Molecular genetic regulation of the vegetative–generative transition in wheat from an environmental perspective

Abstract

The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative–generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular–genetic pathways (Earliness per se, circadian/photoperiod length, vernalization – cold requirement, phytohormonal – gibberellic acid, light perception, ambient temperature perception and ageing – miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.

INTRODUCTION

Wheat is the third most important cereal crop worldwide, and is an essential source of human food and animal feed (Shewry and Hey, 2015). Its production range (67°N to 45°S, Feldman, 1995) is characterized by wide macro- and microclimatic variation, to which plants can only adapt through wide genetic diversity (Cockram et al., 2007; Distelfeld and Dubcovsky, 2010; Dreisigacker et al., 2021). One of the most commonly used methods to investigate adaptation is the study of the transition between the vegetative–generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of the photoperiod, and the composition of the light spectrum (Bullrich et al., 2002; Lewis et al., 2008; Hemming et al., 2012; Karsai et al., 2013; Kiss et al., 2017; Dixon et al., 2019; Monteagudo et al., 2020). In temperate cereals, photoperiod and low-temperature vernalization are the two most decisive environmental factors determining the developmental processes of the plant (Cockram et al., 2007; Distelfeld et al., 2009a). In addition, several other factors fine-tune heading or flowering, including the ambient temperature above vernalizing levels and the various characteristics of light. Temperature has a more complex effect than photoperiod on the dynamics of plant development, as it can vary significantly not only seasonally, but also yearly and daily (Bullrich et al., 2002; Lewis et al., 2008; Hemming et al., 2012). Therefore (in addition to its role in regulating the vernalization requirement), temperature significantly affects the heading (used synonymously with flowering) of cereals, the initiation rate, and number of leaves, tillers and spikelets (Slafer and Rawson, 1994; Atkinson and Porter, 1996; Slafer et al., 2015). The spectral composition and intensity of light play an important role in the production of both primary and secondary metabolites through photosynthesis. Furthermore, they impact the determination of several developmental parameters, such as flowering time, growing process and the regulation of leaf initiation rate (Chen et al., 2004; Darko et al., 2014). However, only limited information is available on the relationship between light spectra variation and the complex genetic regulatory mechanism, including the role of circadian rhythm that determines the intensive stem elongation of hexaploid wheat. Results from experiments on barley confirmed that ambient temperature and spectral composition of light strongly modify plant development, even under fully inductive environmental conditions (saturated vernalization requirement and long-day illumination), which are otherwise optimal for differentiation of the floral meristem (Karsai et al., 2013). Furthermore, while the genotypic effect of ambient temperature depends on the allelic distribution of the major developmental genes, this correlation was not confirmed for the spectral composition of light (Karsai et al., 2013; Monteagudo et al., 2020; Del Río et al., 2023). A similar response to ambient temperature has been described for wheat (Kiss et al., 2017; Dixon et al., 2019).

The molecular genetic regulation of plant development and the transition between the vegetative and generative phases in the dicotyledonous model plant Arabidopsis thaliana and in the monocotyledonous genera Oryza, Brachypodium and Hordeum have been studied most extensively (Schaffer et al., 1998; Fowler et al., 1999; Covington et al., 2001; Izawa et al., 2002; Yu et al., 2002; Karsai et al., 2005; Turner et al., 2005; Yoo et al., 2005; Cockram et al., 2007; Higgins et al., 2010; Campoli et al., 2012a, 2012b, 2013; Cao et al., 2020; Andrade et al., 2022). Several known regulatory pathways exist with numerous interconnection points (Levy and Dean, 1998; Mouradov et al., 2002; Komeda, 2004; Kim et al., 2009; Fornara et al., 2010). These pathways include circadian/photoperiod, vernalization (the effect of low temperature), ambient temperature, phytohormones [gibberellic acid (GA)], earliness per se and ageing regulation [micro-RNA (miRNA)]. The signals from the different regulatory elements are collected by a few integrator genes and transmitted to the floral meristem identity genes, which are responsible for the generative transition of the apex and the regular development of the different floral organs, respectively. The molecular genetic process of the developmental phase in wheat is much less well understood, and only the major components of the vernalization and photoperiod regulation pathways have been identified in detail (Worland, 1996; Dubcovsky et al., 1998; Worland et al., 1998), using either the diploid Triticum monococcum and tetraploid species with a smaller genome size or specific crossing lines (RIL – recombinant inbred line, NIL – near-isogenic line, mutant and transgenic lines) (Trevaskis et al., 2003; Loukoianov et al., 2005; Dubcovsky et al., 2006; Yan et al., 2006; Shimada et al., 2009; Distelfeld and Dubcovsky, 2010; Li et al., 2011; Chen and Dubcovsky, 2012; Kumar et al., 2012; Kippes et al., 2016). Results have revealed significant differences between the regulatory genes and regulatory mechanisms of Arabidopsis and cereals, which is particularly striking in the case of vernalization regulation. The genetic regulation of wheat circadian rhythm and GA synthesis is also not well understood, as vernalization and photoperiod responses can mask their effects, making them extremely difficult to study. Also, little information is available on the extent of variability in the phenotypic effects of different alleles as related to heading under field conditions due to the complex interaction of various environmental factors in different years (Kiss et al., 2019; Horváth et al., 2023). There is also a basic difference, however, between Arabidopsis and cereals from aspects of both the generative development of inflorescences and intensive stem elongation (Fig. 1). In Arabidopsis, these processes occur in parallel, but in cereals they are separated in time: the generative development of inflorescences is already at advanced stages by the time intensive stem elongation actually starts (Kiss et al., 2017; Monteagudo et al., 2020).

In summary, genetic regulatory mechanisms that evolved in response to abiotic environmental (vernalization temperature, photoperiod, ambient temperature, light intensity and composition) factors ensure that flowering and ripening occur under optimal environmental conditions. Detailed molecular genetic analysis of wheat heading time may become even more valuable in the future, as rapidly and unpredictably changing macro- and microclimatic influences will increase the need for breeders to find genetic materials in different breeding programmes to produce new varieties that are best adapted to local environmental conditions. This review focuses on the main molecular–genetic regulatory mechanisms responsible for adaptation in wheat (Fig. 2; Table 1).

THE MAIN GENETIC DETERMINANTS OF TIME TO HEADING

Vernalization pathway

Temperate cereals have various mechanisms that can protect the floral meristem from the adverse effects of low temperatures and allow for heading after saturation of the cold requirement (Cockram et al., 2007; Brambilla et al., 2017; Fernández-Calleja et al., 2021). During breeding, mutations in the genes involved in determining vernalization requirement (VERNALIZATION – VRN) have produced different developmental types of cereal varieties (winter, spring and facultative) with different requirements for low temperatures. Winter types require a longer vernalization period for optimal flowering (Trevaskis, 2010). In wheat, several gene families are involved in the genetic regulation of the vernalization requirement, of which VRN1 (on the homologous group of chromosome 5), VRN2 (on 4B, and on the telomeric region of 5A) and VRN3 (on the homologous group of chromosome 7) have major regulatory roles (Law et al., 1976; Snape et al., 2001; Barrett et al., 2002; Iwaki et al., 2002; Galiba et al., 2009; Distelfeld and Dubcovsky, 2010). However, the data do not provide a detailed understanding of the environmentally determined interconnections between these gene families in regulating the later developmental phases including the process of stem elongation, beyond their roles in the vegetative–generative transition (Trevaskis et al., 2007a; Distelfeld et al., 2009b; Shimada et al., 2009; Distelfeld and Dubcovsky, 2010). In barley, different allele combinations of genes that are responsible for the regulation of vernalization requirement and photoperiod sensitivity lead to different plant development types (Karsai et al., 2008).

The VRN1 gene in wheat encodes an important transcription factor of the MINICHROMOSOME MAINTENANCE1/AGAMOUS/DEFICIENS/SERUM RESPONSE FACTOR (MIKC) family of MADS-box genes, which most closely resembles the APETALA1/FRUITFULL class of Arabidopsis MADS-box genes (AP1/FUL) (Yan et al., 2003; Hyles et al., 2020). These genes are important for regulating the transition from the vegetative shoot apex to the generative phase (Mandel and Yanofsky, 1995; Ferrándiz et al., 2000; Shitsukawa et al., 2007b). In contrast to Arabidopsis AP1/FUL genes, the expression of VRN1 in wheat is increased by prolonged exposure to cold (Danyluk et al., 2003; Murai et al., 2003; Trevaskis et al., 2003; Yan et al., 2003). However, the precise mechanism of the low-temperature induction of VRN1 is not yet understood, but various modifications of histone proteins (H3K27 and H3K4 – DNA methylation) are presumed to play a prominent role. These protein modifications both maintain the repressed state of VRN1 before winter and also induce increased transcription of this gene after the cold requirement (Diallo et al., 2012; Yuan et al., 2013; Hyles et al., 2020; Chen et al., 2023). Oliver et al. (2009) found a correlation between histone protein levels and VRN1 activity. Active histone proteins may be derived from cell organization and may also play a role in cellular ‘vernalization’ memory (Distelfeld et al., 2009a; Oliver et al., 2009; Chen and Dubcovsky, 2012). Transcription of VRN1 is significantly higher in vernalized plants under short photoperiod than in plants without cold treatment (Dubcovsky et al., 2006; Trevaskis et al., 2006; Fu et al., 2007); therefore, VRN1 genes are upregulated by vernalization, independently of the function of the other two important VRN genes (VRN2, VRN3) (Trevaskis et al., 2007a). Similar to VRN1, the WHEAT VEGETATIVE TO REPRODUCTIVE TRANSITION-1 (TaVRT-1) and WHEAT APETALA1 (WAP1) genes encode an APETALA1 (AP1)-like MADS-box gene (presumably VRN1 orthologues). They also play a major role in the vegetative–generative transition of wheat, but they are not sufficient either by themselves or in combination to induce heading (Danyluk et al., 2003; Murai et al., 2003; Trevaskis et al., 2003; Yan et al., 2003). Subsequent studies have shown that these two genes are synonymous with VRN1 (Kane et al., 2007; Shitsukawa et al., 2007a). A number of functional polymorphisms have been found in the promoter, exon and intron regions of VRN-A1, including gene copy number variations (Yan et al., 2004a; Fu et al., 2005; Dubcovsky et al., 2006; Golovnina et al., 2010; Kamran et al., 2014; Shcherban et al., 2015, 2016; Ivaničová et al., 2016; Muterko et al., 2016; Muterko and Salina, 2017; Steinfort et al., 2017; Strejčková et al., 2021; Milec et al., 2023; B. Zhang et al., 2023). The basic allele type of spring/winter is associated with sequence differences detected in several promoter regions, and a larger insertion/deletion size identified in the intron 1 region (Yan et al., 2004a; Fu et al., 2005). For the other two VRN1 genes (VRN-B1 and VRN-D1), much less polymorphism was detected, and the spring–winter allele type is basically related to insertion/deletion of the intron 1 region (Yan et al., 2004a; Fu et al., 2005; Santra et al., 2009; Golovnina et al., 2010; Chu et al., 2011; Efremova et al., 2011; Milec et al., 2012, 2013, 2023; Shcherban et al., 2012; J. Zhang et al., 2012; Kamran et al., 2014; Muterko et al., 2015; B. Zhang et al., 2018,Strejčková et al., 2021; Makhoul et al., 2022). Copy number variation (CNV) has also been found in the VRN1 genes, which is particularly significant for VRN-A1 (Fu et al., 2005; Díaz et al., 2012; Kippes et al., 2015; Würschum et al., 2015; Muterko and Salina, 2019, 2021; Strejčková et al., 2021). The strength of the correlation between VRN-A1 copy number and heading time is strongly influenced by the developmental type of each copy. Thus, wheat genotypes that contain more copies of the winter type allele have a much higher vernalization requirement, and they tend to have later heading (Würschum et al., 2015; Muterko and Salina, 2019, 2021; Strejčková et al., 2021; Chen et al., 2024). In relation to the transcriptional expression of VRN1 genes, Loukoianov et al. (2005) found that the three VRN1 genes (VRN-A1, VRN-B1 and VRN-D1) showed different expression levels in isogenic wheat lines between the one- and six-leaf developmental stages. The transcription of VRN-A1 was already expressed in the first leaf stage, whereas the activity of VRN-B1 and VRN-D1 alleles was only detectable in the second and third leaf stages, which may explain its stronger impact on regulation (Loukoianov et al., 2005). This phenomenon was confirmed to be the result of the different attributes of dominant/recessive allele types associated with the distinct mutations in each subgenome (promoter insertion in genome A, intron deletions of different lengths in genomes B and D) (Trevaskis et al., 2003; Kippes et al., 2018; Hyles et al., 2020). It was also established that VRN1 expression follows a diurnal pattern, but little information is available on its variability across genotypes or on its dependence on various environmental factors and whether these variations may have any phenotypic consequences (Shimada et al., 2009; Nishiura et al., 2014, 2018). The dominant Vrn-A1 allele also determines the spring type that requires no cold treatment at all for heading. In contrast, the dominant Vrn-B1, Vrn-D1 and Vrn4 genes only partially abolish the cold requirement that is essential for the generative phase (Pugsley, 1971, 1972; Kato et al., 2001; Loukoianov et al., 2005).

Two similar ‘zinc-finger CCT’ genes (ZCCT1 and ZCCT2) have been identified in the VRN2 locus which are involved in dominant flowering-inhibitory mechanisms (Yan et al., 2004b). No VRN2 orthologue gene has yet been found either in rice or in Arabidopsis, so it appears that this gene is a distinct regulatory element appearing during the evolution of cereals (Yan et al., 2004b). During vernalization, a steady decrease in the levels of transcription factors produced by ZCCT1 and ZCCT2 was detected in the leaves, while the activity of ZCCT genes remained high in winter types that were kept at room temperature as controls (Yan et al., 2004b). Short photoperiod inhibits, while long day stimulates VRN2 expression (Dubcovsky et al., 2006; Trevaskis et al., 2006). In barley, both phenomic and gene expression analyses have confirmed that VRN2 appears to be controlled by both CONSTANS (CO) and VRN1, suggesting that this gene is a joint element in photoperiod and vernalization regulatory pathways (Karsai et al., 2005, 2006; Mulki and von Korff, 2016). In hexaploid wheat, the phenotypic effects of loss-of-function alleles of VRN2 are extremely difficult to study because the redundancy across the subgenomes may hide the effect of a single recessive allele. However, the induction of new allelic variants of this gene (Dubcovsky and Dvorak, 2007; Distelfeld et al., 2009b; Tan and Yan, 2016; Milec et al., 2023) may also broaden the adaptive capacity of wheat (through increased genetic diversity) (Hyles et al., 2020). Tan and Yan (2016) reported the duplication of the VRN-B2 gene in hexaploid wheat, but they found no significant effect on flowering time.

Wheat FLOWERING LOCUS T (TaFT1), identified as VRN3, encodes a RAF kinase inhibitor protein (highly similar to the FT gene of Arabidopsis) that functions as a signal transduction molecule (an integrator of vernalization and photoperiod regulatory pathways) and, as such, it is an essential element of flowering (Yan et al., 2006; Shi et al., 2019). At least 12 FT-like genetic regions have currently been identified in bread wheat and barley (Lv et al., 2014; Bennett and Dixon, 2021; Pieper et al., 2021), of which Vrn-B3 is the most well characterized; the dominant allele was found to have a 5295-bp repetitive sequence insertion in the promoter region, which showed a strong correlation with early flowering. The recessive (vrn-B3) allele of this gene with the deletion caused late heading (Yan et al., 2006). Moreover, Finnegan et al. (2018) described that the late heading observed in relation to deletion was associated with a prolonged spikelet initiation phase, which increased the number of spikelets during long days. Shaw et al. (2019) reported a weak interaction between TaFT2 and heading as well as a stronger association with spikelet number in tetraploid wheat. Gauley and Boden (2021) also observed a strong correlation between FT2 and PPD1 gene expression and regulation of spikelet number in hexaploid wheat. Gene expression studies revealed that FT3 orthologous genes of tetra- and hexaploid wheat were upregulated only under short photoperiod, similar to the expression of HvFT3 (Halliwell et al., 2016). Six additional single nucleotide polymorphisms (SNPs) were found in the promoter and intron 1 regions, but these mutations did not cause phenotypic differences between the two main allele types (Yan et al., 2006). Chen et al. (2013) and Berezhnaya et al. (2021) identified two additional allele types at the VRN3 locus (VRN-B3b, VRN-B3c and VRN-B3d, VRN-B3e). Other polymorphisms linked to VRN3 have also been reported (Bonnin et al., 2008; Zikhali et al., 2017; Chen et al., 2020a; Dreisigacker et al., 2021; Nishimura et al., 2021), but copy number differences have so far only been detected in barley (Nitcher et al., 2013; Milec et al., 2023). There is a difference in VRN3 signalling between Arabidopsis and wheat. While FT in Arabidopsis directly transmits the signal to the floral meristem identity genes via SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), in wheat, VRN3 is transmitted via VRN1 expressed in the apical meristem. Luo et al. (2024) demonstrated a repressor role for the wheat SOC1 gene in the vernalization and photoperiod regulatory pathway. Kiss et al. (2017) showed that, with the exception of VRN3, ambient temperature also has a significant effect on the expression of the main developmental genes (VRN1, VRN2 and PPD1), the extent of which can be significantly influenced by daylength.

Little information is available on VRN4, and some authors suggest that the dominant allele of VRN-D4 has a low distribution among hexaploid wheat genotypes (Goncharov, 1998, 2003). The extra VRN1 gene copy present at the VRN4 locus (as a probable result of translocation) may be associated with elevated transcription levels of VRN1, which reduces the need for vernalization (Kippes et al., 2014). The intron polymorphisms (SNPs) observed in this translocation explain the high expression of VRN1 in genotypes that carry VRN4 (Hyles et al., 2020). As with other VRN genes, VRN-D4 encodes an AP1 protein that shares a high degree of similarity with the Arabidopsis meristem identity protein AP1 (Shi et al., 2019). Kippes et al. (2015) described the Australian origin of VRN4, which can be traced back to the ʻGaboʼ variety and has a significant role in adapting to local environmental conditions through its strong spring growing habit (Hyles et al., 2020). In wheat, phenotypic values and gene expression patterns have shown that there is a close epistatic interaction between VRN1, VRN2 and VRN3 making it difficult to clearly identify the primary target gene in the vernalization process (Distelfeld and Dubcovsky, 2010). However, VRN1 appears to play a key role (Danyluk et al., 2003; Trevaskis et al., 2003; Yan et al., 2003; Shitsukawa et al., 2007b).

Other vernalization-induced genes have also been described in wheat, such as Vernalization-related 2 (VER2), Wheat vegetative to reproductive transition-2 (TaVRT-2) and T. aestivum glycine-rich RNA binding protein 2 (TaGRP2) (Chong et al., 1998; Yong et al., 2003; Kane et al., 2005; Xing et al., 2009; Xiao et al., 2014). Prior to vernalization, the protein produced by TaGRP2 binds to a specific region of VRN1 and represses the accumulation of its transcript. However, after vernalization, VER2 expression is increased, and the phosphorylated VER2 protein coupled with TaGRP2 protein resolves its inhibitory effect on VRN1 (Xiao et al., 2014). Previous studies have found that the regulation of TaVRT2 is independent of vernalization and photoperiod sensing pathways and that its gene product accumulates in the vegetative phase, which can be directly linked to the CArG box part of the promoter region of VRN1 inhibiting the activity of this gene. This effect is further enhanced by VRN2. After vernalization, the expression of both genes is inhibited, triggering an increase in VRN1 activity (Kane et al., 2005, 2007). However, a series of subsequent studies showed that the expression of TaVRT2 and HvVRT2 (orthologous gene in barley) genes was induced by vernalization (Trevaskis et al., 2007a; Dubcovsky et al., 2008; Winfield et al., 2009; Li et al., 2018); thus, they are promoters of the vernalization regulatory pathway together with TaVRN1 (Xie et al., 2021). TaVRT2 expression increases steadily during vernalization and then decreases significantly, which may prevent the detection of its significant effect on flowering (Xie et al., 2021).

Based on recent models of the vernalization regulation pathway (Chen and Dubcovsky, 2012; Debernardi et al., 2022; Li et al., 2024), in autumn, after germination, when the days are still sufficiently long, the active VRN2 prevents transcription of VRN3, which may play an important role in keeping VRN1 activity low (Trevaskis et al., 2006; Hemming et al., 2008). During vernalization, VRN1 is progressively activated by cold. The increasing amounts of the VRN1 transcription factor inhibit the function of VRN2 (its protein is directly linked to the promoter region of VRN2) and, in parallel, they stimulate VRN3 (its protein is directly linked to the promoter region of VRN3). VRN3 protein thus activated is transported via the phloem to the meristematic tissue of the shoot apex (Trevaskis et al., 2006; Distelfeld et al., 2009a; Deng et al., 2015). The increased amount of VRN3 further enhances the activity of VRN1 and induces heading (Kardailsky et al., 1999; Kobayashi et al., 1999; Abe et al., 2005; Loukoianov et al., 2005; Preston and Kellogg, 2008; Distelfeld and Dubcovsky, 2010; Chen and Dubcovsky, 2012; Fjellheim et al., 2014; Johansson and Staiger, 2014; Deng et al., 2015) (Fig. 2; Table 1). The flowering regulation model reported by Debernardi et al. (2022) was complemented with an ageing regulation pathway. Based on the results of Shaw et al. (2020), the model can be further extended by the finding that, in autumn, PPD1, CO1 and CO2 genes promote the expression of VRN2, and after vernalization, the activated VRN1 downregulates VRN2 and CO1, promoting the expression of FT1, a process that is further enhanced by the PPD1 gene. In barley, the possible photoperiod-dependent relationship between PPD-H1 and VRN-H1 was confirmed by phenomic studies (Karsai et al., 1997; Parrado et al., 2023).

In summary, while there is a similarity in the genetic regulatory mechanism of the vernalization requirement in mono- and dicotyledonous plants (based on epigenetic histone modification of the promoter of the regulated gene), there is a large difference between the target genes. The main regulatory gene for these processes in Arabidopsis is FLOWERING LOCUS C (FLC), which acts as a repressor in the transduction of the floral meristem, whereas in wheat, it is VRN1 demonstrating a central activator role (Sheldon et al., 2000; Loukoianov et al., 2005; Li and Dubcovsky, 2008).

Photoperiod sensitivity

To detect diurnal and seasonal changes in daylength, plants have had to develop different adaptive systems, in which the gene clusters responsible for photoperiod sensitivity (PHOTOPERIOD1/PPD1/), genes regulating the internal circadian rhythm, and primary light-sensing molecules such as phytochromes (PHY) and cryptochromes (CRY) play an important role (Mizuno and Nakamichi, 2005; Hyles et al., 2020). Plants can be divided – according to their photoperiod sensitivity – into long-day, short-day and so-called daylength-neutral classes (Garner and Allard, 1920). Long-day plants, such as wheat, barley, rye and Arabidopsis, need a long-day illumination to flower properly, otherwise their development will be stunted (Laurie, 1997). For short-day crops, such as maize and rice, a shorter daylight is sufficient for flowering (Laurie, 1997). In contrast to the genetic control of vernalization processes, the photoperiod regulatory pathway shows a higher level of similarity in both monocotyledonous and dicotyledonous plants, in which the activity of FT (TaFT1 in wheat) has a central regulatory role under inductive illumination (Kardailsky et al., 1999; Kobayashi et al., 1999) and CO1/CO2 can modulate its activity (Kitagawa et al., 2012). In Arabidopsis, the wild-type dominant CO resulted in late flowering under short days and early flowering under long days. In contrast, in cereals, genotypes containing the recessive co caused late flowering under both daylengths (Laurie, 1997). For long-day plants, a so-called daylength-uninfluenced developmental phase has been described after germination, followed by a light-inducible phase (Roberts et al., 1988). In the period not affected by light, plants do not sense or cannot respond to different daylengths, so their heading time is not affected. The length of this phase may vary between genotypes. When plants enter the so-called light-inducible developmental phase, different daylengths already affect flowering time, but the response of individual genotypes can vary over a wide range (Roberts et al., 1988). In wheat, the gene clusters responsible for the regulation of photoperiod sensitivity (PPD1) mainly determine flowering time, along with the VRN genes. The wild ancestors of wheat are quantitative long-day plants, which are capable of heading under short days, but this process is greatly accelerated by long illumination (Greenup et al., 2009). However, mutations in PPD1 genes (PPD-A1, 2A; PPD-B1, 2B; and PPD-D1, 2D) during breeding resulted in photoperiod-sensitive (Ppd-1b – recessive) and photoperiod-insensitive (Ppd-1a – semi-dominant) types (Pugsley, 1966; Law et al., 1978; McIntosh et al., 2003). In wheat and barley, PPD1 plays a more important role in the regulation of flowering by photoperiod than CO1 and CO2 genes (Alqudah et al., 2014; Shaw et al., 2020). Several studies have shown that under both long- and short-day illumination, photoperiod-insensitive alleles shortened the time needed to heading (under both controlled and field conditions). However, the photoperiod-sensitive allele significantly delays this process in the short day (Worland et al., 1998; Foulkes et al., 2004; Jones et al., 2017). There is evidence that the initial time and length of the stem elongation phase are also highly dependent on the effect of different alleles of the gene responsible for different photoperiod sensing (Miralles et al., 2000; Horváth et al., 2023). This developmental phase is critical to the formation of the total number of fertile florets, which is closely linked to grain yields (Fischer, 1985; Slafer and Rawson, 1994; Reynolds et al., 2009; García et al., 2011; Guo et al., 2018).

PPD1 belongs to the pseudoresponse regulator (PRR) gene family, and is known as PRR37 (Beales et al., 2007). In addition, PPD1 is closely related to the Arabidopsis PRR7 gene which also plays a role in light and temperature sensing of the circadian rhythm, so PPD1 may have a similar role in cereals (Beales et al., 2007; Greenup et al., 2009). Although the regulation of TaPRR37 in wheat is also dependent on circadian genes, this gene is not part of the transcriptional/translational feedback loop that determines circadian rhythm (Kiseleva et al., 2022). In terms of functional polymorphisms, the least information is available on PPD-A1; only a few polymorphisms have been described so far in photoperiod-insensitive varieties (Beales et al., 2007; Wilhelm et al., 2009; Nishida et al., 2013b; Makhoul et al., 2024). Breeders might also use the photoperiod-insensitive allele type PPD-A1a to fine-tune the photoperiod sensitivity of wheat at higher latitudes (Lin et al., 2021). PPD-B1 functional polymorphisms are better known than those of PPD-A1. It was found that the heading time in substitution lines carrying the single-chromosome photoperiod-insensitive allele 2B was shorter than that of the photoperiod-sensitive allele (Scarth and Law, 1984). In Chinese Spring variety, a point mutation in the exon 3 region has been described, and it has also been shown that a multiplication of the PRR gene copy number is behind the photoperiod insensitivity (Díaz et al., 2012). These mutations show co-segregation with the early heading phenotype (Beales et al., 2007; Díaz et al., 2012; Würschum et al., 2015, 2018). Cane et al. (2013), Langer et al. (2014) and Kiss et al. (2014b) in three multi-varietal wheat panels of distinctly diverse geographical origins (Australian vs. mostly European) have independently demonstrated that there is a strong correlation between PPD-B1 gene copy number variants and flowering time in a wide genetic pool under field conditions. PPD-D1 in wheat, which shows similarity to PPD-H1 in barley, has the strongest influence on photoperiod sensitivity (Laurie et al., 1995; Börner et al., 1998; Beales et al., 2007), but there are significant differences between the two genes (Slafer et al., 2023). There is a 2089-bp deletion in the promoter region of the PPD-D1a allele, which is characteristic of the photoperiod-insensitive allelic variant of PPD-D1. As a result of the deletion, the daily cycle of gene expression is significantly modified, the phenotypic consequence of which is early heading under both short- and long-day illumination (Beales et al., 2007). In contrast, for PPD-H1, the strongest functional polymorphism is based on an SNP in exon 6 (SNP48) or in the CCT domain (SNP22), which does not induce a shift in the diurnal cycling between insensitive and sensitive alleles, and it results in contrasting phenotypic effects of the two alleles depending on the photoperiod (Turner et al., 2005; Jones et al., 2008; Slafer et al., 2023). It is generally accepted that, in wheat, the strongest genetic influence is exerted by the semi-dominant Ppd-D1a allele, followed by the dominant Ppd-B1a and Ppd-A1a alleles (Blake et al., 2009; Díaz et al., 2012). The activity of the PPD-D1 gene variant determining the photoperiod-sensitive allele type follows a daily cycle under both long and short days (Beales et al., 2007; Zhao et al., 2016a). In the early morning hours, gene expression level is very low, then reaches its maximum in the morning hours and finally this level starts to decrease. On the other hand, photoperiod-insensitive allele types do not demonstrate this daily fluctuation, and gene activity constantly shows an elevated level, which is closely related to the increase in the activity of TaFT1 (VRN3) and may also affect the decrease in the peak activity of TaCO1 (Yan et al., 2006; Beales et al., 2007; Díaz et al., 2012; Shaw et al., 2012, 2020; Campoli and von Korff, 2014; Hyles et al., 2020; Gauley et al., 2024). However, there is little information available on the extent to which different allele types of the PPD-1 gene regulate floral initiation (Beales et al., 2007; Shaw et al., 2012, 2013; Boden et al., 2015; Gauley and Boden, 2021). It is well known that photoperiod-insensitive allele types significantly reduce spikelet number, floret number and fertility, which are key factors in determining yield potential (Boden et al., 2015; Prieto et al., 2018a; Perez-Gianmarco et al., 2019). Gauley et al. (2024) identified a bZIP and an ALOG transcription factor that suppress flowering and modulate spikelet number and architecture. This new knowledge may help breeders to increase yield potential (Prieto et al., 2018a; Perez-Gianmarco et al., 2019).

There is also little information available on how environmental factors – other than photoperiod – influence the daily activity rhythms of the two allele variants and how they impact flowering.

Circadian clock

The regulatory mechanism of the plant circadian rhythm has already been significantly explored in Arabidopsis, and many homologous genes have been described in wheat (Peng et al., 2015), but only a few of them have been studied in detail (Kiseleva and Salina, 2018). Even less information is available on the internal relationship between the genes responsible for the circadian rhythm, developmental genes and light-sensing receptors in cultivated wheat varieties, and how these gene interactions are influenced by environmental elements, such as ambient temperature and light spectral composition, which fundamentally affect the process of intensive stem elongation. A better understanding of these processes may enhance the ability to manipulate the adaptive capacity of cereals and thereby their productivity and geographical distribution. The circadian rhythm is an internal control mechanism (autonomous oscillator) by which plants coordinate their internal biological processes with the daily changes in temperature and light conditions of the external environment (Johansson and Staiger, 2014; Ford et al., 2016). It also participates in the regulation of photosynthesis, carbohydrate synthesis, and biotic and abiotic stress responses (Bläsing et al., 2005; Fowler et al., 2005; Takeuchi et al., 2014; Hyles et al., 2020; McClung, 2021). In Arabidopsis, the core circadian clock consists of three interconnected major transcriptional/translational feedback loops (negative and positive) that shape the daily rhythm of gene expressions (McClung, 2006, 2021; Hsu and Harmer, 2014). Therefore, morning, daytime and evening/night transcriptional loops can be distinguished (Bendix et al., 2015). CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE-ELONGATED HYPOCOTYL (LHY) genes encoding an Myb transcription factor have their maximum expression in the early morning hours (Schaffer et al., 1998; Cao et al., 2021). Then, expression of the PSEUDORESPONSE REGULATOR [PRR – PRR3, PRR5 (PRR59 and PRR95 in monocotyledons), PRR7 (PRR37 and PRR73 in monocotyledons), PRR9 and TIMING OF CAB EXPRESSION1 (TOC1/PRR1)] genes also increases until the evening hours (Farre et al., 2005; Takata et al., 2010; Cao et al., 2021). In the morning, the CCA1 and LHY genes inhibit the expression of the TOC1 and EC [evening complex ‒ ARRHYTHMO (LUX), EARLY FLOWERING 3 (ELF3), EARLY FLOWERING 4 (ELF4)] genes. In the late afternoon, the expression of TOC1 increases, which reduces the expression of CCA1 and LHY (negative feedback loop) and also affects its own function, reducing its activity (Schaffer et al., 1998; Wang and Tobin, 1998; Matsushika et al., 2000; Strayer et al., 2000; Alabadi et al., 2001; Hazen et al., 2005; Huang et al., 2012a; Bendix et al., 2015). LUX, and ELF3 and ELF4 show maximum expression in the evening and night respectively (Dixon et al., 2011; Herrero et al., 2012; Hyles et al., 2020; Cao et al., 2021) and inhibit the function of PRR5, PRR7, PRR9, TOC1, GIGANTEA (GI) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED1 (LNK1) genes (Kolmos et al., 2009; Dixon et al., 2011; Helfer et al., 2011; Chow et al., 2012; Herrero et al., 2012); as a result, inhibition of the CCA1 and LHY genes is reduced and a new daily cycle begins (Johansson and Staiger, 2014). The circadian rhythm also plays a key role in the regulation of daylength sensitivity among both monocotyledonous and dicotyledonous plants, as it affects the expression of CO, FT and GI genes (central regulatory elements) (Fowler et al., 1999; Kardailsky et al., 1999; Kobayashi et al., 1999; Samach et al., 2000; Distelfeld et al., 2009a; Lazaro et al., 2015; Li et al., 2024). Two homologues of the CO gene have already been described in wheat (TaCO1 and TaCO2), but their effect on flowering time is still poorly understood (Chen et al., 2014). The opposite regulation (positive/negative) of CO on the expression of FT (depending on the photoperiod-insensitive and photoperiod-sensitive alleles of the PPD1) was observed in both barley and wheat independently of daylength (Campoli et al., 2012a; Alqudah et al., 2014; Johansson and Staiger, 2014; Mulki and von Korff, 2016; Shaw et al., 2020). Daily variation in the expression pattern and level of the TaCO1 was also described (Shaw et al., 2013). A decrease in the expression of this gene was observed after the start of illumination; then from 3 to 6 h after this period, the transcription level showed a continuous rise until 15–18 h. The TaHD1 gene has been described in wheat as an orthologue of CO (Hyles et al., 2020). Similar to CO in Arabidopsis, a daily expression pattern (with a peak value during the day) can be observed in TaHD1 under long-day illumination. The daily rhythm of the wheat GI is significantly influenced by daylength (Zhao et al., 2005). It is assumed that the GI of wheat may have a positive effect on CO and indirectly also on the FT gene, which can result in early heading (Zhao et al., 2005; Li et al., 2024). Li et al. (2024) established a complex relationship (a combination of inhibitory and inductive processes) between GI and VRN2, as the daytime expression of VRN2 in tetraploid wheat gi-2 mutant lines differed compared to the wild-type. Furthermore, in the mutant lines, the time required for heading increased significantly compared to the wild-type, a phenomenon that became even more pronounced in the case of the dominant allele type of VRN2. Although TaGI is homologous to GI in Arabidopsis and has a similar function in wheat (regulation of photoperiod sensitivity), the regulatory mechanism is different in the two species (Li et al., 2024). It was found that expression maximum of wheat TaPRR59 and TaPRR95 is in the morning hours, which corresponds to the expression peak value of the homologous gene in rice (Kiseleva et al., 2022; Rees et al., 2022). Furthermore, the expression pattern of TaPRR59 and TaPRR95 resembled the transcription pattern of PRR5 and PRR9 in Arabidopsis (Kiseleva et al., 2022; Rees et al., 2022). The expression pattern of TaPRR73 seems to show similarities to PRR7 in Arabidopsis, which may indicate conservation of the functions of homologous genes between species (inhibition of LHY/CCA1) (Kiseleva et al., 2022). During characterization of TaTOC1 (TaPRR1) identified in wheat, it was found that it has a maximum peak expression value in the evening (Zhao et al., 2016b; Rees et al., 2022), which parallels the daily pattern of activity of the homologous gene in Arabidopsis (James et al., 2008; Rees et al., 2022). Although several haplotypes of this gene have been described, which have been proven to be related to agronomic traits (Zhao et al., 2016b), the signalling mechanism and interaction system of this gene are not yet known (Kiseleva et al., 2022). In wheat, a homologous LUX (WPCL1) gene has been described as a repressor of PPD1 and VRN2 (Mizuno et al., 2016). Furthermore, Nishiura et al. (2018) demonstrated that the upregulation of VRN1 expression after vernalization occurred in the absence of LUX expression. VRN1 was upregulated in the LUX gene deletion mutant (exe3), which resulted in extremely early flowering after vernalization, both in long and short days. Thus, the direct regulation of VRN1 by the circadian pathways independent of the vernalization pathways has also been identified (Nishiura et al., 2018). The wheat ELF3 gene also exerts an inhibitory effect on PPD1 during the night period (Alvarez et al., 2016, 2023), a phenomenon that was also confirmed in Brachypodium distachyon (Woods et al., 2023). The mutations described in this gene led to the constitutive upregulation of PPD1, which was associated with early heading regardless of daylength. Furthermore, TaELF3 has a negative effect on TaGI1 that is consistent with the function of its homologous gene in Arabidopsis (Yu et al., 2008; Zikhali et al., 2016). Wittern et al. (2023) showed that ELF3 is expressed in wheat in the morning period and not in the evening as in Arabidopsis, and consequently the role of ELF3 in circadian rhythm regulation is likely to differ between the two species. Furthermore, the co-expression of ELF3 and LUX is not observed at dusk, which also suggests that the mechanism of the circadian oscillator in wheat might differ from that in Arabidopsis. Therefore, ELF3 is an important regulator of various physiological and developmental processes and its different allele types may help to improve plant adaptation, which will be essential for plant breeding (Zahn et al., 2023). In barley, one such promising allele might be the exotic ELF3 allele type observed by Maurer et al. (2016), Herzig et al. (2018) and Zahn et al. (2023), differing by only one nucleotide from the cultivated ELF3 allele at the ELF3 locus and accelerates the rate of plant development compared to the cultivated ELF3 allele.

Light perception

The spectral composition of the light perceived by plants depends on altitude, latitude, seasons, and climatic and atmospheric factors. During the day (from dawn to dusk), the spectral energy distribution of sunlight changes, so the quality of light also contributes to the precise determination of daylength regulation and circadian rhythm (Morgan and Smith, 1981; Hyles et al., 2020). In Arabidopsis, several different types of photoreceptors may be distinguished, such as red and far-red light-sensing phytochromes (PHY – PHYA, PHYB, PHYC, PHYD and PHYE), cryptochromes (CRY1 and CRY2), phototropins (PHOT1 and PHOT2), the LOV domain-containing F-box proteins (ZEITLUPE/ZTL/, FLAVIN-BINDING KELCH REPEAT F-BOX 1/FKF1/, and LOV KELCH PROTEIN 1 and 2/LKP1 and LKP2/), blue light sensors and UVB-RESISTANCE 8 (UVR8), which is a special UV-B receptor (Guo et al., 1998; Yu et al., 2010; Liu et al., 2011; Ito et al., 2012; Chen et al., 2014; Pham et al., 2018; Sanchez et al., 2020; Cao et al., 2021). The most important photoreceptors in wheat are phytochromes (PHYA, PHYB and PHYC) and cryptochromes (CRY1 and CRY2). In Arabidopsis, PHYA, PHOT1, PHOT2, CRY1, CRY2, FKF1 and UVR8 have a positive effect on flowering (Valverde et al., 2004; Sawa et al., 2007; Liu et al., 2011; Arongaus et al., 2018; Kong and Zheng, 2020), while PHYB, PHYC, PHYD, PHYE, ZTL and LKP2 negatively influence this process (Devlin et al., 1998, 1999; Schultz et al., 2001; Monte et al., 2003; Valverde et al., 2004; Takano et al., 2005; Kim et al., 2007; Chen et al., 2014). In wheat, by contrast, PHYC and PHYB play a positive regulatory role in the control of flowering under long-day illumination, while the role of PHYA is unknown (Chen et al., 2014; Pearce et al., 2016; Kiseleva and Salina, 2018). There is also no information on possible wheat homologous genes PHOT, UVR8 and FKF1 (Cao et al., 2021). Kiseleva et al. (2022) highlighted the difference in the expression pattern of the ZTL and LKP2 homologous genes of wheat and Arabidopsis. In barley, the positive correlation of HvPhyC with HvFT1 promoting the reproductive transition of the floral meristem has already been described, an effect that was independent of the circadian cycle and HvCO1 (Nishida et al., 2013a). According to other studies, however (Pankin et al., 2014), HvPhyC had an effect on the circadian oscillation, and it was also related to PPD-H1, thus promoting flowering. Similarly, in diploid wheat (Triticum monococcum), PHYB and PHYC upregulate PPD1 during long days, which results in early flowering through the activation of FT1 (VRN3) and CO (Chen et al., 2014; Pearce et al., 2016). In Arabidopsis, the photoreceptor PHYB has been described also to function as a temperature signal transmitter (Jung et al., 2016; Legris et al., 2016). However, this has not yet been investigated in temperate cereals (Cao et al., 2021). The regulatory mechanisms of TaCRY1 and TaCRY2 have also not been investigated. In Arabidopsis, these two genes also play an important role in proper functioning of the internal oscillator (Yu et al., 2010; Sanchez et al., 2020). It has been described that CRY2 positively affects one of the genes responsible for regulating the circadian rhythm (CO), which, however, also depends on the photoperiod (Guo et al., 1998; Suárez-López et al., 2001).

Ambient temperature perception (thermosensory)

This section summarizes the genetic regulatory mechanism of the optimal environmental temperature (between 17 and 23 °C). Temperatures outside of this range can trigger either developmental responses as was discussed in the section on the vernalization pathway or various stress responses in plants (Porter and Gawith, 1999; Acevedo et al., 2009). The latter is not the aim of this review. Slafer and Rawson (1995) described that in wheat, raising the temperature from 10 to 19 °C accelerated reproductive development, whereas temperatures above 19 °C delayed terminal spikelet initiation and reduced the number of spikelet primordia. The average optimum temperature required for grain filling was found to be around 20 °C, but a temperature above 35 °C is harmful (Porter and Gawith, 1999). So lower or higher than optimal temperatures inhibit growth and reproductive development, but this effect is strongly modified by daylength (Hemming et al., 2012). A higher ambient temperature (25 °C) was observed to have inhibited reproductive development with non-inductive daylength (especially in the early development phases), but accelerated the reproductive phase with inductive daylength (Rawson and Richards, 1993; Kiss et al., 2017). This may be a form of adaptive advantage for temperate plants (Jacott and Boden, 2020). Although an increasing number of detailed results are available on the perception of the cold effect (vernalization) by plants and the molecular genetic mechanism of regulation, the related effects of the ambient temperature (as a secondary environmental factor) have been much less well explored. In Arabidopsis, several genes have already been identified to be linked to ambient temperature sensing. These include red and far-red light-sensing phytochromes (PHY), blue light-sensing cryptochromes (CRY), UVR8, genes involved in GA biosynthesis, and SHORT VEGETATIVE PHASE (SVP), PRR7, PRR9, GI, CO, LUX and ELF3 genes (Samach et al., 2000; Halliday et al., 2003; Valverde et al., 2004; Salome and McClung, 2005; Samach and Wigge, 2005; Fernández et al., 2016; Findlay and Jenkins, 2016). At low temperatures, the transcriptional repressor ELF3 forms a complex with the LUX and ELF4 genes preventing the activation of FT that is necessary for flowering. In response to an increase in temperature, the ELF3 protein undergoes a molecular structural change that results in the dissociation of the repressor complex and, consequently, in the derepression of FT. The PrD (Prion-like domain) structure provides a molecular switch that allows ELF3 to alter cell organization in response to temperature changes. In barley, it has already been observed that depending on the allele types of PPD-H1 and HvELF3, 28 °C (compared to 20 °C) delayed or accelerated reproductive development (Ejaz and von Korff, 2017; Zhu et al., 2023). In spring barley genotypes that carry the mutant ppd-H1 allele, expression of FT1 was inhibited at higher ambient temperatures, and late heading and a reduced number of grains per spike were observed compared to the control. In introgression lines carrying the wild-type PPD-H1 or the mutant Hvelf3 allele, on the other hand, floret primordia initiation was accelerated (through the increased activity of the FT1), and a higher seed number were also observed. Similarly, in spring wheat, higher ambient temperatures either reduce or do not significantly affect FT1 expression (Kiss et al., 2017; Dixon et al., 2018). Furthermore, it was observed that ending of the repressive effect of ELF3 at a higher ambient temperature (25 °C) involved an increase in the expression of the GI, LUX and PRR genes (Ford et al., 2016). Thus, at higher temperatures, ELF3 can play a central role in the regulation processes of photoperiod-dependent flowering (Ford et al., 2016). In wheat, Ochagavía et al. (2019) described those differences between alleles of TaELF3 that resulted in different levels of sensitivity to temperature, according to which precociousness in hexaploid wheat was associated with increased sensitivity to temperature in the late reproductive phase. The same study also showed a temperature-dependent inhibition of TaGI controlled by TaELF3. Genes involved in vernalization also show a strong interaction with temperature (Kiss et al., 2017; Dixon et al., 2019). Delayed flowering of winter wheat genotypes (following exposure to higher ambient temperatures during and after cold treatment) was described to be genetically closely linked to VRN1 (highlighting VRN-A1) (Dixon et al., 2019). Furthermore, higher ambient temperature (25 °C) led to increased expression of VRN2 associated with reduced levels of VRN1 and FT1 transcripts compared to gene activities at moderate (18 °C) and low (11 °C) temperatures (Kiss et al., 2017; Dixon et al., 2019). The gene expression values influenced by the ambient temperature observed by the authors were significantly dependent on the photoperiod-insensitive and photoperiod-sensitive allele type of PPD-D1. Allele types of VRN1 also influence the expression of flowering-promoting factors in barley. In the treatments at higher ambient temperature, the inhibition of expression of FT1 was more pronounced in the winter compared to the spring genotypes, related to a stronger repression of VRN1 (Ejaz and von Korff, 2017).

Earliness per se

Allelic variants of ‘Earliness per se’ (Eps) genes can cause differences in flowering time of a few days, independent of environmental effects (Worland, 1996; Snape et al., 2001; Bullrich et al., 2002; Zikhali et al., 2014). A close relationship was also established with the PPD and circadian genes, so their interrelated effect determines the final level of photoperiod sensitivity of a given genotype (Worland, 1996; Hyles et al., 2020). The most important function of the Eps genes is fine-tuning of flowering time (Hoogendoorn, 1985; Valárik et al., 2006; Griffiths et al., 2009; Horváth et al., 2023). Thus, some allelic variants of these genes may be used in the creation of new genotypes that, with their earliness, can avoid the early summer dry period, thus increasing the productivity of the varieties, and therefore also increasing crop security. ‘Earliness per se’ is a quantitative trait determined by a number of genes with smaller effects (Kato and Wada, 1999). In bread wheat, numerous quantitative trait locus (QTL) analyses have already indicated the existence of genes on most chromosomes that may be associated with earliness (Snape et al., 2001; Hanocq et al., 2007; Chen et al., 2010; Basavaraddi et al., 2021). These QTL effects were independent of the effects of the main genes of the VRN and PPD regulatory pathways. However, Horváth et al. (2023) identified several eps loci in a wheat association panel during field developmental studies, the detectability of which was closely related to the allele type of PPD-D1. In most of the cases, the genes behind these earliness loci are not yet known. However, several examples are available where the gene was cloned and characterized and, in some cases, proved to belong to the circadian clock. Zikhali et al. (2016) identified that the gene of the Eps-3A^m locus in Triticum monococcum is orthologous to LUX/PCL1 of Arabidopsis (Shindo et al., 2002; Gawroński and Schnurbusch, 2012; Mizuno et al., 2012; Gawroński et al., 2014). The photoperiod-insensitive mutant version of this gene was associated with early heading and showed increased expression of the TmFT, Ppd-1, WCO1 and TmHd1 genes, and it was also associated with sensitivity to temperature, similar to the Eps-A^m1 (T. monococcum 1A^m) gene (Bullrich et al., 2002; Lewis et al., 2008; Gawroński et al., 2014). Bullrich et al. (2002) identified a QTL in a mapping population that was closely linked to a major Eps gene (Eps-A^m1). This is one of the best characterized Eps loci that is located on chromosome 1A^m of T. monococcum (Bullrich et al., 2002; Valárik et al., 2006; Lewis et al., 2008; Faricelli et al., 2016) and is considered to be an orthologue of TaELF3 (Alvarez et al., 2016; Wang et al., 2016). The early allele type of this gene (Eps-Am1-e) significantly accelerated the time required for flowering, while the late allele type (Eps-Am1-l) significantly delayed it. The different temperature optimum of these two allele types was also described by Bullrich et al. (2002) and verified by Appendino and Slafer (2003) in aestivum wheats. In hexaploid wheat, Zikhali et al. (2014) detected a QTL responsible for earliness on chromosome 1DL (Eps-D1, homologous to Eps-A^m1) of hexaploid wheat, the effect of which was confirmed in NIL populations under both field and controlled conditions. They also identified TaELF3 as the gene responsible for this effect (Zikhali et al., 2016). In those lines that carried the deletion of the Eps-D1 gene, the expression of TaELF3 was significantly reduced and the expression of TaGI changed compared to the wild-type. The temperature-dependent relationship between the early and late allele type of Eps-D1 and several yield-related components with an emphasis on the number of fertile florets, leaf development dynamics and heading time was analysed in detail (Prieto et al., 2020). Eps genes probably affect almost all development phases, such as the vegetative/generative transition, early and late spike differentiation, the stem elongation phase, heading, and spike fertility, which also have a significant role in determining grain yield (Lewis et al., 2008; Griffiths et al., 2009; Ochagavía et al., 2018; Prieto et al., 2018b). Buckley et al. (2024) found that the deletion of Eps-D1 affects ageing processes and the protein content of the grains.

Gibberellin response pathways

Plant height is also a key factor determining environmental adaptation. The regulation mechanism of endogenous GA hormone synthesis plays a prominent role in the formation of the final plant height. Gibberellins are pentacyclic diterpene compounds that stimulate growth, so they play an important role in germination, the stem elongation phase, leaf development, the reproductive developmental phase and the regulation of various environmental stress responses (Olszewski et al., 2002; MacMillan et al., 2005; Yamaguchi, 2008; Llanes et al., 2016). Their effect is manifested in the fact that they degrade the growth-inhibiting DELLA proteins. These proteins are encoded by GAI, RGA, RGL1, RGL2 and RGL3 in Arabidopsis, by SLR1 in rice, and by RHT in wheat (Peng et al., 1997; Ikeda et al., 2001). GA is sensed by the protein receptor GID1 (GIBBERELLIN-INSENSITIVE DWARF1), which was first identified in gibberellin-insensitive dwarf mutants of rice (Ueguchi-Tanaka et al., 2005). Three GID1 orthologues have been described in Arabidopsis (AtGID1a, AtGID1b and AtGID1c) with overlapping functions (Nakajima et al., 2006). In AtGID1, the triple mutant in Arabidopsis GA sensing did not work, and as a result, the plants became extremely dwarfed. This phenotypic effect did not appear in the single mutants, but it did in the double mutants (Griffiths et al., 2006; Iuchi et al., 2007; Willige et al., 2007). Over the last 10 years, the GA signalling mechanism by the GID1 protein and the details of GA biosynthesis itself have been elucidated through biochemical, genetic and structural analyses in rice and Arabidopsis (Ueguchi-Tanaka et al., 2005; Griffiths et al., 2006; Jiang and Fu, 2007; Murase et al., 2008; Hirano et al., 2010). Seven different types of enzymes may be highlighted in GA biosynthesis, such as ent-copaly1 diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), ent-kaurenoic acid oxidase (KAO), GA20 oxidase, GA3 oxidase and GA2 oxidase (Yamaguchi, 2006). Orthologues of the genes responsible for the synthesis of these enzymes have already been described in wheat (Spielmeyer et al., 2004; Appleford et al., 2006; Y. Zhang et al., 2007; Khlestkina et al., 2010; Huang et al., 2012b; Tang et al., 2019) and their expressions were shown to be tissue- and developmental stage-specific (Huang et al., 2012b). The role of GA in flowering appears to be species-dependent as it promotes flower initiation in Arabidopsis, but inhibits this process in several perennials (Mutasa-Göttgens and Hedden, 2009). Pearce et al. (2013) demonstrated that in wheat, VRN3 also upregulates GA biosynthesis through GA20ox and inhibits the expression of GA2ox1 through indirect and direct ways. The increased level of GA and the transcriptional activity of VRN1 upregulate the function of the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-1 (SOC1-1) and LEAFY (LFY) genes, a process required for normal spike development (Pearce et al., 2013). In hexaploid wheat, GA signalling factors and DELLA proteins are also encoded by RHT (Peng et al., 1999). The DELLA genes are located at three homologous loci, Rht-A1, Rht-B1 (formerly RHT1) and Rht-D1 (formerly RHT2) on chromosomes 4A, 4B and 4D (Börner et al., 1996; Flintham et al., 1997; Peng et al., 1999; Febrer et al., 2009). In the Rht-B1b and Rht-D1b GA-insensitive (mutant) alleles, degraded proteins are produced that are unable to form the appropriate GA–GID–DELLA protein complex, and as a result, the DELLA protein cannot be degraded, but instead accumulates and inhibits the growing processes (Peng et al., 1999; Hyles et al., 2020). These mutant alleles reduce the length of the internodes that results in reduced plant height (Keyes et al., 1989; Hoogendoorn et al., 1990) and can also be associated with reduced leaf size (Allan, 1989; Ellis et al., 2004). Although the decrease can be observed between all internodes, the largest absolute decrease is found in the last internode length (Hoogendoorn et al., 1990). The shorter last internode allows more assimilates to be used for growth and development of the differentiating spikelet (Youssefian et al., 1992), and as a result, more fertile florets can be formed that also increase the potential seed number. Recently, Song et al. (2023a) identified an Rht-B1 null mutant in wheat segregation lines where a natural deletion of about 500 kb within the ZnF-B gene (encoding a RING-type E3 ligase) was observed. This deletion resulted in semi-dwarf plants with more compact plant architecture and significantly increased grain yield (up to 15.2 %) in field experiments compared to Rht-B1b and Rht-D1b mutants. Further genetic analyses confirmed that deletion of ZnF-B in the absence of Rht-B1b and Rht-D1b alleles caused the semi-dwarf trait by weakening brassinosteroid (BR) sensing. Hence, Rht-B1 null mutants can be a promising source for the production of new cultivars with high yield and desired height. Dong et al. (2023) reported that GLYCOGEN SYNTHASE KINASE 3 (GSK3) phosphorylates Rht-B1b modification through the BR pathway, thus causing reduced plant height. Other authors (Li et al., 2010; Chen et al., 2020b) described that the BR sensing pathway in Arabidopsis is also related to the regulation of flowering time; however, the molecular–genetic regulatory mechanism of this process remains unclear. In addition, Cui et al. (2023) demonstrated that GSK3 is in physical contact with VRN1 and regulates its intracellular accumulation through VRN3. Other RHTs have also been identified as individual allelic variants of RHT1 and RHT2 (RHT3, RHT4, RHT5, RHT6, RHT7, RHT8, RHT9, RHT10, RHT11, RHT12, RHT13, RHT14, RHT15, RHT16, RHT17, RHT18, RHT19; RHT20, RHT21, RHT22, RHT23, RHT24, RHT25, RHT26 and RHT27); although their exact genetic regulation is not yet sufficiently known, their effect on plant height has already been proven (Flintham and Gale, 1983; Konzak, 1987; Loskutova, 1998; Peng et al., 1999, 2011; Ellis et al., 2004, 2005; Haque et al., 2011; Divashuk et al., 2012; Li et al., 2012; Bazhenov et al., 2015; Chen et al., 2015; Lu et al., 2015; Würschum et al., 2017; Yan and Zhang, 2017; Du et al., 2018; Ford et al., 2018; Mo et al., 2018; Mohan et al., 2021; Zhao et al., 2021; Song et al., 2023b; Liu et al., 2024). There is also little information available about the mechanism of regulation and the relationship between RHT genes and other genetic components responsible for flowering regulation in cereals.

Use of Rht-B1b and Rht-D1b alleles in new breeding lines (‘Green Revolution’ – 1960/1970s) made it possible to replace the tall, lodging-sensitive varieties in the past with short, less lodging-sensitive varieties. The introduction of these genes resulted in higher average grain yields, due to which those cultivars harbouring any combinations of Rht mutant allelles spread rapidly in breeding and cereal production (Gao and Chu, 2020). Combining the adequate alleles of the RHT genes is extremely important in breeding to avoid adverse phenotypic effects. It has been described that combining the Rht-B1b and Rht-D1b alleles with the RHT8 gene resulted in extremely dwarfed plants with reduced spike fertility rates (Worland and Law, 1986). The allelic combinations of RHT15 and RHT1 reduced the grain yield per plant (Zhao et al., 2023). Cseh et al. (2024) also observed that Rht-B1 and Rht-D1 mutants are prone to meiotic aberrations (reduced spike fertility rate) even at optimal temperatures and showed a higher level of sensitivity to heat stress than the taller genotypes. In addition, the reduced fertility may be linked to the reduced recombination level of homologous chromosomes and the frequency of defective chromosome separations. Regarding cereal development, genetic regulation of GA biosynthesis lies in the intricate regulation cascade system of plant development, including the vegetative–generative transitions and the stem elongation phase, which is much less well understood.

Ageing pathway

In Arabidopsis, senescence-related genetic factors are also among the most important elements of flowering regulation (Rehman et al., 2023) and several SQUAMOSA PROMOTER BINDING LIKE (SPL) genes regulated by miRNAs have now been described (Xu et al., 2016). In Arabidopsis, the concentration of SPL transcription factors increases continuously with ageing (Fornara et al., 2010). These factors promote flowering and ripening, and during this process they also induce the expression of several transcription factors [LFY, FRUITFULL (FUL) and SOC1]. miRNAs include short (21–24 nucleotides) non-coding nucleic acid sequences that participate in gene expression regulation (through mRNA cleavage or translation inhibition) (Bartel, 2009; Chellappan et al., 2010). miR156 and miR172 are one of the miRNA families showing the greatest degree of conservation in plants (Rehman et al., 2023). SPL proteins correlate negatively with miR156, the level of which is significantly higher in young than in older leaves (Fornara et al., 2010), while SPL genes activate the expression of miR172 in leaves. An increased level of miR172 inhibits the expression of APETALA2-like (AP2L) genes (flowering-inhibitory transcription factors) promoting flowering competence (Wu et al., 2009; Debernardi et al., 2022; Li et al., 2024). Furthermore, it was described that the synthesis of miRNAs is a temperature-dependent process (e.g. miR156 and miR169 are upregulated at 16 °C) thus preventing precocious flowering at sub-optimal temperatures (Kim et al., 2012; Quiroz et al., 2021). Other miRNA families have already been identified in wheat by genome-wide association analysis (Yao et al., 2007; Sun et al., 2014). However, the functions of the identified miRNAs and their role in genetic regulation of plant development are not yet sufficiently detailed. The wheat miR5200 is homologous to that described in Brachypodium distachyon and it also inhibits the expression of FT1 in short-day conditions (Wu et al., 2013; Li et al., 2014; Pearce et al., 2016). These studies also demonstrated that PHYC of wheat has a negative effect on this molecule. An miRNA has also been described in wheat (tae-miR408) associated with flowering time (Zhao et al., 2016b). This molecule exerts a negative effect on the TaTOC1 circadian rhythm gene, and as a result, the expression level of TaFT1 that plays an important role in flowering regulation also increases.

Why is it so important to study the stages of plant development in wheat?

Vernalization requirement and photoperiod sensitivity are the basic components influencing plant developmental phases in cereals grown under continental conditions. After the saturation of these major developmental factors, there are other components (circadian rhythm, light perception, hormonal regulation and earliness per se) that sense subsidiary environmental signals, such as light intensity and ambient temperature. This continuous adjustment to environmental conditions ensures the fine-tuning of adaptive plant growth (Fornara et al., 2010). As climatic anomalies (taken here to mean weather conditions that are unusual at any given time of year) increase both in magnitude and in frequency, they affect not only fine-tuning mechanisms but also the major plant developmental responses (Porter and Semenov, 2005). It is therefore essential to establish the extent to which disturbances in plant developmental patterns negatively affect yield formation and to obtain detailed physiological and genetic knowledge on the starting date and length of various plant developmental phases. This will enable breeders to modify both the transition from the vegetative to the generative phase of the genotypes by changing the scale of photoperiod-sensitivity and vernalization requirements and the effectiveness of fine-tuning mechanisms (González et al., 2005; Borràs et al., 2009; Chen et al., 2009, 2010; Maurer et al., 2016; Zahn et al., 2023). The length of the various developmental phases is an important factor determining the extent to which the yield potential of a genotype may be achieved under a given set of ecological conditions (Slafer and Rawson, 1996; Araus et al., 2002; González et al., 2005; McMaster, 2005; Borràs et al., 2009; Chen et al., 2009; Foulkes et al., 2011). One such adaptation process is a time shift in the rapid stem elongation phase (Fischer, 1985; Slafer and Rawson, 1994; Reynolds et al., 2009; García et al., 2011). The later timing of stem elongation helps to avoid frost damage in early spring, whereas earlier maturity helps to avoid hot dry weather during summer. Similarly, the relative duration of any two consecutive phases can be also important in determining the various yield components. A longer vegetative phase generates more biomass (due to the longer nutrient storage period), and an extended stem elongation phase is required to achieve a higher number of fertile florets or spikelets, whereas a longer grain-filling period may lead to increased grain weight in the spikes (Kirby, 1988; Slafer and Rawson, 1996; Miralles and Richards, 2000; Whitechurch and Slafer, 2001, 2002; Araus et al., 2002; González et al., 2002, 2003, 2005; Kiss et al., 2011; Dreccer et al., 2014; González-Navarro et al., 2015, 2016). The time between first node appearance and the start of rapid stem elongation has a significant effect on the number of reproductive tillers, and a close association was observed between the second half of rapid stem elongation (from the boot stage to heading) and the number of spikelets per spike (Miralles and Richards, 2000; Whitechurch and Slafer, 2001, 2002; Kiss et al., 2011, 2014a). Guo et al. (2018) further subdivided the stem elongation phase into seven sub-phases to investigate their effects on yield components. The most important finding of their study was the potential strategies for controlling the narrow time windows (sub-phases) during the stem elongation phase to increase floret fertility and grain number. At the time of stem elongation, it is important that the development of node initiation and elongation of the internodes are appropriate for the yield. However, it is still unclear how these events are spatiotemporally coordinated (Huang et al., 2024). This approach to cereal stem development may be traced back to information obtained from diploid barley. The main body axis of barley represents a simple and continuous segmentation of phytomers (apex-derived organ form) wherein both vegetative and reproductive organs coexist at opposite ends (Huang et al., 2024). In addition to the phytohormones (such as gibberellin), the FLOWERING LOCUS T (FT)/TERMINAL FLOWERING 1 (TFL1) family genes also play a crucial role in the formation of plant structure (Taoka et al., 2011; Eshed and Lippman, 2019; McKim, 2020). In barley, the HvFT1 gene integrates signals from vernalization (VERNALIZATION 1, 2 – VRN-H1, VRN-H2), photoperiod (PHOTOPERIOD 1 – PPD-H1) and circadian (EARLY FLOWERING 3 – HvELF3) regulatory pathways for floral induction (Turner et al., 2005; Faure et al., 2012; Boden et al., 2014; Deng et al., 2015). Mutations in these flowering time genes may cause significant changes in both vegetative and reproductive phytomeric iterations (Huang et al., 2023). However, little information is available on how phytomer initiation and elongation are coordinated during morphogenesis (Huang et al., 2024). The effects of vernalization requirement and photoperiod sensitivity on plant developmental stages are much better known than the effects of secondary environmental elements (ambient temperature, light spectra). Temperature affects each phase, and a higher ambient temperature generally accelerates growth and development rates in crop species (Slafer and Rawson, 1994, 1995; Atkinson and Porter, 1996; Slafer et al., 2015). However, it is not clear whether the response to temperature is independent of growth rate and development (Kronenberg et al., 2021). In relation to the light spectrum, it should be pointed out that the far-red spectrum increases plant internodal length, petiole length, plant height and gibberellin content, among others (Kurepin et al., 2010; Hitz et al., 2019). The effect of this spectrum has been studied mainly as shade avoidance responses, which are changes in the growth and development pattern of plants caused by shifts in the light spectrum (in the red:far-red light ratio) caused by neighbouring vegetation (Casal et al., 1986). In Arabidopsis, the regulation of this process is well documented; however, in wheat, it remains limited (Wille et al., 2017). In Arabidopsis, sunlight activates PHYB and CRY1 to repress shade avoidance responses. The loss-of-function mutants of these photosensory receptors show shade avoidance responses under full sunlight (Mazzella and Casal, 2001). Warm conditions reduce the activity of PHYB, which operates as a temperature sensor and further increases the activities of PHYTOCHROME INTERACTING FACTORs (PIF4 and PIF7) by independent temperature sensing mechanisms (Casal and Fankhauser, 2023).

In summary, a more comprehensive and quantitative understanding of the physiological and genetic determinants of time to heading and the partitioning of time among the phenophases of preflowering development would allow the fine-tuning of adaptation and the optimization of development for maximum yield potential under both present and future conditions. Extending the duration of phase intervals with a decisive influence on yield components without modifying the total time to anthesis has been proposed as a promising breeding tool, but this requires detailed information on the mechanism of the genetic and environmental regulation of the start and duration of various phases and their interactions (Chen et al., 2009, 2010). However, variations in environmental parameters in different years under field conditions may produce considerable variability in phenotypic responses, often leading to contradictory results (Snape et al., 1985; Worland, 1996; Worland et al., 1998; Kato et al., 2000). The importance of this research field is also underlined by the fact that neither the changes caused by global climatic change on local climate conditions nor their effects on plant developmental strategies can be exactly predicted (Kiss et al., 2011).

CONCLUSIONS

Studying the genes that determine flowering in Arabidopsis provides a good foundation for mapping orthologous genes in wheat. This can be of great help for further dissecting and analysing QTLs and genes identified by different molecular genetic and genomic tools as well as for studying their functions and interactions in cereals. This review has provided an overview of the regulatory system of the most important genes that determine the vegetative–generative transition of wheat shoot apex (Fig. 2; Table 1). These genes may be organized around four main regulatory pathways, such as earliness per se, light/photoperiod sensitivity, vernalization (cold requirement), hormonal (GA synthesis) and ageing regulation. The results so far have proven the significant differences between the genes determining the vernalization processes of Arabidopsis and crop plants, but the regulatory processes show a high degree of similarity in both mono- and dicotyledonous plants. In wheat, the genetic factors of the vernalization, photoperiod and circadian rhythm control pathways (especially the VRN1, VRN2, VRN3, PPD1, CO and GI genes) integrate signals from the environment (vernalizing temperature, daylength), defining the vegetative–generative transition phase, while the importance of GA synthesis and earliness regulation lies in the fine-tuning of further plant development dependent on a set of partially different environmental factors (ambient temperature, daylength, light intensity, spectral composition of light). This complex process has a fundamental effect on the intensive stem elongation phase, which determines various parameters of grain yield. Several studies have already reported on the major regulatory genes responsible for environmental adaptation in wheat and the role of their allelic variants. These results have been established by experiments with diploid (Triticum monococcum) and tetraploid (Triticum turgidum subsp. durum) species with smaller genome sizes or with specific crossing lines (RIL, NIL, mutant and transgenic lines). However, this review also highlights that the current knowledge of the light and temperature control in the process of wheat heading (especially bread wheat) is not yet comprehensive, with only elements of vernalization and photoperiod control being described in detail. Even less is known about complex regulatory pathways such as the circadian rhythm of wheat and its effect on development, the regulatory pathway of GA, or the genetic regulation of earliness and ageing. These areas are extremely difficult to study because vernalization and photoperiod responses, being the most determining, can hide the effects of other regulatory pathways. However, the number of studies linking new genes to the wheat heading process is increasing year by year, further confirming that this information will be an essential task for the future. Elucidating how the epistatic effects of particular allelic variants in different varieties may influence the expression of particular genes under different environmental conditions and how these may be linked will also be important. In summary, detailed omics-based discovery of wheat’s ability to adapt may become increasingly valuable. Due to rapidly and unpredictably changing climatic effects, the need for breeders to find the genetic materials from which they can produce varieties that are most adaptable to local environmental conditions is increasing. In the future, cultivation of these varieties may ensure adequate quality and quantity of yield.

FUNDING

Funding of this research was provided by TKP2021-NKTA-06 (from the National Research, Development and Innovation Fund, financed under the TKP2021-NKTA funding scheme), and by NKFI-FK-134234 and NKFI-K-142934 (from the National Research, Development and Innovation Fund). T.K. and A.C. were supported by János Bolyai Research Scholarships of the Hungarian Academy of Sciences (BO/00396/21/4 and BO/00416/23/4, respectively).

AUTHOR CONTRIBUTIONS

T.K. and I.K. conceived the article. T.K., Á.D.H., A.C., Z.B. and K.B. wrote the first draft. All authors were involved in revision of the draft manuscript and have agreed to the final content.

CONFLICT OF INTEREST

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

LITERATURE CITED