLG1-mediated thermotolerance is positively correlated with thiolated tRNA level. SLG1 differentiated between indica (SLG1^Ind) and japonica (SLG1^TeJ) rice, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance of indica rice.

Genes involved in protein homeostasis maintenance

Heat stress could induce misfolding of proteins and their accumulation in the endoplasmic reticulum (ER), which initiates the unfolded protein response (UPR) in plants (Liu and Howell 2010). UPR plays an important role in protein homeostasis under heat stress. ER stress activates UPR with two arms of the signaling pathway. One is the splicing of bZIP60 mRNA by a dual protein kinase (IRE1), and another involves membrane-associated bZIP transcription factors. IRE1 is one of the major sensors of UPR in eukaryotes. ER stress allows IRE1 activation through autophosphorylation. At high temperatures, activated IRE1 triggers irregular mRNA splicing of rice homologous bZIP74/bZIP50 of AtbZIP60 to generate nuclear localization forms and activate the expression of UPR-related genes (Lu et al. 2012; Hayashi et al. 2012). The expression of bZIP39 and bZIP60 is upregulated by heat stress (Cheng et al. 2019).

As molecular chaperones, HSPs can maintain the normal physiological metabolism by stabilizing unfolded proteins and promoting the renaturation of aggregated proteins induced under heat stress and play essential roles in the tolerance to stress (Fig. 2B) (Müller and Rieu 2016). A most recent study revealed that 79 out of 100 HSF and HSP genes are differentially expressed under heat stress analyzed by transcriptome analysis in rice (Cui et al. 2020). Under heat stress, the expression of HSP18.0 rapidly increases and reaches its peak in a short time. Overexpressing HSP18.0 increases seed germination, plant height, and chlorophyll content under heat stress, thus improving the heat tolerance of rice (Kuang et al. 2017). The expression of HSP26.7, HSP23.2, HSP17.9A, HSP17.4, and HSP16.9A are induced by heat stress, which was more dramatic in heat tolerance rice. HSP17.4 and HSP17.9A proteins exhibit chaperone activity, and ectopic expressing HSP17.4 and HSP17.9A improves thermotolerance in tobacco and Arabidopsis (Sarkar et al. 2019). Similarly, the protein abundance of HSP101, HSP90, and HSP70 also increased significantly under heat stress (Lin et al. 2014; Scafaro et al. 2010).

The ubiquitin-proteasome pathway is an important way to regulate protein stability in the signal transduction process under heat stress (Lyzenga and Stone 2012). The ubiquitin/26S proteasome system is an essential proteolytic complex responsible for degrading proteins conjugated with ubiquitin. Many RING finger ubiquitin E3 ligases, such as heat-induced RING finger protein 1 (HIRP1; Kim et al. 2019), heat tolerance at the seedling stage (HTAS) (Liu et al. 2016), and heat and cold induced 1 (HCI1; Lim et al. 2013), are reported to be indispensable for rice tolerance to heat stress and may function in recognizing and ubiquitinating their target proteins for subsequent degradation by the 26S proteasome. Overexpression of their genes would increase heat tolerance. Under heat stress, the expression of HIRP1 is significantly increased, while the expression levels of Aldo/Keto Reductase 4 gene (ARK4) and HIRP1-Regulated Kinase I gene (HRK1) are reduced in rice seedlings. HIRP1 ubiquitinates ARK4 and HRK1 for degradation via Ub/26S protease. Arabidopsis expressing rice HIRP1 shows higher heat tolerance (Fig. 2C) (Kim et al. 2019), while drought-, heat-, and salt-induced RING finger protein 1 (DHSRP1) acts as a ring-H2 E3 ligase and negatively regulates rice heat stress, whose gene expression is upregulated in rice seedlings under heat stress (Kim et al. 2020). The Arabidopsis overexpressing rice DHSRP1 exhibits hypersensitivity to heat stress. In addition, the cloning of TT1 from African rice encodes a 26S proteasome α2 subunit, which achieves more effective elimination of cytotoxic denatured proteins than its Asian rice allele, thereby protecting cells from heat damage (Li et al. 2015).

Strategies for breeding thermotolerance rice

Breeding of thermotolerance rice cultivar might be an effective method to reduce the damage of heat stress on growth and development, and thus improve the yield and quality of rice. Conventional breeding methods are normally based on phenotypic selection related to the heat tolerance of rice, and the most appropriate breeding methods are selected according to different regional climates (Driedonks et al. 2016). Therefore, accurate assessment of the heat tolerance of rice, selection of heat-tolerant rice varieties or breeding lines, and successful stable inheritance of heat-tolerant traits in specific varieties with excellent yield and quality are important for breeding selection.

Accumulating data suggest that using genes or QTLs for improving rice tolerance to high temperatures is technically possible and the necessary resources are available. The available candidates include SLG1^Ind and QTLs derived from African rice TT1, TT2, and TT3, all of which regulate tolerance to heat stress at both seedling and adult stages, and some other genes that play roles in rice heat stress response. These genes encode diverse proteins involved in various pathways, which provide a wide range of choices for heat-tolerant rice breeding. Based on this information, a single gene or multi-gene combination may be used for improving rice thermotolerance via the following approaches.

The first strategy is using gene marker-assisted selection to transfer a single gene or pyramid of genes of interest and maintain the genetic background of the cultivar with superior agronomic traits by crossing and backcrossing. SLG1^Ind can be used by using this approach. By analysis of the sequences of 4219 Asian cultivated rice accessions (Xu et al. 2020), 2527 out of 2691 (93.9%) indica accessions carry SLG1^Ind, which provides lots of choices for selection by breeders. TT1, TT2, TT3, and some other QTLs can also be used in this way. In addition, some genes, such as NTL3 and WR2, that enhance rice heat tolerance or contribute to QTLs may also be used by this approach. Because this type of genes-mediated heat tolerance frequently requires a higher level of gene expression, identification of alleles with markedly high expression levels under heat stress is a prerequisite. Rice is rich in germplasm resources (Zhang 2007), which makes this requirement feasible. The advantage of molecular markers has further assisted breeders in shortening the breeding period and consequently enhancing the efficiency and precision of conventional crop breeding. However, being a random process, the identification of a desirable genotype after crossing is an extremely laborious and time-consuming process.

The second strategy is directly transforming a positive regulator gene into the genetic background of elite cultivars. Higher transcript levels of these genes are required to achieve tolerance improvement. The expression level and coding sequence variation of SLG1 contribute to its function and overexpressing SLG1^TeJ enhances rice tolerance to heat stress (Xu et al. 2020). Thus, SLG1 is a gene that can be used in this way. Similarly, TT3.1 also can be used by using this approach. However, constitutive high level expression of some genes can result in fitness costs or be negatively involved in other physiological activities.

The development of genome editing technologies offers new possibilities for addressing the food security challenge and simultaneously the core issues of legislation on transgenic plants. Genome editing systems can introduce stably inherited point modifications, fragment deletions, insertions, and substitutions, including elimination of genes, introduction of desired genes, and altering regulatory sequences controlling the gene expression, at precise locations in the plant genome. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system has been used to generate marker-free (without antibiotic resistance genes) and excess genetic material-free (without remnants of delivery tools) genetically modified crops (Wang et al. 2019; Zhang et al. 2016). These aims could not be achieved through traditional breeding methods or even transgenesis. Genes functioning either positively roles or negatively can be used by exploring genome editing technologies. As positive regulators (like WR2, and ANN1), these technologies can be used to substitute their native promoters with strong ones. As negative regulators (like TT2, and RBOHA), these technologies can be used to knock out or knock down their functions. Theoretically, these technologies could be used to generate plants with the designed genotype.

Conclusion and perspectives

In recent years, global temperatures have gradually risen, posing a serious threat to crops. The problem of grain yield and quality has aroused great concern. In order to meet the growing food demands, effective breeding methods and improvement of agronomic traits as well as the cultivation of heat-resistant varieties are the primary tasks for coping with elevated temperature stress at present. At the same time, rice and other plants have also evolved complex and effective high-temperature response regulation mechanisms to maintain normal growth and development under high-temperature environments. This involves the activation of a variety of functional proteins and RNAs. It is worth noting that some of the studies on heat-tolerant rice varieties mainly reveal the expression of heat-tolerant genes in response to heat stress, but there are few studies on the regulatory genes and their applications in breeding. Therefore, future studies should pay more attention to the upstream and downstream regulatory mechanisms in response to high temperature, and identify heat-tolerant genes through a large number of phenomics, gene editing, and alternative genetic engineering techniques. In particular, the application of gene editing technologies provides different approaches to the field of traditional transgenesis, and is crucial to elucidate the mechanisms of rice heat stress response and heat tolerance gene networks, offering better prospects for improving crop tolerance.

Author contribution

All the authors Z.M., J.L., W.W., D.F., S.L., Y.K., and P.Y. discussed and created the outline, Z.M. and J.L. wrote the manuscript, and Y.K. and P.Y. revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Foundation of Hubei Hongshan Laboratory.

Data availability

Not applicable.

Declarations

Conflict of interest

The authors declare no competing interests.