ABSTRACT
As global temperatures increase, heat stress has become a key limiting factor affecting crop yield and quality. Against the backdrop of growing global food demand and increasingly frequent extreme high‐temperature events, this dual pressure poses a threat to global food security. This review systematically analyzes the physiological effects of heat on major crops, focusing on source–sink relationships and nutrient transport processes. We summarize key heat‐related genes identified in these crops through forward and reverse genetic approaches, elucidating the mechanisms underlying heat signal perception and transduction across genetic, transcriptional, protein, metabolic, cell membrane, nuclear, and organellar levels. Furthermore, we explore the complex crosstalk between heat and other abiotic/biotic stresses in crops. Finally, we discuss current challenges and future avenues for breeding heat‐resilient crops to ensure stable agricultural productivity.
Keywords: crops, heat‐related genes, heat stress, heat‐tolerant breeding, regulatory mechanisms, stress crosstalk
This review integrates molecular networks and physiological adaptation to reveal how heat stress disrupts source‐sink dynamics in crops, and highlights key thermotolerance genes and regulatory modules that enable precision breeding of heat‐resilient varieties, thereby providing a roadmap for safeguarding global food security under climate warming.
INTRODUCTION
Global warming has intensified over recent decades, posing a substantial threat to agricultural systems worldwide. Between 1880 and 2025, the average global temperature increased by more than 1°C (Intergovernmental Panel on Climate Change IPCC, 2021; National Aeronautics and Space Administration NASA, 2025), and it is projected to increase by 2.3°C–2.5°C by the end of this century (United Nations Environment Programme UNEP, 2025). According to the World Meteorological Organization (WMO), the period from 2015 to 2025 marked the warmest 11‐year interval on record, and the past 3 years (2023–2025) have been the warmest 3 consecutive years, with 2024 being the hottest individual year in recorded history, when the global mean near‐surface temperature reached approximately 1.55°C above the 1850–1900 average, indicating that the global warming trend is continuing (World Meteorological Organization WMO, 2025, 2026). Rising temperatures pose an increasingly severe threat to crop production. The growing demand for food, coupled with the increasing frequency of extreme heat events, has led to significant declines in both crop yield and quality. For instance, a 2°C increase during the growing season can result in yield losses of 3%–13% (Zhao et al., 2017; Wang et al., 2020b). Projections further indicate that rising minimum temperatures could lead to a potential 41% reduction in rice yield by 2100 (Riaz et al., 2024). These trends underscore the urgency of elucidating the molecular and physiological mechanisms underlying heat stress tolerance to safeguard future agricultural productivity.
Heat stress causes substantial yield losses by impairing key plant processes, including growth, phenology, pest resistance, seed setting, grain filling, and senescence onset (Zhu et al., 2021). At the molecular level, plants deploy a multi‐layered response system to heat stress, involving early sensing, signal transduction, osmolyte synthesis, and antioxidant defense, culminating in heat stress‐associated gene expression. Heat stress responses are orchestrated by a multi‐layered regulatory network that includes heat stress transcription factors, microRNAs, and other transcriptional regulators, forming a complex regulatory circuit. Studies in model plants such as Arabidopsis have identified numerous genes and metabolites involved in heat perception and adaptation (Ding et al., 2020; Zhang et al., 2022e), revealing the complexity and multi‐component nature of the heat stress response.
Crops are highly vulnerable to climate change, which causes substantial losses in productivity. Rice, wheat, and maize, the world's major cereal crops, collectively provide 48% of total calories and 42% of daily proteins, accounting for approximately 75% of global food production. With the global population projected to exceed 9.8 billion by 2050, the demand for these staples will intensify, placing additional pressure on agricultural systems (Pandey et al., 2024). However, climate change‐induced temperature increases are expected to cause severe yield losses in cereals if current warming trends continue. Beyond staple grains, heat stress also imposes severe constraints on high‐value crops. Tomato is the world's second most important vegetable crop, with an annual global production exceeding 180 million tons (FAO, 2023a). Tomato fruits are rich in phytochemicals that protect against chronic degenerative diseases and serve as an important source of various vitamins (Ali et al., 2021). Nevertheless, high‐temperature stress frequently limits tomato yields, as temperatures are often elevated in many tomato‐growing regions, particularly during the critical stages of flowering and fruit set (Miller et al., 2021; Ayenan et al., 2019). Given its status as a widely cultivated fruit crop, even a slight increase in temperature can lead to substantial production losses at the global level (Ayenan et al., 2019). Heat‐induced yield losses in tomato pose a direct threat to dietary diversity and nutritional security, particularly in regions reliant on its vitamin and antioxidant content (Singh et al., 2022). Cotton, a major cash crop, is a vital fiber crop for the global textile industry, supplying around 31% of the world's textile raw material, and also serves as a source of edible oil; it also has emerging applications in the biopharmaceutical sector. Cotton is cultivated in nearly 35 countries; China, India, and the United States collectively contribute around 60% of total cotton production (Luqman et al., 2025a; FAO, 2023b). However, cotton production faces continuous threats from climate change, particularly heat stress (Luqman et al., 2025a). Heat stress disrupts key biological processes in cotton, especially at the bud and boll stage (Luqman et al., 2025b; Bista et al., 2025), leading to considerable declines in growth, yield, and fiber quality (Ijaz et al., 2024). Similarly, soybean is a leading source of vegetable oil and dietary protein. Soybean products and soybean oil play a significant role in agricultural commodities (Hartman et al., 2011). Furthermore, soybean meal serves as the major source of both protein and energy in animal feed, thereby underpinning the livestock industry (Hartman et al., 2011). The yield growth of soybean has been consistently constrained by abiotic stress factors (Jumrani and Bhatia, 2018). In particular, heat stress frequently compromises soybean yield (Djanaguiraman et al., 2011; Siebers et al., 2015). When temperatures exceed 35°C, soybean plants experience impaired photosynthetic efficiency, disrupted flowering, and poor pod setting, collectively contributing to significant yield loss (Raineri et al., 2025).
Given that high‐temperature stress has become a major constraint on crop production, exploration of heat‐tolerant genetic resources and development of heat‐resilient crop varieties hold strategic importance. However, research into the molecular and genetic bases of crop heat tolerance has historically lagged behind studies in model organisms. The past decade has witnessed growing research interest in this field, yielding several notable advances. However, many aspects of the molecular mechanisms underlying heat tolerance and their regulatory networks remain poorly understood (van Es, 2020; Li and Howell, 2021; Singh et al., 2022; Li et al., 2023; Cai et al., 2024; Ijaz et al., 2024; Kalantar Ahmadi and Daneshian, 2025; Prado et al., 2025; Xiong et al., 2025; Zheng et al., 2025b). Furthermore, although studies have identified key heat‐tolerance genes in crops and noted their phenotypic linkages to abiotic/biotic stress and hormone signaling, the functional crosstalk between these associated pathways is still largely unclear (Gu et al., 2023; Rahman et al., 2024).
In this review, we first systematically analyze the physiological impacts of high‐temperature stress on major crops (e.g., rice, maize, wheat, tomato, soybean, and cotton), emphasizing the source–sink relationships and assimilate partitioning. Subsequently, we summarize representative heat‐related genes identified through forward and reverse genetics, synthesizing them into an integrated regulatory network of core thermotolerance mechanisms. We then present the crosstalk between heat stress and other abiotic/biotic stresses. Finally, we discuss the current challenges and shortcomings in heat‐tolerant crop breeding and propose future research directions, aiming to provide a theoretical framework for enhancing global food security under a warming climate.
HIGH‐TEMPERATURE EFFECTS ON CROP PHYSIOLOGY: SOURCE, SINK, AND TRANSPORT
Crop yield is determined by the synergistic interaction among the photosynthetic capacity of source tissues, the storage capacity of sink tissues, and the efficiency of the translocation system that connects them. High productivity depends on adequate sources, robust sinks, and unimpeded flow. Photosynthates are translocated via the phloem from source tissues (such as leaves) to heterotrophic sink tissues (including root tips, shoot apices, and reproductive tissues) to sustain their growth and metabolism, thereby driving overall plant development and yield formation (Lou et al., 2025). Although source, sink, and transport processes are all susceptible to heat stress throughout the entire crop growth cycle, encompassing the vegetative, reproductive, and grain‐filling stages, the primary impacts vary depending on the developmental stage (Li et al., 2023; Xiong et al., 2025). During vegetative growth, heat stress primarily impairs source tissues (leaves) by reducing photosynthetic capacity (Schapendonk et al., 2007; Hastilestari et al., 2018). During the reproductive and grain‐filling stages, heat stress mainly damages sink tissues (flowers, seeds, and fruits) by disrupting fertility and storage compound accumulation (Harding et al., 1990; Zhang et al., 2018). The transport processes connecting the source and sink are affected across all developmental stages (Zhang et al., 2018). Taking rice as an example, high temperatures severely inhibit seed germination, reduce tiller number and plant height at the seedling stage, and cause irreversible declines in spikelet fertility and grain quality during the reproductive and grain‐filling stages (Li et al., 2023). Heat stress impairs crop performance by disrupting source activity, sink strength, and translocation processes (Figure 1).
Figure 1.
Effects of high temperature on crop physiology
High temperatures adversely affect crops throughout their life cycle, with source tissues, sink tissues, and the associated transport processes (i.e., source–sink flow) each showing sensitivity to heat stress (top left panel). From the perspective of source–sink dynamics, the primary targets of high‐temperature stress shift across growth stages. During vegetative growth (bottom left panel), source tissues (leaves) bear the brunt of heat stress, which impairs photosynthesis by disrupting chlorophyll biosynthesis, photochemical reactions, electron transport, and CO2 assimilation. In addition, heat stress damages chloroplast and mitochondrial ultrastructure, and triggers a burst of reactive oxygen species (ROS). During the reproductive and maturation stages (bottom right panel), the predominant impact shifts to sink tissues (flowers, seeds, and fruits), where heat stress often reduces fertility, disrupts starch biosynthesis, and compromises grain quality. Source–sink transport processes (top right panel) are compromised throughout the entire life cycle. This systemic disruption of source–sink coordination ultimately hampers reproductive development, leading to substantial losses in both yield and quality.
Impairment of source tissue function under heat stress
Crops are vulnerable to heat stress throughout their life cycle. During vegetative growth, including the seedling stage, source tissues—primarily leaves—are relatively more severely affected by heat stress than sink tissues or transport processes (Zhu et al., 2021; Lou et al., 2025). Extensive research over the past several decades has revealed that chloroplasts, the photosynthetic organelles of plants, are highly vulnerable to heat stress, which disrupts chlorophyll biosynthesis, photochemical reactions, electron transport, and CO2 assimilation, collectively undermining photosynthetic performance (Hu et al., 2020). The damage primarily manifests as a severe cellular energy imbalance, fundamentally stemming from heat‐induced alterations in the redox states closely linked to thylakoid membrane damage. This energy deficit directly undermines source tissues' capacity to produce and export photosynthates, initiating a cascade of source‐limitation effects that ultimately constrain yield.
Chloroplasts are not merely passive targets of heat stress; they also serve as central hubs for its perception, signaling, and metabolic acclimation. Heat stress induces a rapid and conserved disruption of chloroplast ultrastructure, including loosening and swelling of thylakoid membranes, reduced granal stacking, and increased plastoglobuli (Hu et al., 2020; Ahmad et al., 2024). These structural perturbations are closely linked to decreased photosynthetic efficiency, as high temperatures impair the oxygen‐evolving complex of PSII, inhibit Rubisco activase, and disrupt electron transport chains, leading to reduced carbon assimilation and ROS overproduction (Hu et al., 2020; Scafaro et al., 2023; Qu et al., 2023). Chloroplasts also initiate retrograde signaling cascades that reprogram nuclear gene expression to establish thermotolerance. In parallel, chloroplast‐derived signals, including ROS, the isoprenoid intermediate methylerythritol cyclodiphosphate (MEcPP), and the phosphonucleotide PAP, are mobilized to orchestrate a coordinated heat shock response (Hu et al., 2020; Tang et al., 2020). This signaling web is further reinforced by chloroplast‐localized chaperones and proteases, such as the casein kinase cpCK2, which phosphorylates and stabilizes the small heat shock protein sHSP26 to protect PSII, while the FtsH11 metalloprotease degrades the ATP synthase assembly factor BFA3 to regulate the proton gradient and prevent photodamage under heat stress (Yue et al., 2023; Zhao et al., 2025c). Collectively, these findings position chloroplasts as high‐temperature sensing sites and signaling hubs where morphological, physiological, and molecular responses are integrated. Harnessing this essential organelle may represent a key strategy for plant survival and reproductive success under a warming climate.
The photosynthetic apparatus, such as Photosystem I (PSI), Photosystem II (PSII), the cytochrome b 6 f (Cytb 6 f) complex, and Rubisco, is directly impaired under elevated temperatures (Mathur et al., 2014; Chen et al., 2020; Zhang et al., 2022a). Among these, PSII is particularly heat‐sensitive. High temperatures increase thylakoid membrane fluidity, leading to the dislodgement of PSII light‐harvesting complexes and the oxygen‐evolving complex (OEC). This damage compromises PSII integrity, inhibits electron transfer from the OEC to the acceptor side, and consequently inhibits photosynthetic electron transfer and ATP synthesis (Mathur et al., 2014). Furthermore, heat stress often coincides with oxidative stress, and together, they might inhibit the repair of the damaged PSII by inhibiting key PSII protein synthesis, such as the D1 protein, leading to a sustained decline in photosynthetic efficiency in plants (Chen et al., 2020).
Chlorophyll (Chl), the primary photosynthetic pigment located within the thylakoid membranes, plays a central role in the initial stages of photosynthesis by harvesting light energy and driving electron transfer (Saini and Debnath, 2023). Under normal growth conditions, Chl levels remain stable due to a balance between its synthesis and degradation. However, under environmental stress such as high temperature, this equilibrium is disrupted: The Chl content declines, leading to leaf senescence or chlorosis (Hörtensteiner, 2006). Heat stress upregulates the activity of chlorophyllase and Chl‐degrading peroxidase, accelerating Chl breakdown and significantly reducing photosynthetic pigment levels (Shen et al., 2022; Ahmad et al., 2024). Consequently, sustaining the balance of chlorophyll metabolism is critical for optimal photosynthetic apparatus functionality, on which overall crop productivity and yield stability critically depend.
Rubisco (Ribulose‐1,5‐bisphosphate carboxylase/oxygenase) plays a dual role in plants as the key carboxylase in photosynthesis and as an oxygenase in photorespiration (von Caemmerer, 2020). Its activation is governed by Rubisco activase, which becomes a limiting factor in photosynthesis when the atmospheric temperature exceeds the optimum range for plants (Crafts‐Brandner and Salvucci, 2000). Under moderately elevated temperatures, the Rubisco activase activity is inhibited, resulting in the thermal inactivation of Rubisco (Scafaro et al., 2023). Under more extreme heat, the stability of Rubisco's chaperone‐activating enzyme decreases, further suppressing photosynthetic capacity (Feller et al., 1998; Ristic et al., 2009; Kumar et al., 2016; Degen et al., 2021). In addition to these direct effects, photosynthesis is also indirectly impaired by stomatal closure, a response to reduce water loss that consequently increases leaf temperature and promotes Rubisco's oxygenase activity (Losciale et al., 2014). As the temperature increases, the affinity of Rubisco for CO2 decreases, favoring photorespiration. This shift reduces net photosynthetic efficiency and contributes to yield loss (Hu et al., 2020). Conversely, increased stomatal density may enhance transpirational cooling and photosynthetic efficiency (Rathnasamy et al., 2023).
Heat stress also damages chloroplast and mitochondrial ultrastructure, triggering a burst of reactive oxygen species (ROS), such as singlet oxygen, superoxide anion, and hydrogen peroxide. ROS accumulation causes oxidative damage to nucleic acids, lipids, and proteins. Protein denaturation induced by high temperature results in oxidation, misfolding, and aggregation, which can induce cell death in the absence of effective chaperones and proteolytic systems (Huang et al., 2022a). Recent studies have identified genes such as HTH5, which reduces ROS accumulation by increasing the pyridoxal 5′‐phosphate content and enhances rice heat tolerance at the heading stage (Cao et al., 2022), and PSL50, which regulates H2O2 accumulation and photosynthetic acclimation, integrating heat response with the control of leaf senescence (He et al., 2021).
Heat‐induced dysfunction of sink tissues
During the reproductive and grain‐filling stages, sink tissues (flowers, seeds, and fruits) experience relatively greater impairment than source tissues or transport processes (Jagadish, 2020; Zhu et al., 2021; Resentini et al., 2023). Crop yield relies on successful seed production, a process highly vulnerable to elevated temperatures. Seed set requires the coordinated development of male and female gametophytes, successful fertilization, and subsequent embryonic and endosperm growth—all sensitive to thermal extremes (Jagadish, 2020). Reproductive development is particularly vulnerable to temperature fluctuations, with heat stress frequently leading to impaired fertility across species (Zhu et al., 2021).
The male reproductive components show exceptional sensitivity to high temperatures. Anther and pollen development are more affected by temperature fluctuations than other stages of gametophyte development, fertilization, and seed set (Resentini et al., 2023; Zhao et al., 2025a). In cotton, elevated temperatures significantly slow pollen tube growth within pistils under field conditions (Snider et al., 2011), with temperatures exceeding 35°C strongly suppressing both pollen tube development and fertilization efficiency (Song et al., 2015). Similarly, rice experiences exacerbated pollen sterility and inhibited pollen germination on stigmas under heat stress (Firon et al., 2012; Mo et al., 2023; Zhao et al., 2025a), while soybean shows shortened flowering duration, reduced pollen germination rates, diminished pollen size, and impaired pollen tube elongation—all contributing to decreased seed output (Jumrani and Bhatia, 2018). This broad reproductive susceptibility stems primarily from the high heat sensitivity of developing pollen grains (Firon et al., 2012; Mo et al., 2023; Zhao et al., 2025a).
Beyond direct impacts on fertilization, heat stress triggers phenotypic adjustments that further constrain yield potential. Plants often accelerate development under high temperatures, shortening the grain‐filling period and consequently reducing the temporal window for resource accumulation into seeds (Xiong et al., 2025). In rice, for instance, yield declines by approximately 7% per 1°C increase in nighttime temperature and 6% per 1°C increase in daytime temperature beyond optimal levels (28°C day/22°C night), with seed set rate identified as the most temperature‐sensitive yield component (Su et al., 2023).
High‐temperature stress profoundly impacts sink strength and grain yield by disrupting the highly coordinated processes of starch biosynthesis and degradation, particularly in cereal crops. Starch constitutes 60%–75% of the final grain dry weight, and its accumulation is highly temperature‐sensitive. During grain filling, heat stress typically accelerates the filling rate but shortens the overall duration of grain filling, leading to insufficient starch accumulation and reduced grain weight (Karim et al., 2020; Zhang et al., 2021b). High temperatures suppress the activity and expression of key starch biosynthetic enzymes, including ADP‐glucose pyrophosphorylase (AGPase), soluble starch synthase (SSS), and granule‐bound starch synthase I (GBSSI, encoded by the Wx gene), thereby reducing both total starch and amylose contents (Zhang et al., 2014; Zhang et al., 2021b). Concomitantly, heat stress enhances the expression and activity of starch‐hydrolyzing enzymes, particularly α‐amylases in developing endosperm, which actively degrade starch granules and contribute to chalky, opaque grains with poor milling quality and diminished market value (Yamakawa and Hakata, 2010; Nakata et al., 2017). This imbalance between reduced synthesis and accelerated degradation directly compromises sink strength, limiting grain storage capacity and reducing both kernel number and size (Shi et al., 2017). Moreover, high night temperatures exacerbate these effects by increasing respiratory carbon losses, further depleting carbohydrate reserves available for grain filling (Bahuguna et al., 2017; Impa et al., 2021). Key regulators such as the rice FLOURY ENDOSPERM 24 (FLO24), encoding an HSP101, and the transcription factor OsbZIP58 help maintain starch biosynthesis and endosperm development under heat stress by preserving enzyme function and repressing α‐amylase gene expression, respectively (Xu et al., 2020a; Wu et al., 2024).
Grain quality parameters are equally compromised under high‐temperature conditions. Cereals frequently show increased chalkiness, reduced milling recovery, and altered cooking, eating, and nutritional qualities under thermal stress (Su et al., 2023). Chalkiness, a complex trait governed by multiple quantitative trait loci, results from disrupted endosperm development during grain filling. In this process, high temperatures impair the deposition and organization of storage compounds (Li et al., 2025b). In wheat, heat stress produces smaller, lighter grains characterized by diminished starch content and elevated grain protein concentration, further reducing processing quality and market value (Wardlaw et al., 2002).
In summary, enhancing crop reproductive heat tolerance is a key objective in crop breeding. Promising strategies include selecting genotypes with sustained reproductive function under high temperatures (Mehmood et al., 2025), as well as exploiting phenotypic traits such as shifted flower opening times to avoid peak heat periods, coupled with improved pollen and pistil viability to mitigate heat damage during flowering (Bheemanahalli et al., 2017; Jagadish, 2020).
Disruption of source–sink transport under heat stress
Source–sink transport processes are compromised across all developmental stages (Zhang et al., 2018; Sun, et al., 2021; Li et al., 2023; Lou et al., 2025). Plant carbohydrate allocation encompasses a series of tightly regulated processes, including carbon assimilation, sucrose synthesis, phloem loading, long‑distance transport, and unloading in sink tissues (Braun et al., 2014). In source leaves, sucrose is synthesized from triose phosphates via the action of sucrose–phosphate synthase (SPS) (Li et al., 2024a). Sucrose is then loaded into phloem sieve elements through either an apoplastic pathway (mediated by sucrose transporters, SUTs) or a symplastic pathway via plasmodesmata (Julius et al., 2017). In many crop plants, apoplastic loading is predominant and requires active transport against a concentration gradient, a process that is highly sensitive to energy supply and membrane integrity. After long‐distance transport, sucrose reaches developing seeds or fruits, where it is unloaded and metabolized. Sucrose can enter sink cells either as a disaccharide or be hydrolyzed by cell‐wall invertases (CWINs) or sucrose synthase (SuSy) into hexoses, which then fuel grain development and starch accumulation (Ruan, 2014; Stein and Granot, 2019).
Heat stress disrupts the source–sink balance in plants, resulting in inadequate energy supply in sink tissues, impaired reproductive development, and ultimately yield and quality reduction (Kan et al., 2023; Lou et al., 2025). High temperatures inhibit SPS activity, leading to reduced sucrose production in source leaves and suppressing SuSy activity in sink tissues, which limits hexose supply and starch biosynthesis (Zhao et al., 2013; Parihar et al., 2025). Central to this imbalance is the compromised function of cell‐wall invertases (CWINs), which are essential for providing nutrients, energy sources, and signaling molecules for plant growth, yield, and stress responses. CWINs are highly sensitive to heat stress and are typically downregulated under heat stress. RNA interference or loss of function of cell‐wall invertases LIN5, Mn1, and GIF1 produces stunted fruits and reduces yield in tomato (Zanor et al., 2009), maize (Cheng et al., 1996), and rice (Wang et al., 2008), respectively. In particular, heat stress rapidly represses CWIN expression and activity in reproductive organs, thereby reducing the conversion of imported sucrose into glucose and fructose, and causing carbon starvation in developing fruits and seeds (Li et al., 2012; Lou et al., 2025). The resulting shortage of carbon assimilates triggers selective abortion of grains or ovaries, and ultimately reduces yield. Furthermore, high temperatures affect phloem transport efficiency by altering callose deposition at sieve plates, reducing phloem sap flow, and accelerating sieve‑tube occlusion (Slewinski, 2012). In cereals like rice, heat stress downregulates the expression of sucrose transporters such as OsSUT1 during grain filling, further compromising sucrose unloading (Miyazaki et al., 2013; Kusano et al., 2025).
Despite efforts to enhance carbon partitioning via ectopic CWIN expression, these interventions frequently fail to improve yield and may even reduce it, empirically demonstrating that successful engineering requires a finely tuned source–sink balance. Recently, progress has demonstrated that engineering source–sink relations can effectively mitigate heat‑induced yield losses. Heat shock elements (HSEs) insertion through a prime‐editing system has been shown to endow CWINs with heat‐responsive upregulation without altering their spatial expression pattern in both controlled and field environments, enhancing carbon partitioning to grain and fruits, resulting in per‐plot yield increases of 25% in rice and 33% in tomato under heat stress without fruit quality loss (Lou et al., 2025). This strategy highlights the potential of fine‑tuning carbohydrate transport processes to create climate‑smart crops.
Beyond carbon metabolism, phytohormones such as ABA also contribute to thermal acclimation in plants. The majority of the ABA present in rice caryopses is transported from leaves, and this leaf‐to‐caryopsis ABA transport is regulated by a multidrug and toxic compound extrusion transporter in a temperature‐sensitive manner that functions to ensure normal seed development in response to variable temperatures (Qin et al., 2021). In addition, plant root systems are also affected by heat stress, which in turn influences the yield of crops. Heat stress restructures root architecture, leading to reduced primary root length, fewer lateral roots, and less root branching, which limits water and nutrient uptake (Kumar et al., 2025). Selection for ideal root traits represents an effective strategy to improve yield under abiotic stress. Single‐cell transcriptomes reveal that cortex size strongly correlates with heat tolerance in maize (Wang et al., 2025b). Furthermore, nitrogen retranslocation is coordinately regulated by two splice isoforms of OsNRT2.3. OsNRT2.3a (with a 42‑bp 5′UTR) is expressed in the root xylem and mediates long‑distance nitrate transport to shoots, whereas OsNRT2.3b (with a 247‑bp 5′UTR) is expressed in the shoot phloem and facilitates nitrate redistribution, pH buffering, and ion homeostasis. Under high nighttime temperatures, the HTNE‑2 haplotype maintains higher OsNRT2.3b protein levels via two SNPs that reduce the small RNA sNRT2.3‑1, which otherwise binds OsNRT2.3a mRNA to promote its repression. The resulting higher OsNRT2.3b/OsNRT2.3a ratio sustains nitrate transport and pH buffering, improving nitrogen uptake and grain yield in a temperature‑dependent manner (Zhang et al., 2022c).
HEAT SIGNAL PERCEPTION AND TRANSDUCTION
Heat stress sensing and early signaling
The mechanisms by which plants perceive high‐temperature signals remain largely elusive, although several thermosensors have been identified in the model plant Arabidopsis thaliana (Kan et al., 2023; Yadav et al., 2025). These thermosensors can be roughly divided into those that detect mild temperature elevation to drive thermomorphogenesis (Jung et al., 2016, 2021; Chung et al., 2020; Zhang et al., 2021a) and those that respond to acute heat stress, often via protein liquid–liquid phase separation (LLPS). In Arabidopsis, for instance, the intrinsically disordered protein FuSang Tree1 (FUST1) directly senses heat and promotes stress granule assembly; its loss delays granule formation and impairs both basal and acquired heat tolerance (Geng et al., 2025). Similarly, THERMO‐WITH ABA‐RESPONSE1 (TWA1) undergoes conformational changes at high temperatures, enabling interaction with JASMONATE‐ASSOCIATED MYC‐LIKE (JAM) transcription factors, TOPLESS (TPL), and TOPLESS‐RELATED (TPR) proteins to form a transcriptional repressor complex essential for thermotolerance (Bohn et al., 2024). Additionally, heat shock transcription factor 1b (Hsf1b) has been reported to moonlight as an adenylate cyclase that perceives heat and modulates stomatal closure (Zhang et al., 2025d). In crop plants, thermosensors are much less understood. Rice E3 ligase TT3.1 is implicated as a potential heat sensor: Under perceiving heat stress, it translocates from the plasma membrane to endosomes, where it ubiquitinates TT3.2 for vacuolar degradation, thereby protecting chloroplasts and enhancing heat tolerance (Zhang et al., 2022a).
Membrane lipids also play a pivotal role in early heat signaling. High temperature can alter the fluidity and permeability of cellular phospholipid membranes, triggering rapid cytosolic Ca2+ increases that activate downstream heat‐responsive gene expression. In tobacco, trienoic fatty acids enhance chloroplast membrane fluidity in plants grown under low‐temperature conditions, while silencing ω‐3 desaturase to suppress their accumulation improves thermotolerance (Murakami et al., 2000). In rice, Ca2+ channels including CYCLIC NUCLEOTIDE‐GATED ION CHANNELs (CNGCs) and Ca2+‐permeable transporters annexins (ANNs) help regulate Ca2+ dynamics, while TT2 is required for heat‐triggered activation of Calmodulin 2 (CaM2) and inhibition of calmodulin‐binding transcriptional activators SCT1 (Sensing Ca2+ Transcription Factor 1) and SCT2 (Kan et al., 2022), underscoring the critical role of Ca2+ influx in heat stress signaling in crops. Reactive oxygen species (ROS), including 1O2, O2 −, H2O2, and OH−, also act as early signaling molecules that regulate downstream gene expression to aid plant heat acclimation (Mittler et al., 2022). Under heat stress, ROS accumulate notably in chloroplasts, mitochondria, and at the plasma membrane, leading to oxidative membrane and protein denaturation. The NAC transcription factor SNAC3 confers heat and drought tolerance in rice by activating genes encoding H2O2‐scavenging enzymes (Fang et al., 2015), highlighting the importance of ROS homeostasis under thermal stress. Nitric oxide (NO), a key reactive nitrogen species, is also involved in plant adaptation to both biotic and abiotic stresses, though its specific signaling role in crops remains unclear (Sarma et al., 2025). Phosphoinositide‐specific phospholipases C (PLCs) are important for phosphoinositide (PI) signaling and G protein‐coupled receptor‐mediated transduction. Overexpressing AtPLC9 in rice improves heat tolerance and affects the expression of Ca2+‐related signaling genes (Liu et al., 2020b). Additionally, HIGH TEMPERATURE SENSITIVE 1 (HTS1), a thylakoid membrane‐localized β‐ketoacyl carrier protein reductase, is required for de novo fatty acid biosynthesis, lipid metabolism, and heat stress signaling in rice, thereby maintaining membrane stability and chloroplast integrity under high temperatures (Chen et al., 2021). Heat stress also induces cell membrane lipid remodeling. The plasma membrane‐localized diacylglycerol kinase 7 (DGK7) converts diacylglycerol into phosphatidic acid (PA), which binds and activates metal‐dependent phosphodiesterase (MdPDE1), promoting its nuclear translocation to degrade cyclic adenosine monophosphate (cAMP), thereby transducing heat signal into the nucleus and driving transcriptional reprogramming to enhance heat tolerance (Kan et al., 2025; Figure 2). In Arabidopsis, the malectin‐like receptor kinase FERONIA forms sterol‐rich nanoclusters on the plasma membrane to activate heat shock transcription‐mediated downstream signaling (Wang et al., 2026).
Figure 2.
Molecular networks of heat stress responses in crops
Research has identified numerous heat‐responsive genes in crops, with rice being a primary model. These genes encode components across the cell membrane, nucleus, and organelles, each contributing to thermotolerance. Putative core sensors (e.g., TT3.1), key integrative nodes (ROS, Ca2+, and hormones such as ABA and GA), and the broadly conserved HSF–HSP chaperone axis are central to crop thermotolerance. Heat stress activates a coordinated cellular defense network, beginning with signal perception via (1) Calcium‐mediated pathways (e.g., CNGC14/16 and ANN1); (2) A plasma membrane ROS burst (generated by Rbohs); and (3) Signaling peptides such as GhRALF30L. These signals are potentially perceived by components including TT3.1, heterotrimeric G proteins, OsREM1.5, and OsNTL3, initiating downstream adaptive responses. The systemic defense program integrates interconnected modules: (i) Organelle and protein homeostasis (chaperone‐assisted protein folding, ubiquitin‐proteasome degradation); (ii) Metabolic and structural adaptation (lipid/wax biosynthesis for membrane remodeling, water retention, and chloroplast stabilization); and (iii) Transcriptional and post‐transcriptional reprogramming (transcription factor‐driven antioxidant induction, RNA processing for stability). Arrows and barred lines indicate positive and negative regulation, respectively; dashed lines denote indirect regulation or putative pathways.
Signal cascades and subcellular translocation
A transient cytosolic Ca2+ influx from the extracellular space to the cytosol is recognized as an early event in HSR. As a second messenger, Ca2+ is perceived by calcium sensor proteins, enabling rapid transduction of external heat signals into the cell. Calmodulin (CaM), a Ca2+‐binding protein, plays a central role in transducing heat stress signals in plants (Zhang et al., 2009). In particular, CaM3 interacts with calmodulin‐binding protein kinase 3 (CBK3) and protein phosphatase 7 (PP7), which, respectively, promote phosphorylation and dephosphorylation of HSFA1. Disruption of either CBK3 or PP7 leads to a thermosensitive phenotype (Liu et al., 2008). In rice, heat‐induced cytosolic Ca2+ elevation activates sensors including calmodulin (OsCaM1‐1) and calcium‐dependent protein kinases (CDPKs) such as OsCDPK25/OsCPK25. OsCaM1‐1 overexpression enhances thermotolerance and upregulates CBK3, PP7, HSFs, and HSPs, while CDPKs sense Ca2+ via their EF‐hand domain and transduce signals via kinase domains, with their heat‐induced upregulation implicating them in thermotolerance (Wan et al., 2007; Wu et al., 2012, 2018). Heat‐induced chloroplast, mitochondrial, and plasma membrane damage triggers ROS overaccumulation, which functions as secondary messengers (Li et al., 2018a; Xu et al., 2021). H2O2 directly activates HSFA1a and promotes HSP promoter binding (Liu et al., 2013b). ROS also activates mitogen‐activated protein kinases (MAPKs) that phosphorylate HSFs: MAPK6 phosphorylates HSFA2 at Thr249 to facilitate the HS‐induced nuclear accumulation (Evrard et al., 2013), while MAPK3 and MAPK6 phosphorylate HSFA4a at Ser309 to mitigate oxidative damage by heat (Andrási et al., 2019). In rice, heat stress induces H2O2 overproduction and upregulates annexin OsANN1, which enhances thermotolerance by boosting SOD and CAT activities through interaction with OsCDPK, suggesting crosstalk between ROS and Ca2+ signals in HSR (Qiao et al., 2015).
Beyond ionic and redox signaling, heat stress triggers the nuclear import of certain NAC transcription factors via proteolytic release from membrane anchors or phosphorylation‑dependent mechanisms, positioning this process as a key regulatory mechanism in crop high‑temperature responses (Liu et al., 2020a). In rice, membrane‐anchored OsNTL3 undergoes proteolytic cleavage and translocates from the plasma membrane to the nucleus upon heat or ER stress, activating downstream thermotolerance genes via direct binding to the OsbZIP74 promoter (Liu et al., 2020a). Additionally, heat‐ and drought‐induced dephosphorylation of OsREM1.5 facilitates ONAC023 nuclear import through importin‐α, where ONAC023 regulates redox homeostasis, water transport, and alternative splicing to enhance stress resilience (Chang et al., 2024; Figure 2).
Heat stress also triggers subcellular relocalization of other signaling proteins. TT3.1 translocates from the plasma membrane to endosomes, where it ubiquitinates TT3.2 for vacuolar degradation, protecting chloroplast stability (Zhang et al., 2022a). ZmCDPK7 detaches from the membrane to the cytosol in a duration‐dependent manner, participating in ABA signaling and thermotolerance via phosphorylation of sHSP17.4 and RBOHB (Zhao et al., 2021). In wheat, heat‐inhibited phosphorylation of TaBZR2 by TaSERL2 allows non‐phosphorylated TaBZR2 to accumulate and translocate from the cytoplasm to the nucleus, promoting heat tolerance (Hao et al., 2025; Figure 2).
Accumulating evidence indicates that phase separation plays a critical role in regulating heat tolerance in crops. For example, in maize, ZmCTU2 acts as a stress granule scaffold protein, recruiting ZmPOX and ZmCTU1 into stress granules. This ensures proper tRNA modification to prevent protein misfolding while stabilizing antioxidant enzymes to scavenge ROS, thereby reducing oxidative damage, maintaining redox homeostasis, and ultimately enhancing heat tolerance (Xu et al., 2026). Certain splicing cofactors also promote the correct splicing of their target genes through phase separation under heat stress. In rice, the splicing auxiliary factor OsU2AF35a undergoes LLPS via its C‑terminal intrinsically disordered region (IDR) to form nuclear condensates, which facilitate its nuclear accumulation and promote accurate splicing of the Oshsa32 pre‐mRNA, thereby enhancing heat tolerance (Liu et al., 2025a; Figure 2).
Organellar responses to heat stress
Chloroplasts are highly sensitive to heat stress (Hu et al., 2020). They possess an independent genome encoding primarily ribosomal proteins and core components of the photosynthetic apparatus (Zhang et al., 2023b). Under elevated temperatures, protein aggregation and denaturation frequently occur, with PSII being a primary target of thermal damage (Momcilovic and Ristic, 2006; Allakhverdiev et al., 2008). The consequent inhibition of plastid translation can trigger retrograde signaling, leading to the downregulation of nuclear‐encoded photosynthetic genes (Sugimoto et al., 2004; Qiu et al., 2018; Li et al., 2018c). One effective strategy is to ensure an adequate supply of PSII proteins, such as the D1 subunit, which increases thermotolerance and grain yield in rice (Chen et al., 2020). Retrograde signaling from chloroplasts to the nucleus plays a central role in regulating nuclear gene expression during stress (Gao et al., 2023). Chloroplast ribosomal protein S1 (RPS1), a heat‐responsive protein, plays a key role in retrograde signaling during heat stress. Mutations in rps1 and Rabe1b disrupt the induction of nuclear heat‐responsive genes governed by HSFA2 (Yu et al., 2012). Since most chloroplast proteins are nuclear‐encoded and imported from the cytosol, proper organelle function requires coordinated homeostasis. For example, heat stress‐induced TT3.2 accumulation contributes to chloroplast damage, although the underlying mechanism remains to be fully elucidated (Zhang et al., 2022a). Therefore, chloroplast protein quality control is essential for plant heat stress responses. Damaged proteins in chloroplasts are rapidly degraded to maintain photosynthesis (Ling et al., 2019). Heat stress also induces expression of protective chaperones that are essential for thermotolerance, chloroplast development, and photosynthetic maintenance (Park et al., 2016; Kang et al., 2017). For instance, chloroplast‐localized small heat shock proteins such as sHSP26 improved chloroplast performance under heat stress in wheat and maize by interacting with specific proteins that help sustain photosynthetic function (Chauhan et al., 2012; Hu et al., 2015).
Mitochondria serve as essential energy hubs in plant cells, supporting critical developmental processes such as spikelet formation under heat stress (Wang et al., 2025a). In maize, the mitochondrial ATP‐dependent metalloprotease ZmFTSH10 maintains reproductive meristem activity by preserving redox balance and auxin homeostasis, thereby ensuring organogenesis under high‐temperature conditions (Liu et al., 2019). Cellular lipid homeostasis, particularly within mitochondria, is also critical for thermal adaptation. For instance, EXTRA GLUME 1 (EG1), which encodes a mitochondria‐localized lipase, promotes floral robustness under fluctuating temperatures by protecting floral identity gene expression via a temperature‐responsive lipid pathway (Zhang et al., 2016). Additionally, elevated temperature induces the accumulation of mitochondrial small heat shock proteins (15–30 kDa) (Banzet et al., 1998; Lund et al., 1998). sHSPs protect respiratory complexes, particularly Complex I (the most heat‐sensitive component), against thermal denaturation and proteolytic degradation (Downs and Heckathorn, 1998; Figure 2).
HEAT STRESS RESPONSES IN CROPS
Key genes for heat tolerance
Over the past two decades, significant progress has been made in deciphering the molecular mechanisms underlying plant responses to extreme temperatures, particularly in the model plant Arabidopsis thaliana, spanning processes from signal perception, transduction, and transcriptional regulation (Zhang et al., 2022e; Kan et al., 2023). In contrast, heat tolerance in crops is typically a quantitative trait governed by complex genetic networks that remain poorly understood (Xu et al., 2021; Kan et al., 2023; Xiong et al., 2025). Although numerous quantitative trait loci (QTLs) associated with thermotolerance across seedling and reproductive stages have been reported, only a limited number of causal genes have been successfully cloned and functionally validated to date (Xu et al., 2021; Xiong et al., 2025). Forward and reverse genetic approaches have uncovered several key heat stress‐related genes; yet, the repertoire of well‐characterized genes remains scarce, particularly in soybean and cotton. Indeed, functional genetic studies show a marked disparity among crops: Approximately 150 genes in rice, around 50–65 in maize, wheat, and tomato, but fewer than 10 in soybean and cotton (Table 1). A deeper mechanistic understanding of thermotolerance in crops is therefore still needed. To clarify the regulatory logic of the heat stress response network, we have classified the genes listed in Table 1 into six functional categories based on their hierarchical positions within the signaling and response cascade (Table 1). Primary sensors (e.g., TT3.1) directly perceive temperature increases; for example, TT3.1 perceives temperature and promotes TT3.2 degradation to protect chloroplasts. Signal transducers (e.g., TT2, ZmCDPK7, MAPKs, and E3 ligases) relay and amplify the signal. Central regulatory nodes (e.g., HSFs, NACs, WRKYs, NAT1, and bZIPs) orchestrate downstream gene expression programs and serve as master switches; for example, NAT1 negatively regulates bHLH110, which in turn activates CER1/CER1L for wax biosynthesis. Effector proteins (e.g., HSPs, chaperones, proteases, and antioxidant enzymes) directly execute protective functions. Metabolic modifiers (e.g., ATT1/2, CER1, CWINs, and GA20‐oxidases) remodel metabolic pathways to enhance stress adaptation. Post‐transcriptional/epigenetic regulators (e.g., miRNAs, RNA methyltransferases, histone modifiers, and splicing factors) fine‐tune gene expression at the RNA and chromatin levels. This hierarchical framework reveals that upstream sensors and central regulatory nodes are particularly attractive targets for engineering heat‐resilient crops, as they orchestrate broader adaptive responses.
Table 1.
Key genes regulating heat tolerance in major crops (rice, maize, wheat, tomato, soybean, and cotton)
| Gene | Functional description | Subcellular localization | Functional classification | Functional stages | Multiple stress tolerance | References |
|---|---|---|---|---|---|---|
| Rice | ||||||
| ATT1&2 * | GA20‐oxidase | Cytoplasm | Metabolic modifier | Seedling, grain filling | Saline‐alkali | Guo et al. (2025a) |
| DGK7 * | Diacylglycerol kinase 7 | Cell membrane | Signal transducer | Seedling, grain filling | — | Kan et al. (2025) |
| NAT1 * | C2H2 family transcription factor | Nucleus | Central regulatory node | Seedling, grain filling | — | Lu et al. (2025) |
| OsU2AF35a * | U2 snRNP auxiliary factor small subunit | Nucleus (phase separation) | Post‐transcriptional regulator | Seedling, grain filling | — | Liu et al. (2025a) |
| QT12 * | Sec. 61 translocon β subunit | Endoplasmic reticulum | Signal transducer | Seedling, grain filling | — | Li et al. (2025b) |
| GIF1 * | Cell wall invertase | Cell wall | Metabolic modifier | Reproductive stages | Biotic stress and saline‐alkali | |
| OsPRMT6b | Arginine methyltransferase 6b | Nucleus | Post‐transcriptional regulator | Seedling | — | Jin et al. (2025) |
| HsfA1 | Heat shock transcription factor | Nucleus | Central regulatory node | Seedling | Biotic stress | Qiu et al. (2025a) |
| OsCNGC14&15&16 | Cyclic nucleotide‐gated channel proteins | Cell membrane | Signal transducer | Seedling | Drought and cold | Luo et al. (2025) |
| HTT1 | Stearoyl‐acyl carrier protein desaturase | Chloroplasts | Metabolic modifier | Seedling | — | Zhang et al. (2025c) |
| OsHsfA4d | Heat shock transcription factor | Nucleus, cytoplasm | Central regulatory node | Seedling | Biotic stress | Fang et al. (2025b) |
| OsNAC023 * | NAC transcription factor | Nucleus, cytoplasm (stress‐induced nuclear import) | Central regulatory node | Seedling, grain filling | Drought | Chang et al. (2024) |
| RMI1 | A component of the RTR complex | Nucleus | Effector protein | Seedling, grain filling | — | Liu et al. (2024) |
| OsPRMT6a | Protein arginine methyltransferases | Nucleus | Post‐transcriptional regulator | Reproductive stages | — | Dong et al. (2024) |
| HDA714 | Histone deacetylase | Cytoplasm, stress granules | Epigenetic regulator | Seedling | — | Chen et al. (2024) |
| OsSGS3a | SUPPRESSOR OF GENE SILENCING 3 | Cytoplasmic granules | Post‐transcriptional regulator | Seedling, grain filling | Biotic stress | Gu et al. (2023) |
| OsEDS1 * | Immune activator | Nucleus, cytoplasm | Signal transducer | Seedling, grain filling | Biotic stress | |
| TTL1 * | Encode a C4HC3‐type RING‐v domain and a DUF3675 domain | Nucleus, cell membrane | Central regulatory node | Seedling, grain filling | — | Lin et al. (2023) |
| TT3.1 * | RING‐type E3 ligase | Plasma membrane → endosomes | Primary sensor | Seedling, grain filling | — | Zhang et al. (2022a) |
| TT3.2 * | Unknown transmembrane protein | Chloroplasts | Effector protein | Seedling, grain filling | — | |
| TT2 * | Gγ subunit | Cytoplasm | Signal transducer | Seedling, grain filling | — | Kan et al. (2022) |
| HTG3 (HSF2d) | Heat shock factor2d | Nucleus | Central regulatory node | Seedling, reproductive stages | — | Wu et al. (2022b) |
| OsMS1 | Histone binding protein | Nucleus, cytoplasm | Central regulatory node | Grain filling | — | Wu et al. (2022a) |
| HTH5 * | Pyridoxal phosphate‐binding protein | Mitochondrion | Effector protein | Grain filling | — | Cao et al. (2022) |
| OsNRT2.3 * | Nitrate transporter | Cell membrane | Metabolic modifier | Grain filling | — | Zhang et al. (2022c) |
| HTS1 | β‐ketoacyl carrier protein reductase | Chloroplasts | Metabolic modifier | Seedling | — | Chen et al. (2021) |
| SLG1 * | Cytosolic tRNA 2‐thiolation protein 2 | Unknown | Effector protein | Seedling, reproductive stages | — | Xu et al. (2020b) |
| OsbZIP58 * | bZIP transcription factor | Unknown | Central regulatory node | Grain filling | — | Xu et al. (2020a) |
| OsNTL3 | NAC transcription factor | Plasma membrane to nucleus | Signal transducer | Seedling | — | Liu et al. (2020a) |
| OsNSUN2 | RNA 5‐methylcytosine methyltransferase | Nucleus | Post‐transcriptional regulator | Seedling | Salt | |
| LS1 | A subunit of the RNase H2 complex | Nucleus | Effector protein | Seedling | Light | Qiu et al. (2019) |
| OsHTAS | RING Finger Ubiquitin E3 Ligase | Nucleus, cytoplasm | Metabolic modifier | Seedling | Drought and salt | Liu et al. (2016) |
| TT1 * | α2 subunit of the 26S proteasome | Cytoplasm | Effector protein | Seedling, grain filling | — | Li et al. (2015) |
| SNAC3 | NAC transcription factor | Nucleus | Central regulatory node | Seedling, grain filling | Drought and arsenic | |
| OsANN1 | Annexin protein | Cell periphery, cytoplasm | Signal transducer | Seedling | Drought and biotic stress | |
| OsHsp70CP1 | Heat shock protein 70 | Chloroplast stroma | Effector protein | Seedling | — | Kim and An (2013) |
| OsWRKY11 | WRKY transcription factor | Unknown | Central regulatory node | Seedling | Drought and biotic stress | |
| Maize | ||||||
| ZmATG8c * | AuTophaGy‐related 8 protein | Autophagosome | Effector protein | Vegetative, reproductive stages | — | Ma et al. (2025) |
| ZmHSFA2d | Heat shock transcription factor | Nucleus | Central regulatory node | Seedling | Drought | Cao et al. (2025) |
| ZmHSF12 | Heat shock factor12 | Nucleus | Central regulatory node | Seedling | — | Qi et al. (2025) |
| ZmHSFA2B | Heat shock transcription factor | Nucleus | Central regulatory node | Seedling | — | Song et al. (2025) |
| ZmHSF20 | Heat shock factor20 | Nucleus | Central regulatory node | Seedling | — | Li et al. (2024b) |
| ZmMPK20 | MAP kinase | Nucleus, cytoplasm | Signal transducer | Seedling, reproductive stages | — | Cheng et al. (2023) |
| HSP101 | Heat shock protein | Membrane, nucleus, cytoplasm | Effector protein | Reproductive stages | — | Li et al. (2022) |
| ZmCDPK7 | Calcium‐dependent protein kinases | Membrane to cytoplasm | Signal transducer | Seedling | — | Zhao et al. (2021) |
| ZmRPP13‐LK3 | RPP13‐like protein 3 | Mitochondrion | Signal transducer | Seedling | — | Yang et al. (2021a) |
| NUT1 | NAC transcription factor | Nucleus | Central regulatory node | Reproductive stages | Drought | Dong et al. (2020) |
| bZIP60 | bZIP transcription factor | Nucleus | Central regulatory node | Seedling | Drought and salt | |
| ZmFTSH10 | ATP‐dependent metalloprotease | Mitochondrion | Effector protein | Reproductive stages | — | Liu et al. (2019) |
| Wheat | ||||||
| TaHsfA2h * | Heat shock transcription factor | Nucleus | Central regulatory node | Seedling, grain filling | — | Wei et al. (2025) |
| TaFAD8‐D * | Fatty acid desaturase 8 | Chloroplasts | Metabolic modifier | Seedling, grain filling | — | Yu et al. (2025) |
| TaIRE1 | Inositol‐requiring enzyme 1 | Endoplasmic reticulum | Signal transducer | Seedling, grain filling | — | Li et al. (2025a) |
| TaBZR2 * | Brassinazole‐resistant transcription factors | Cytoplasm to nucleus | Signal transducer | Grain filling | — | Hao et al. (2025) |
| TaHSP90 | Heat shock protein 90 | Membrane, cytoplasm | Effector protein | Seedling | — | Wang et al. (2025c) |
| TaSG‐D1 | STKc_GSK3 kinase | Cytoplasm, nucleus | Signal transducer | Seedling, grain filling | — | Cao et al. (2024) |
| TaHSFA6e | Heat shock transcription factor | Nucleus | Central regulatory node | Seedling | — | Wen et al. (2023) |
| TaHsfA1 | Heat shock transcription factor | Nucleus | Central regulatory node | Seedling | — | Wang et al. (2023a) |
| HvMADS1 | SEPALLATA MADS‐box protein | Unknown | Central regulatory node | Reproductive stages | — | Li et al. (2021b) |
| Tomato | ||||||
| LIN5 * | Cell wall invertase | Cell wall | Metabolic modifier | Reproductive stages | — | Lou et al. (2025) |
| SlJA2L | NAC transcription factor | Nucleus | Central regulatory node | Seedling, fruit ripening | — | Liang et al. (2025) |
| TMF * | A prion‐like transcription repressor | Nucleus | Central regulatory node | Reproductive stages | — | Huang et al. (2025a) |
| BAG5b | Bcl‐2‐associated athanogene proteins | Unknown | Effector protein | Seedling | — | He et al. (2025b) |
| SlHSFB2b | Heat shock factor B2b | Unknown | Central regulatory node | Seedling | Light | He et al. (2025a) |
| MiR164a | MicroRNA164a | Unknown | Post‐transcriptional regulator | Seedling | — | Huang et al. (2025b) |
| SlWRKY55 | WRKY transcription factor | Nucleus | Central regulatory node | Seedling | — | Ma et al. (2024) |
| HSFA1a | Heat shock transcription factor | Nucleus | Central regulatory node | Seedling | Cadmium | |
| CPK28 | Calcium‐dependent protein kinases | Unknown | Signal transducer | Seedling | — | Hu et al. (2021) |
| SmHSFA8 | Heat shock factor | Unknown | Central regulatory node | Seedling | — | Liu et al. (2025b) |
| Soybean | ||||||
| GmBSK1 * | Brassinosteroid‐signaling kinase 1 | unknown | Signal transducer | Seedling, maturation period | — | Hou et al. (2025) |
| GmDIS1 | SINA E3 ligase | Unknown | Signal transducer | Seedling | Drought | Tiwari et al. (2025) |
| MiR156b | MicroRNA156b | Unknown | Post‐transcriptional regulator | Seedling | — | Ding et al. (2023) |
| GmEF8 | Elongation factor Tu family protein | Cytoplasm, nucleus | Effector protein | Seedling | Drought | Zhang et al. (2022b) |
| GmHsp90A2 | Heat shock protein 90 s | Plasma membrane, cytoplasm | Effector protein | Seedling | — | Huang et al. (2019) |
| Cotton | ||||||
| GhCKI * | Casein Kinase I | Unknown | Signal transducer | Reproductive stages | — | Li et al. (2025c) |
| GhRALF30L | An intrinsically disordered small peptide | Extracellular | Signal transducer | Reproductive stages | — | Zhang et al. (2025b) |
Superior genes that enhance heat tolerance without yield penalty are indicated by an asterisk.
Heat shock transcription factors (HSFs)
Hsfs function as primary regulators of plant responses to heat stress, modulating both basal and acquired thermotolerance in plants. They activate transcriptional cascades that drive the expression of genes involved in heat shock response (HSR), including those encoding ROS scavenging enzymes, metabolic enzymes, and heat shock proteins (HSPs) (Gong et al., 2020). HSFs have been functionally characterized across diverse plant species, such as Arabidopsis, tomato, wheat, soybean, cotton, rice, and maize (Andrási et al., 2021). Plant HSFs are encoded by large gene families, showing significant diversity in their expression patterns and functions. They are grouped into classes A, B, and C. Each shows modular structural features comprising several conserved domains: Class A HSFs possess C‐terminal activator motifs essential for transcriptional activation (e.g., AHA motif); class B members carry a conserved LFGV tetrapeptide repressor domain, while the function of class C HSFs remains unclear (Guo et al., 2016). The HSF family shows strong diversification of expression patterns and functions within the HSF family. HSFA1 serves as a central regulator, inducing the expression of other HSF genes, such as HSFA2, HSFA3, HSFA7A/B, and HSFB1/2 A/2B, and directly activating DREB2A (Andrási et al., 2021). Heat‐induced HSFA2 and HSFA3 enhance responses to heat and other stresses. In tomato, HSFA2 is required for the expression of HSFA1‐controlled genes and promotes thermotolerance (Mishra et al., 2002). Overexpression of HSFA2/A3 improved thermotolerance in Arabidopsis, while hsfa2 and hsfa3 mutants were hypersensitive to high temperatures (Banti et al., 2010). In wheat, heat tolerance was enhanced by overexpression of TaHsfA2h and compromised by RNA interference (Wei et al., 2025), underscoring the critical role of these transcription factors in heat stress adaptation.
In contrast, class B HSFs typically repress heat shock responses. HSFB1 and HSFB2B suppress multiple class A HSFs and several HSP genes, and yet, still support acquired thermotolerance (Ikeda et al., 2011; Andrási et al., 2021). Tomato HSFB1 serves dual regulatory functions under heat stress. It acts as a co‐activator of HsfA1a for certain heat shock protein genes while exerting transcriptional repression on other Hsfs, including HsfA1b and HsfA2. This bifunctional nature enables HSFB1 to activate chaperones to enhance protection while modulating the balance between growth and stress responses, depending on its homeostatic levels (Fragkostefanakis et al., 2019). In thermotolerant tomato cultivars, reduced HSFB4a expression and elevated HSFA7 levels govern downstream heat stress‐responsive genes to confer thermotolerance (Rao et al., 2022a). In maize, ZmHSFA2B produces two splicing variants: the full‐length ZmHSFA2B‐I and a truncated ZmHSFA2B‐II. Overexpression of ZmHSFA2B‐I improved heat tolerance in maize and Arabidopsis, but caused growth retardation. Further studies showed that ZmHSFA2B‐II attenuates the transactivation activity of ZmHSFA2B‐I, reducing the adverse effects of its overaccumulation. This indicates that alternative splicing of ZmHSFA2B forms a self‐regulatory loop fine‐tuning the heat stress response in maize (Song et al., 2025).
Other transcription factors in heat stress response
Beyond Hsfs, other transcription factor (TF) families, including MYB, ERF, BBX, MBF1, WRKY, and NAC, also regulate plant responses to heat stress (Wu et al., 2009; El‐Kereamy et al., 2012; Qin et al., 2015; Wang et al., 2018; Park et al., 2021; Bandara et al., 2022; Tian et al., 2022; Chang et al., 2024; Ma et al., 2024; Wang and Zhan, 2024; Liang et al., 2025; Zhu et al., 2025a; Zhao et al., 2025b). MYB transcription factors contribute significantly to thermotolerance; for example, ZmMYB104 regulates cuticle permeability under heat stress and influences high‐temperature tolerance in maize by modulating the downstream gene ZmCAT2 (Zhang et al., 2025a), while tomato SlMYB41 enhances thermotolerance through activation of SlHSP90.3 (Wang et al., 2023b). Among AP2/EREBP family members, OsERF115/AP2EREBP110, classified into Group‐IIIc, is strongly induced by heat and drought in rice. Its overexpression improves thermotolerance in seeds and vegetative tissues, accompanied by increased expression of the proline biosynthesis gene P5CS1, alongside water‐saving traits under the combined stress of heat and drought (Park et al., 2021). Similarly, SlBBX17 overexpression in tomato increases heat tolerance, as reflected by improved membrane stability, higher antioxidant enzyme activities, and reduced ROS accumulation (Xu et al., 2022).
MULTIPROTEIN BRIDGING FACTOR 1 (MBF1) acts as a typical transcriptional coactivator that mediates gene activation by physically bridging TFs, thereby regulating diverse developmental processes across various organisms. In plants, MBF1 functions as a critical regulator of heat stress responses and thermotolerance. In Arabidopsis, knockout of AtMBF1c significantly reduces heat tolerance, while its overexpression enhances seedling survival under heat treatment (Suzuki et al., 2008). The wheat gene TaMBF1c is heat‐induced, and its knockdown and knockout increase heat sensitivity and affect heat shock protein translation (Tian et al., 2022), while its overexpression confers heat tolerance to rice and yeast (Qin et al., 2015).
WRKY TFs are involved in both biotic and abiotic stress responses. In rice, WRKY10 is induced by multiple stresses, and its role in disease resistance has been established. WRKY10 overexpression leads to ROS accumulation, elevates the expression of NAC4, OxO4, and SGR, and causes thermosensitivity, whereas its mutation improves thermotolerance. VQ8 interacts with WRKY10, suppresses its DNA‐binding activity, and positively regulates HSRs (Chen et al., 2022a). In tomato, SlWRKY55 cooperates with SlVQ11 to activate SlHsfA2 and enhance thermotolerance (Ma et al., 2024). Overexpression of ZmWRKY106 improves heat and drought tolerance in Arabidopsis via ABA‐mediated regulation of stress‐related genes and enhanced superoxide dismutase (SOD), peroxidase dismutase (POD), and catalase (CAT) activities (Wang et al., 2018).
NAC TFs form a large, conserved family essential for heat stress adaptation. Overexpression of ZmNAC074 in Arabidopsis enhances thermotolerance by modulating stress metabolites, including ROS, antioxidants, malondialdehyde (MDA), proline, soluble protein, chlorophyll, and carotenoids (Xi et al., 2022). In tomato, SlJA2L integrates ethylene signaling to co‐regulate thermotolerance and fruit ripening via the SlJA2L–SlACO1 module and SlCRTISO activation for carotenoid accumulation, thus mediating ethylene's positive effect on heat tolerance (Liang et al., 2025). Other NAC members in rice, including SNAC3 and OsNAC006, contribute to heat and drought tolerance through ROS regulation (Fang et al., 2015; Wang et al., 2020a). Notably, heat‐induced nuclear translocation of NAC TFs—exemplified by OsNTL3 (Liu et al., 2020a) and ONAC023 (Chang et al., 2024)—is discussed in detail in the “Signal cascades and subcellular translocation” section.
The C2H2 family transcription factor NAT1 regulates wax biosynthesis and forms the NAT1–bHLH110–CER1/CER1L module for enhanced rice thermotolerance. NAT1 represses bHLH110 activity, inhibiting wax synthesis, while bHLH110 directly activates OsWR2 expression, establishing wax deposition as a crucial thermotolerance mechanism (Kan et al., 2022; Lu et al., 2025; Sonkar and Singh, 2025).
MicroRNA‐mediated regulation
MicroRNAs (miRNAs) are ubiquitous regulatory molecules that negatively modulate gene expression at the post‐transcriptional level, either by directing mRNA cleavage or by inhibiting translation, depending on the degree of complementarity with their target sequences (Zhang, 2015). Accumulating transgenic evidence underscores the vital role of miRNAs in plant abiotic stress tolerance. For instance, miR444b.2, a temperature‐responsive miRNA in rice, directly suppresses HsfA1 expression by targeting its second exon. Under heat stress, suppression of miR444b.2 expression releases HsfA1 from repression to enhance blast resistance (Qiu et al., 2025a). In wheat, TaIRE1 promotes heat stress tolerance through unconventional splicing of membrane‐localized TabZIP60 mRNA to generate nuclear‐localized TabZIP60s protein and mis‐cleavage of miR172 precursors (Li et al., 2025a). In tomato, miR164a responds rapidly to heat stress, while its target NO APICAL MERISTEM 3 (NAM3) displays a complementary expression pattern. Mutants deficient in miR164a/b‑5p and plants overexpressing NAM3 show heightened heat sensitivity, whereas lines with reduced NAM3 levels show improved heat tolerance (Huang et al., 2025b). Additionally, miR156b regulates male fertility in a cytoplasmic male sterility‐based restorer line of soybean under heat stress (Ding et al., 2023). The miR169 family, which participates in plant abiotic and biotic stress responses as well as developmental processes such as root architecture and nodulation, targets multiple Nuclear Factor‐YA (NF‐YA) genes. In Arabidopsis and tomato, miR169‐mediated downregulation of At‐NF‐YA2 and Sly‐NF‐YA9/10, respectively, enhances thermotolerance and influences HSF expression. Notably, NF‐YA transcriptionally modulates HSR genes, including HSFs, which in turn feed back control NF‑YA expression via miR169, forming a finely tuned regulatory loop (Rao et al., 2022b).
Key thermotolerance QTLs and their mechanisms
Several key QTLs conferring thermotolerance across rice developmental stages have been identified. Thermo‐tolerance 1 (TT1), the first cloned heat tolerance QTL in crops, encodes an α2 subunit of the 26S proteasome that degrades ubiquitinated denatured proteins. Its introduction into cultivated rice enhanced thermotolerance (Li et al., 2015). The SUMO‐conjugating enzyme SCE1, which interacts with TT1, acts as a negative regulator; reducing SCE1 levels significantly enhanced grain yield under high‐temperature stress by improving the seed‐setting rate and rice grain filling (Yu et al., 2024). TT2 (GS3) encodes a G protein γ (Gγ) subunit that negatively regulates wax biosynthesis and thermotolerance in rice. Functional TT2 is required for heat‐triggered elevation of cytosolic Ca2+ levels, which suppresses the SCT1/SCT2‐OsWR2 pathway, reducing wax accumulation and thermotolerance. Natural loss‐of‐function TT2 alleles enhance wax deposition and heat tolerance (Kan et al., 2022; Zhang et al., 2023a). The TT3 genetic locus consists of TT3.1, a plasma membrane‐localized E3 ligase, and TT3.2, a chloroplast precursor protein. Upon perception of heat stress, TT3.1 translocates to endosomal compartments, ubiquitinating TT3.2 precursor for vacuolar degradation, thereby enhancing thermotolerance and reducing yield losses caused by heat stress (Zhang et al., 2022a). Furthermore, ALKALI‐THERMAL TOLERANCE 1/2 (ATT1/2), the QTLs encoding GA20 oxidases, improves alkali–thermal tolerance by fine‐tuning endogenous gibberellin (GA) levels to medium levels, showing potential for developing heat‐resilient rice varieties (Guo et al., 2025a). QT12, together with the NF‐Y transcription factor, constitutes a naturally occurring heat‐activated gene switch; natural variation in this system reduces rice sensitivity to high temperatures, preserves endosperm storage homeostasis, and thus maintains both grain quality and yield under hot field conditions (Li et al., 2025b). Unlike genes identified predominantly under controlled greenhouse conditions—which often impose yield penalties, depend on constant artificial heat stress, and lack validation under fluctuating field conditions—the alleles derived from adaptive natural variation offer fundamental advantages: Having been selected by natural selection, they typically do not cause yield reductions or result in only minor losses under normal field conditions; they confer stable heat tolerance, thereby mitigating yield losses under variable natural heat stress conditions in the field. Furthermore, these elite alleles can be directly introgressed into high‐yielding varieties through marker‐assisted selection, offering promising practical value for breeding heat‐tolerant rice.
Key regulators governing source–sink dynamics and grain quality under heat stress
Heat stress disrupts the source–sink balance, leading to inadequate energy supply in sink tissues, impaired reproductive development, and consequent yield loss (Pressman et al., 2002; Suwa et al., 2010). It rapidly inhibits carbon partitioning into sink tissues and triggers selective abortion of grains or ovaries, representing a major cause of yield reduction in cereal and fruit crops (Li et al., 2012; Liu et al., 2013a). Cell‐wall invertases (CWINs) are essential for supplying energy, nutrients, and signaling molecules to support growth, yield, and stress responses (Cheng et al., 1996; Wang et al., 2008). However, attempts to ectopically express CWINs for improved carbon allocation often lead to yield penalties, underscoring the need for precise regulation of source–sink relationships (Lou et al., 2025). As detailed in the “Disruption of source–sink transport under heat stress” section, the prime editing‐mediated insertion of a heat shock element into CWIN promoters (e.g., LIN5 in tomato and GIF1 in rice) has proven effective in enhancing carbon partitioning and mitigating heat‐induced yield losses (Lou et al., 2025). Grain chalkiness is a heat‐sensitive quantitative trait indicating quality deterioration (Yang et al., 2021b). QT12, as a key QTL, encodes a Sec. 61 translocon β subunit, which facilitates the co‐translational translocation of nascent peptides. Field trials revealed that QT12 negatively regulates quality thermotolerance by disrupting endosperm homeostasis via unfolded protein response (UPR) overactivation. An NF‐Y switch modulates QT12: High temperature weakens the NF–YB9/NF–YC10–NF–YA8 interaction to derepress QT12, whereas low QT12 expression improves quality and boosts elite rice yield under field heat stress (Li et al., 2025b).
High‐temperature tolerance and yield trade‐off
Achieving stable or increased crop yield under adverse environmental conditions is a long‐standing goal in crop science; yet, yield and stress tolerance are often negatively correlated. Notably, however, a positive correlation between heat tolerance and yield/quality traits has emerged from studies on several well‑characterized genes that simultaneously enhance both attributes. For example, the TT3.1–TT3.2 genetic module in rice enhances thermotolerance and increases grain yield under heat stress without yield penalty under normal conditions (Zhang et al., 2022a). In wheat, overexpression of TaHsfA2h or TaHsfC2a improves both heat tolerance and yield‐related traits such as 1,000‐grain weight and grain yield under heat stress (Wei et al., 2025). The CROCS strategy, which involves knocking a heat shock element into the promoters of cell‐wall invertase genes LIN5 (tomato) or GIF1 (rice), enhances carbon partitioning and increases yield under normal conditions while reducing heat‐induced yield losses (Lou et al., 2025). Fine‐tuning gibberellin levels via ATT2 in rice achieves moderate GA levels that simultaneously improve alkali–thermal tolerance and grain yield (Guo et al., 2025a). In soybean, GmBSK1 positively regulates heat tolerance and yield under heat stress (Hou et al., 2025). Overexpression of the autophagy gene ZmATG8c in maize increases grain yield under heat stress without compromising normal growth (Ma et al., 2025). Editing the negative regulator NAT1 in rice enhances wax biosynthesis and thermotolerance, leading to higher seed‐setting rates and grain yield under heat stress (Lu et al., 2025). Additionally, TTL1 simultaneously enhances thermotolerance and increases grain size in rice (Lin et al., 2023). Further exploration of this positive correlation mechanism holds great promise for developing climate‑resilient crops, thereby safeguarding food security in an era of global warming.
CROSSTALK BETWEEN HEAT STRESS AND OTHER STRESSES IN CROPS
As sessile organisms, plants not only face heat stress but also experience various other abiotic challenges (e.g., salinity, drought, flooding, and heavy metals) as well as biotic stresses (bacteria, fungi, nematodes, oomycetes, and herbivorous animals) (Ali et al., 2020; Poveda, 2021; Lv et al., 2026). Over the past decade, while significant progress has been made in deciphering plant responses to individual stresses, it is increasingly clear that these conditions rarely occur in isolation. In natural field environments, the interplay between heat stress and other adversities poses a severe threat to global crop productivity, especially in the context of climate change (Mittler, 2006; Suzuki et al., 2014). This section, therefore, synthesizes recent advances toward our understanding of plant adaptation to combined stresses, with a particular focus on the crosstalk between heat and abiotic stresses (e.g., drought and salinity) as well as heat and biotic stresses (Figure 3).
Figure 3.
Crosstalk between heat stress and other abiotic/biotic stresses in crops
Under natural field conditions, heat stress frequently co‐occurs with other biotic (e.g., pathogens) and abiotic (e.g., salinity and drought) stresses, creating combined stress effects that severely limit crop growth and productivity. Research in major crops has primarily focused on interactions such as heat–pathogen and heat–drought stress. Several regulatory factors responsive to multiple stresses have been identified. These include common regulators that function consistently across different stresses—exerting either positive (e.g., ATT2, ONAC023, and ZmWRKY106) or negative (e.g., TT2 and GmDIS1) effects, while others mediate trade‐off regulation between stress response pathways through antagonistic interactions (e.g., PWL1, OsHSFA4d, and OsSGS3a/b). Arrows and barred lines indicate positive and negative regulatory actions, respectively; dashed lines indicate indirect regulation or putative pathways.
Crosstalk with abiotic stresses
Heat and drought: A prevalent and damaging duo
The concurrence of high temperature and drought stress is perhaps the most common and detrimental stress combination in agriculture. These two stresses are intrinsically linked: high temperatures accelerate plant transpiration and soil water evaporation, thereby exacerbating drought conditions; conversely, drought‐induced stomatal closure compromises evaporative cooling, leading to a further increase in leaf surface temperature and intensifies the impact of heat (Zandalinas et al., 2018). The synergistic impact of this combination leads to more severe damage to crop yield than either stress alone. For instance, the reduction in individual grain weight of wheat under combined heat and drought stress can reach a staggering 43%–83%, far exceeding the 13%–27% reduction observed under drought stress alone (Mahrookashani et al., 2017).
The physiological basis for this yield penalty often lies in the collapse of photosynthetic systems. This is exemplified in sorghum, where sustained water loss under heat exposure precipitates a sharp increase in canopy temperature, causing severe damage to the PSII system (Pradhan et al., 2022). Similarly, maize hybrids facing the combined stress produce higher levels of ROS and malondialdehyde (MDA) than those exposed to a single stress, resulting in oxidative damage that reduces photosynthetic efficiency, limits nutrient uptake, and ultimately lowers yield (Hussain et al., 2019). A critical point of no return is often reached under combined stress; for example, tomato plants subjected to drought alone can fully recover their electron transport rate (ETR) and PSII efficiency (ΦPSII) after rewatering, whereas those exposed to combined heat and drought fail to do so, indicating irreversible damage (Zhou et al., 2019).
To cope with these challenges, plants have evolved integrated molecular mechanisms. Drought and heat stress signaling pathways share common regulatory elements and interact at multiple levels, enabling coordinated responses (Mittler et al., 2022). Several transcription factors and proteins have been reported to function under both drought and heat stress (Nishizawa et al., 2006; Li et al., 2020a), among which DREB2A has been extensively studied for its role in mediating crosstalk between drought and heat responses (Liu et al., 1998; Sakuma et al., 2006a, 2006b). In maize, the stress‐inducible splicing variant ZmDREB2A functions as a transcriptional activator that confers multi‐stress tolerance: It upregulates the expression of late embryogenesis abundant (LEA) and detoxification‐related genes for drought tolerance, while under heat stress, it can activate heat shock genes such as AtHsfA3 and subsequently downstream heat shock protein (HSP) genes (e.g., HSP70 and chloroplast‐small HSPs) to maintain protein homeostasis and promote heat tolerance (Sakuma et al., 2006a; Qin et al., 2007, 2008).
Beyond DREB2A, other transcriptional regulators have also been implicated in combined stress resilience. Overexpression of the rice OsMYB55 gene in maize significantly enhances tolerance to both heat and drought. Transcriptome analysis revealed that OsMYB55 upregulates a wide range of abiotic stress‐related genes, including those encoding heat shock proteins, lipid transfer proteins, and transcription factors from the MYB, WRKY, and AP2 families. These genes are involved in processes such as ROS scavenging, membrane protection, and stress signaling (Casaretto et al., 2016). Similarly, overexpression of the OsRab7 gene in rice improves performance under combined heat and drought stress by modulating osmolyte accumulation, ROS homeostasis, and the expression of stress‐responsive genes such as OsSOD‐Cu/Zn, OsAPX2, OsCATA, and OsCATB, ultimately contributing to higher grain yield under adverse conditions (El‐Esawi and Alayafi, 2019).
Heat and salinity: An intensifying challenge
Apart from the effects caused by drought stress, soil salinization and alkalization have emerged as critical constraints to global crop production (Kopittke et al., 2019). Over the past half‐century, increasing soil salinity, coupled with global warming, has substantially reduced arable land area and crop yields worldwide (Munns and Gilliham, 2015). High salt concentrations reduce the soil water potential, thereby limiting water uptake by roots (Parihar et al., 2014), while excessive accumulation of sodium (Na+) and chloride (Cl−) ions within cells causes toxicity and disrupts nutrient balance, impairing normal growth and metabolism (İbrahimova et al., 2021). Moreover, heat stress compounds the deleterious effects of salinity. Elevated temperatures typically increase transpiration rates, thereby promoting the accumulation of salts in the aerial parts of plants and intensifying overall salt injury (Wen et al., 2004; Suzuki et al., 2014).
Recent studies have elucidated sophisticated mechanisms that help plants manage combined salt–heat stress. In rice, precise regulation of plant hormone GA enhances combined alkali–thermotolerance (Guo et al., 2025a). GA biosynthesis genes ATT1/Sd1 and ATT2/GNP1 encode GA20 oxidases that regulate active GA levels. High GA levels reduce SLR1/DELLA protein accumulation (Sasaki et al., 2002; Ueguchi‐Tanaka et al., 2005), lowering peroxidase activity and ROS‐scavenging capacity, leading to ROS overaccumulation and sensitivity to alkali–heat stress (Guo et al., 2025a). Conversely, low GA levels promote SLR1–NGR5 interaction (Wu et al., 2020), which recruits histone methyltransferase activity (H3K27me3) to repress a broad spectrum of stress tolerance genes (e.g., OsNAAT1 and OsHsfA2d), also resulting in sensitivity. Notably, moderate GA levels maintain SLR1 homeostasis, balancing ROS production and H3K27me3 repression to confer combined alkali and heat tolerance (Guo et al., 2025a).
Other key genes provide additional layers of regulation. OsNCED1, a rate‐limiting enzyme in abscisic acid (ABA) biosynthesis, enhances antioxidant capacity and improves heat tolerance during heading and flowering. Overexpression of OsNCED1 increases pollen viability, seed‐setting rate, and the activities of superoxide dismutase (SOD) and peroxidase (POD) under heat stress (Zhou et al., 2022). It also interacts with the transcription factor OsNAC15 to regulate abscisic acid (ABA) biosynthesis, contributing to salt stress adaptation (Ao et al., 2024). The ORANGE (OR) gene in rice, OsOr, particularly the OsOr‐R115H variant, enhances tolerance to heat and salt through distinct regulatory pathways. Under heat stress, overexpression of OsOr increases chlorophyll and proline contents, reduces electrolyte leakage and malondialdehyde (MDA) levels, and upregulates ROS‐scavenging enzyme genes such as OsAPX2 and OsCATA, as well as stress‐responsive genes including OsLEA3 and OsDREB1A, thereby mitigating oxidative damage (Jung et al., 2021). Under salt stress, CRISPR‐Cas9‐mediated mutation of OsOr in rice calli increases carotenoid accumulation, strengthens ROS‐scavenging capacity, reduces H2O2 accumulation, and maintains higher relative water content (RWC), thereby mitigating combined oxidative and dehydration stress (Kim et al., 2022).
Crosstalk with biotic stresses
The interplay between heat and biotic stresses introduces a complex layer of physiological and molecular trade‐offs in plants. Temperature fluctuations can reshape plant–pathogen interactions, often by modulating the core hormonal signaling networks that govern immunity (Cheng et al., 2013; Desaint et al., 2021). This crosstalk can lead to a broad suppression of defense responses, such as cytosolic calcium influx and ROS production (Cheng et al., 2013; Hilleary et al., 2020). It also inhibits effector‐triggered immunity (ETI) by regulating the activity of nucleotide‐binding leucine‐rich repeat (NLR) immune receptors (Zhu et al., 2010). Ultimately, this renders plants more susceptible to infections and leads to substantial yield losses (Sanogo, 2004; Pandey et al., 2015; Kumar et al., 2022).
Heat and fungal pathogens
The combination of heat stress and fungal diseases represents a major threat to cereal crops. For example, high temperatures increase barley's susceptibility to powdery mildew (Schwarczinger et al., 2021), enhance wheat's sensitivity to root rot disease (Sharma et al., 2015), and make rice more vulnerable to sheath blight (Shen et al., 2023). At the molecular level, the OsCDPK24/28–OsHSFA4d regulatory module illustrates a direct trade‐off (Fang et al., 2025b). Heat stress activates the kinase activities of OsCDPK24/28, enabling them to form a complex with the transcription factor OsHSFA4d and promote its phosphorylation at serine 146, allowing it to bind to the heat shock elements (HSEs) in the promoter of the HSP101 gene and activate its expression and confer thermotolerance (Scharf et al., 2011). Concurrently, OsHSFA4d upregulates CslF6, a gene involved in mixed‐linkage glucan (MLG) deposition in the cell wall (Vega‐Sánchez et al., 2012). This cell wall modification, however, suppresses PAMP‐triggered ROS bursts and reduces the expression of pathogenesis‐related genes, ultimately weakening rice resistance to fungal pathogens like rice blast (Fang et al., 2025b). Similarly, the transcription factor WRKY82 is induced by both heat and fungal pathogens (e.g., rice blast and sheath blight) (Peng et al., 2011). It functions in the nucleus as a transcriptional activator to promote heat‐responsive genes, likely via the jasmonic acid and ethylene (JA/ET) signaling pathways, thereby enhancing thermotolerance. During pathogen challenge, it binds to W‐box elements in the promoters of defense‐related genes, activating their transcription and enhancing resistance through the same JA/ET pathway, representing a dual‐function component in stress cross‐talk (Peng et al., 2011).
Heat and bacterial pathogens
Heat stress also compromises plant defenses against bacterial pathogens. In rice, this is evidenced by increased susceptibility to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight, under high temperatures (Webb et al., 2010). A key regulatory node in this trade‐off is the OsSGS3–tasiRNA–OsARF3 module, which controls the balance between heat tolerance and disease resistance in rice (Gu et al., 2023). OsSGS3a/b promote the biosynthesis of tasiRNAs to suppress the expression of OsARF3a/b/la/lb (negative regulators of thermotolerance), thereby enhancing heat tolerance via OsCATA‐mediated ROS scavenging. In contrast, the module functions oppositely in the regulation of disease resistance: OsSGS3a negatively regulates rice resistance to bacterial leaf blight and rice blast pathogens, and in OsSGS3 RNAi plants, the upregulation of the OsARF3 gene family enhances disease resistance, leading to shorter lesion lengths and reduced pathogen proliferation; consistently, osarf3 mutants show significantly increased susceptibility to both pathogens, confirming that the OsARF3 gene family acts as a positive regulator of disease resistance (Gu et al., 2023).
Crosstalk with signaling molecules
Plant responses to combined stresses involve the synergistic action of multiple signaling pathways. Among these, the ABA signaling pathway is a core hub for high temperature, drought, and salt stress. Under stress, accumulated ABA binds to PYR/PYL/RCAR receptors, inhibiting PP2C phosphatase and activating SnRK2 kinases, which phosphorylate AREB/ABF transcription factors to induce downstream stress‐responsive genes and promote stomatal closure (Yang et al., 2006; Zhu et al., 2025b). In maize, under combined drought and heat stress, ABA induces H2O2 production, which promotes HSP70 synthesis and enhances antioxidant enzyme activities (Hu et al., 2010). In pumpkin, ABA directly induces the heat shock transcription factor CmHSF30, enhancing heat tolerance (Liu et al., 2025c). In rice, the J‐domain protein OsDjC46, strongly induced by ABA, interacts with the zinc finger protein ZFP36 to increase superoxide dismutase and catalase activities, effectively scavenging ROS and enhancing plant tolerance to drought and salt stress (Huang et al., 2022b).
Salicylic acid (SA) plays a central signaling role in both biotic and high‐temperature stress responses (Nadarajah et al., 2021). Following pathogen invasion, induced SA synthesis alters the cellular redox state, causing NPR1 oligomers to dissociate into active monomers that translocate to the nucleus and interact with TGA transcription factors to activate pathogenesis‐related genes (Zavaliev and Dong, 2024). Concurrently, SA binding to NPR3/4 relieves transcriptional repression of immune genes (Ding et al., 2018). NPR1 also mediates the degradation of negative immune regulators, synergistically activating defense programs (Guo et al., 2025b). In thermotolerance, SA acts as an upstream signal to induce HsfA2 expression in a mitochondrial ROS‑dependent manner (Nie et al., 2015). Activated HsfA2 upregulates heat shock protein expression to enhance basal thermotolerance and is also an essential factor for systemic acquired resistance. Localized pathogen inoculation can confer heat tolerance by activating HsfA2 (Nishad et al., 2025).
GA and BR also serve as central integrators of heat and combined stress responses. Under heat stress, bioactive GA levels decrease, leading to DELLA protein accumulation. DELLAs upregulate ROS‑detoxification enzyme genes, reducing ROS levels and delaying cell death to promote stress tolerance (Achard et al., 2008). The GA–DELLA module interfaces with multiple stress signaling pathways. Under combined stress, medium GA levels maintain DELLA protein SLR1 homeostasis, balancing ROS production and H3K27me3 epigenetic repression to confer alkali–thermal tolerance in rice (Guo et al., 2025a). Under heat–salt stress, NO‑mediated S‑nitrosylation of DELLA stabilizes these repressors, integrating salt signals with GA signaling to coordinate growth inhibition and stress adaptation (Chen et al., 2022b). Under heat–drought stress, DELLA proteins directly interact with ABF transcription factors, linking ABA and GA signaling (Wang et al., 2020c). In rice, knockout of the GA signaling repressor SLR1 enhances heat tolerance and yield (Zhu et al., 2025c). Thus, the GA–DELLA module represents a key node integrating heat signals with those from drought, salt, and alkali stresses.
BR signaling, through the BIN2–BZR1/BES1 cascade, integrates heat with other abiotic stresses. BIN2 kinase is the core regulatory node: Under non‐stress conditions, BIN2 phosphorylates BZR1, retaining it in the cytoplasm and suppressing BR signaling (Nolan et al., 2020; Zhang et al., 2022d). Under heat–salt stress, BIN2 accumulates in the nucleus and phosphorylates BZR1, inhibiting BR signaling; the BR receptor mutant bri1‐119 shows hypersensitivity to salt stress at high temperature, while BRI1 overexpression enhances salt tolerance under heat (Ren et al., 2022; Zhang et al., 2022d). Under heat–drought stress, BR and ABA signaling are linked through BIN2 kinase, which serves as a molecular node for stress integration and memory formation (Bulgakov et al., 2020). In soybean, the GmBSK1–GSK1–BES1.5 module positively regulates heat tolerance by enhancing ROS scavenging (Hou et al., 2025). Field application of 24‐epibrassinolide (EBR) in peanut reduced heat‐induced yield loss by 26.9% in tolerant cultivars and by 55.2% in sensitive cultivars (Lai et al., 2024). Together, BR signaling coordinates responses to heat, drought, and salinity through conserved modules.
ROS play a dual role under high‐temperature stress. High levels cause oxidative damage, photoinhibition, and lipid peroxidation (Bao et al., 2024). At non‐lethal levels, ROS act as signals: Heat shock activates NADPH oxidase to produce H2O2, which interacts with calcium signaling and the MAPK cascade to regulate heat shock factors and proteins (Zheng et al., 2025a). Drought‐induced ROS trigger stomatal closure to reduce water loss. Maintaining ROS homeostasis is also critical for root architecture; for example, the rice transcription factor WOX11 activates peroxidase OsPRX130 to promote crown root development and enhance drought tolerance (Tan et al., 2025). In Lilium pumilum, the LpbHLH115–LpFRO7 module maintains ROS homeostasis by boosting antioxidant enzymes and improving bicarbonate stress tolerance (Zhang et al., 2024). In biotic stress, ROS levels are tightly controlled, as seen in the rice blast immunity module OsFBX388–OsFIP1–OsCatA: OsFIP1 inhibits catalase OsCatA to elevate H2O2 for defense, while OsFBX388 degrades OsFIP1 to prevent ROS overaccumulation and ensure cell survival (Qiu et al., 2025b).
Despite the central roles of these signaling molecules, translation of this knowledge into agricultural practice faces challenges. Exogenous hormone application requires precise optimization of concentration, timing, and delivery; improper use can cause growth penalties or even exacerbate stress damage (Feng et al., 2018; Raghunath and Beena, 2021). Moreover, most studies have examined individual hormones in isolation, whereas ABA, GA, BR, and SA operate in an integrated, often synergistic network. Understanding how they coordinately regulate thermotolerance—and how their crosstalk can be harnessed—remains a critical knowledge gap. Future research integrating hormone profiling, functional genomics, and field trials will be essential to develop practical strategies for managing heat‑resilient crops.
TRENDS, SHORTAGES, AND CHALLENGES IN BREEDING FOR HEAT TOLERANCE
Research directions and entry/key points
In the context of climate change and the increasing frequency of extreme heat events, development of heat‐tolerant crops has become a critical task for ensuring global food security. Although traditional agronomic practices and chemical treatments can partially alleviate the damage caused by heat stress (Sarwar et al., 2019; Yadav et al., 2022; Liu et al., 2023), their widespread application is often constrained by economic costs and environmental concerns. Consequently, genetic improvement has emerged as a major research focus for breeding heat‐tolerant varieties. Modern breeding techniques have been transformed from a reliance on conventional phenotypic selection toward integrated frameworks that leverage genomic tools, high‐throughput phenotyping, and gene editing, significantly accelerating the development of climate‐resilient crops with enhanced efficiency, precision, and predictability (Hill and Li, 2022; Figure 4).
Figure 4.
Strategies and challenges in breeding for heat‐tolerant crops
The development of heat‐tolerant crop varieties has been greatly accelerated by integrating advanced tools such as genomic selection, high‐throughput phenotyping, and gene‐editing technologies, which enhance the efficiency, precision, and predictability of breeding programs. However, progress is hindered by several interconnected challenges, including the genetic complexity and context‐dependent expression of heat‐tolerant genes, limited diversity in available germplasm resources, persistent technical bottlenecks, and mounting socio‐economic pressures.
The rapid advancement of sequencing technologies has propelled molecular breeding approaches, such as marker‐assisted selection (MAS), genomic selection (GS), and genome editing, to become mainstream in crop improvement (Kumar et al., 2024; Mangal et al., 2024). Heat tolerance, as a complex quantitative trait controlled by combined effects of alleles at many loci, relies on the identification of QTLs to elucidate its genetic mechanisms. In recent years, a growing number of QTLs associated with heat tolerance, involving morphological, physiological, and yield‐related traits, have been identified in major cereal crops, including rice, wheat, maize, and barley (Longmei et al., 2021; Kumar et al., 2023; Huang et al., 2023a; Wang et al., 2023c). Genome‐wide association studies (GWAS) have further expanded the scope and resolution of QTL detection, enabling systematic dissection of marker‐trait associations and laying a solid foundation for marker‐assisted breeding (Ravikiran et al., 2022).
Genomic selection (GS), which utilizes genome‐wide markers associated with the cumulative effects of target traits, has emerged as an important breeding tool for developing high‐yielding and climate‐resilient crop varieties, especially those tolerant to combined stresses such as heat and drought (Juliana et al., 2018). When combined with high‐throughput phenotyping, GS has the potential to reduce the challenges associated with breeding high‐yielding crops under multi‐environment conditions (Cabrera‐Bosquet et al., 2012). By integrating multi‐environment trials and high‐throughput phenomics, GS significantly enhances the predictability of trait performance under stress conditions. This approach allows breeders to identify stable genetic regions with broader adaptability, thereby improving selection efficiency for challenging scenarios such as combined heat–drought stress (Shahi et al., 2022). For instance, under multi‐environment field conditions, GS has been successfully applied in wheat and maize by aggregating previously reported heat tolerance‐associated genomic regions, leading to simultaneous improvements in grain yield, physiological resilience, and nutritional quality (Neiff et al., 2023; Tolley et al., 2023). Furthermore, the incorporation of machine learning models further strengthens the predictive accuracy of GS, offering a powerful platform for optimizing genotype selection under complex environmental constraints (Xu et al., 2024).
Moreover, the rapid development of genome editing technologies has yielded new avenues for precise improvement of thermotolerant crop trait design. The molecular response to heat stress involves a complex signaling network that includes heat shock transcription factors, MYB family transcription factors, and related stress‐responsive genes (González‐Schain et al., 2015). The application of CRISPR‐based systems has enabled significant advances across multiple species, permitting targeted enhancement of thermotolerance through the editing or overexpression of key genetic components. For example, overexpression of OsMYB55 or ZmCDPK7 in maize can enhance antioxidant capacity, improve photosynthetic performance, and reduce membrane lipid peroxidation, thereby increasing heat tolerance (Casaretto et al., 2016; Zhao et al., 2021), Similarly, in barley, overexpression of TaHsfA6bT augments thermotolerance through the coordinated regulation of heat shock proteins and antioxidant genes (Poonia et al., 2020). Notably, certain transcription factors, such as HSFs, DREBs, and WRKYs, show functional conservation across diverse crops and are often implicated in responses to multiple stresses, providing important targets for breeding crops with broad‐spectrum stress resilience (Liu et al., 2016; El‐Esawi and Alayafi, 2019; Wei et al., 2022). Moving beyond single‐gene manipulation, recent studies have begun to elucidate higher‐order regulatory modules with profound impacts on thermotolerance. This is exemplified in rice by modules such as TT3.1–TT3.2, NF‐YA8–QT12, and NAT1–bHLH110–CER1/CER1L, which enhance yield/quality‐related traits under heat stress by modulating distinct physiological processes (Zhang et al., 2022a; Lu et al., 2025; Li et al., 2025b). Such examples highlight a shift from single‐gene editing toward pathway‐level engineering.
The positive correlation between heat tolerance and yield observed across rice, wheat, maize, soybean, and tomato provides a strong rationale for gene pyramiding. The functional classification in Table 1 offers a rational framework to guide this strategy (Table 1). Optimal breeding outcomes could potentially be achieved by combining genes from complementary hierarchical layers (e.g., a primary sensor, a metabolic modifier, and a central regulatory node). For example, in rice, pyramiding TT3.1 (sensor), GIF1‐HSE (metabolic modifier), and NAT1 knockout (regulatory node) would simultaneously target heat perception, carbon partitioning, and wax biosynthesis through independent mechanisms, possibly enabling additive or synergistic effects (Zhang et al., 2022a; Lou et al., 2025; Lu et al., 2025). In wheat, stacking TaBZR2 (signal transducer) with TaHsfA2h/TaHsfC2a (regulatory nodes) might amplify the heat shock response (Hao et al., 2025; Wei et al., 2025), while in maize, combining ZmATG8c (effector) with NUT1 (regulatory node) could provide both immediate protection and transcriptional reprogramming (Dong et al., 2020; Ma et al., 2025). Several challenges, however, may need to be considered. First, trait trade‐offs are common when manipulating central regulators; for instance, constitutive activation of OsHSFA4d enhances thermotolerance but compromises blast resistance (Fang et al., 2025b). This could potentially be mitigated using stress‐inducible or tissue‐specific promoters. Second, genotype‐by‐environment (G × E) interactions affect allele performance across genetic backgrounds and temperature regimes; the QT12 locus, for example, shows differential effects between indica and japonica backgrounds (Li et al., 2025b). Genomic selection incorporating multi‐environment data may help predict optimal allele combinations. Third, epistatic interactions might produce non‐additive effects, which would necessitate empirical validation of pyramided lines in field trials. Given recent advances in multiplex genome editing, simultaneous modification of three to five genes is now becoming feasible. We therefore suggest that future breeding programs could prioritize pyramiding functionally complementary genes across hierarchical layers (Table 1), combined with environment‐specific deployment and rigorous field validation.
In summary, breeding crops for heat tolerance is shifting from traditional phenotype‐based selection toward precision breeding supported by multi‐omics approaches. The integrated application of techniques such as QTL mapping, marker‐assisted selection, genomic selection, and gene editing has significantly improved both the efficiency and the predictability of selecting for heat‐tolerant traits. The future of heat tolerance breeding lies in the smart integration of multi‐omics data to design crops that are not only high‐yielding but also resilient to the unpredictable challenges of a warming climate.
Challenges and shortcomings
Although researchers have conducted extensive work over the past decades on the physiological mechanisms of heat tolerance, the genetic basis of heat‐tolerant traits, and the development of breeding technologies, breeding crops for high‐temperature tolerance is still at a plateau (Figure 4).
Genetic complexity and context dependency
The complex genetic architecture of heat tolerance and the difficulties in its dissection constitute the primary challenges. Heat tolerance is a quantitative trait jointly controlled by multiple genes, and the mechanisms underlying high‐temperature responses often vary across different developmental stages. Although a series of heat‐related loci have been identified in various crops through QTL mapping (Xu et al., 2021; Kan et al., 2023; Xiong et al., 2025), these loci only explain a limited proportion of the observed phenotypic variations. Furthermore, the detection power of QTL is significantly reduced when the mapping population is small, leading to an expansion of the confidence intervals that encompass the QTL regions. Simultaneously, the linkage between molecular markers and the corresponding genes or QTL is often not tight, and recombination may occur when the distance between them is large. Even markers initially determined to be closely linked may undergo recombination, resulting in separation between the marker and the target gene (Thomas, 2003). Genetic background and environmental factors can also interfere with molecular breeding, as QTLs identified in specific populations frequently show no effect when tested in different genetic backgrounds (Steele et al., 2005; Bohnert et al., 2006). Moreover, interactions or epistatic effects among QTLs can lead to variations in QTL expression across different genetic contexts (Méndez‐Vigo et al., 2013; Singh et al., 2019). Meanwhile, QTLs often show genotype‐by‐environment interactions, meaning that even if certain QTLs show consistent expression across environments, their effect size and direction may change under different environmental conditions, with smaller‐effect QTLs being particularly sensitive to environmental influences (Li et al., 2018b). These multi‐layered complexities collectively limit the reliable identification of heat tolerance‐related QTLs and their effective utilization in breeding programs.
Limited diversity in breeding germplasm and phenotyping gaps
The development of heat‐resilient crops is significantly hindered by the lack of genetic diversity in modern breeding programs and the underutilization of superior heat‐tolerance genes. Long‐term domestication through directed selection in staple crops has led to genetically uniform cultivars with narrow adaptive capacity, while wild relatives and local landraces retain rich reservoirs of untapped heat‐adaptive alleles (Ortiz et al., 2008). For instance, wild diploid wheat accessions carry loci that support grain filling under high temperatures (Peng et al., 2013), and certain weedy rice lines from Malaysia can withstand temperatures of up to 44°C (Peng et al., 2013; Stallworth et al., 2021; Sarker et al., 2024). However, the introgression of such valuable traits into elite cultivated varieties is often impeded by hybridization barriers and linkage drag (Sarker et al., 2024), where heat tolerance is genetically coupled with undesirable characteristics—such as poor plant architecture, high shattering, or low yield—thus reducing breeding utility (Song et al., 2014; Liberty et al., 2024). Compounding the germplasm limitation, current phenotyping approaches remain fragmented, often relying on single time‐point assessments (such as seedling vigor or electrolyte leakage) rather than coordinated multi‐trait profiling across the full growth cycle (Palermo et al., 2025). These approaches overlook stage‐specific tolerance mechanisms and contribute to a discrepancy between laboratory and field performance. As a result, many potentially valuable resources remain underutilized, and materials selected under controlled conditions may not always show consistent adaptability in field trials.
Technological and regulatory hurdles
While gene‐editing tools such as CRISPR/Cas9 offer promising avenues for precise modification of heat‐tolerance genes (Sun et al., 2021), their application, particularly in polyploid crops like wheat, still faces substantial challenges (Wei et al., 2025). Genomic complexity increases off‐target risks and precise modulation of the expression of edited genes, such as achieving an optimal expression level rather than simple knockout, is technically demanding (Arif et al., 2025). Currently, only a few major‐effect heat‐resistance genes have been functionally validated, while the functions of most genes and their potential impacts on other traits after editing remain unclear. Moreover, the potential for pleiotropic effects post‐editing is poorly understood, raising concerns about unintended trade‐offs between heat tolerance and agronomic performance. Finally, the heterogeneous and evolving global regulatory landscape for gene‐edited crops introduces uncertainty and can significantly delay the commercialization and deployment of improved varieties (Liberty et al., 2024).
Exacerbating environmental and socio‐economic pressures
The challenges of breeding for heat tolerance are further compounded by a range of environmental and socio‐economic factors. Climate change intensifies these challenges by increasing the frequency, intensity, and duration of extreme heat events, presenting a moving target for breeders. Simultaneously, the development of heat‐tolerant cultivars themselves requires substantial financial investment and is a lengthy process (Ravikiran et al., 2024), often spanning more than a decade from laboratory research to field application. This long developmental cycle is exacerbated by uncertain market returns and a lack of robust economic incentives tied to climate‐resilient traits, which collectively discourage sustained investment. Furthermore, the lack of unified international regulatory frameworks for gene‐edited crops delays the approval and commercialization of improved varieties (Yang et al., 2024), impeding the translation of genetic advances into practical solutions for farmers.
CONCLUSIONS AND FUTURE PERSPECTIVES
The escalating frequency of extreme high‐temperature events critically threatens global crop production and food security. Plant thermotolerance is a complex quantitative trait shaped by intricate genetic networks. While significant progress has been made in identifying thermotolerance genes—with approximately 150 functionally validated in rice—critical knowledge gaps remain. Staples like cotton and soybean are notably understudied, with fewer than 10 characterized genes. Furthermore, many genes have been validated only during vegetative growth, leaving reproductive‐stage tolerance and cross‐species functional mechanisms poorly understood.
Perhaps the most pressing frontier is breeding applications under field conditions, where heat stress rarely occurs in isolation. It typically coincides with other abiotic stresses (e.g., drought, salinity) and biotic pressures (e.g., pathogens), creating combined stressors that can synergistically impact plants. Yet, research on such stress combinations is still nascent, and the identification of hub genes or master regulators that integrate multiple stress response pathways is a crucial unmet need. Finally, beyond the mere presence of tolerance genes, fine‐tuned spatiotemporal regulation of their expression is emerging as a critical determinant of phenotype, an area where our understanding remains particularly limited.
To synthesize these mechanistic insights and guide practical applications, we propose a conceptual framework that links heat‐induced source–sink dysfunction to regulatory networks and breeding strategies (Figure 5). This framework views thermotolerance as a systemic trait requiring coordinated protection of source, transport, and sink tissues, each tending to be more severely affected at developmental stages, though all remain susceptible throughout the life cycle. It connects physiological outputs to transcriptional modules (e.g., HSF/NAC, MYB/WRKY, and bZIP/ERF) and hormone–stress crosstalk, and highlight key genes (e.g., TT3.1‐TT3.2, NF‐Y‐QT12, HSE‐CWIN, and NAT1) for pyramiding and field deployment. Overall, the framework offers a roadmap for translating mechanistic knowledge into precision breeding.
Figure 5.
Conceptual model of heat‐induced disruption to source–sink dynamics and strategies for molecular breeding
This model integrates heat damage to leaves, phloem, and grains across developmental stages. Top panel from left to right: leaf source (photosystem damage, ROS, and heat‑sensing cascades), phloem transport (inhibition of carbon translocation), and grain sink (disrupted starch metabolism and chalkiness). The bottom panel combines regulatory networks and precision breeding tools toward the goal of heat‑resilient crops with stable yield and quality. Key genetic modules are listed in Table 1.
Therefore, strategic future efforts should prioritize (i) deploying advanced genomics and gene‐editing technologies in understudied crops to close gaps in gene discovery; (ii) systematically elucidating stage‐specific tolerance mechanisms, with particular attention to reproductive tolerance mechanisms; (iii) decoding stress crosstalk to identify integrator genes for combined stress tolerance; and (iv) advancing precision breeding through mapping and engineering of gene‐regulatory networks for optimized resilience. Addressing these interconnected priorities will be essential for engineering a new generation of climate‐resilient crops to ensure sustainable agri‐food systems in a warming world.
CONFLICTS OF INTEREST
The authors declare no conflicts of interest.
AUTHOR CONTRIBUTIONS
Y.L. conceived and supervised the work. L.G. and J.R. wrote the manuscript and prepared the figures; Q.Y. assisted with reference collection and contributed to the writing. Y.L. revised the manuscript. All authors have read and approved the contents of this paper.
ACKNOWLEDGEMENTS
We apologize to authors whose work could not be cited owing to space limitations. This work was supported by the National Key Research and Development Program of China (grant no. 2024YFF1000402), the National Natural Science Foundation of China (grant no. 32525046), the Shanghai Jiao Tong University 2030 Initiative (WH510363003/015), the Shanghai Post‐doctoral Excellence Program (2023366, 2024343), the Natural Science Foundation of Shanghai (24ZR1431200), and the China Postdoctoral Science Foundation (2024M751984). 1, 2, 3, 5 were created with BioRender.com.
Biographies
Guo, L. , Ruan, J. , Yu, Q. , and Lin, Y. (2026). Integrating molecular networks and physiological adaptation for heat‐resilient crops. J. Integr. Plant Biol. 68: 2624–2657.
Edited by: Zhizhong Gong, China Agricultural University, China
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