Plant clock modifications for adapting flowering time to local environments

Identification of the causal mutation in early heading mutant of bread wheat (Triticum aestivum L.) using MutMap approach

In bread wheat (Triticum aestivum L.), fine-tuning the heading time is essential to maximize grain yield. Photoperiod-1 (Ppd-1) and VERNALIZATION 1 (Vrn-1) are major genes affecting photoperiod sensitivity and vernalization requirements, respectively. These genes have predominantly governed heading timing. However, Ppd-1 and Vrn-1 significantly impact heading dates, necessitating another gene that can slightly modify heading dates for fine-tuning. In this study, we developed an early heading mutant from the ethyl methanesulfonate-mutagenized population of the Japanese winter wheat cultivar "Kitahonami." MutMap analysis identified a nonsense mutation in the clock component gene Wheat PHYTOCLOCK 1/LUX ARRHYTHMO (WPCL-D1) as the probable SNP responsible for the early heading mutant on chromosome 3D. Segregation analysis using F2 and F3 populations confirmed that plants carrying the wpcl-D1 allele headed significantly earlier than those with the functional WPCL-D1. The early heading mutant exhibited increased expression levels of Ppd-1 and circadian clock genes, such as WPCL1 and LATE ELONGATED HYPOCOTYL (LHY). Notably, the transcript accumulation levels of Ppd-A1 and Ppd-D1 were influenced by the copy number of the functional WPCL1 gene. These results suggest that a loss-of-function mutation in WPCL-D1 is the causal mutation for the early heading phenotype. Adjusting the functional copy number of WPCL1 will be beneficial in fine-tuning of heading dates.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01478-5.

Flowering time: From physiology, through genetics to mechanism

Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.

The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem

Plants undergo a series of developmental phases throughout their life-cycle, each characterized by specific processes. Three critical features distinguish these phases: the arrangement of primordia (phyllotaxis), the timing of their differentiation (plastochron) and the characteristics of the lateral organs and axillary meristems. Identifying the unique molecular features of each phase, determining the molecular triggers that cause transitions and understanding the molecular mechanisms underlying these transitions are keys to gleaning a complete understanding of plant development. During the vegetative phase, the shoot apical meristem (SAM) facilitates continuous leaf and stem formation, with leaf development as the hallmark. The transition to the reproductive phase induces significant changes in these processes, driven mainly by the protein FT (FLOWERING LOCUS T) in Arabidopsis and proteins encoded by FT orthologs, which are specified as 'florigen'. These proteins are synthesized in leaves and transported to the SAM, and act as the primary flowering signal, although its impact varies among species. Within the SAM, florigen integrates with other signals, culminating in developmental changes. This review explores the central question of how florigen induces developmental phase transition in the SAM. Future research may combine phase transition studies, potentially revealing the florigen-induced developmental phase transition in the SAM.

Light quality-dependent roles of REVEILLE proteins in the circadian system

Several closely related Myb-like activator proteins are known to have partially redundant functions within the plant circadian clock, but their specific roles are not well understood. To clarify the function of the REVEILLE 4, REVEILLE 6, and REVEILLE 8 transcriptional activators, we characterized the growth and clock phenotypes of CRISPR-Cas9-generated single, double, and triple rve mutants. We found that these genes act synergistically to regulate flowering time, redundantly to regulate leaf growth, and antagonistically to regulate hypocotyl elongation. We previously reported that increasing intensities of monochromatic blue and red light have opposite effects on the period of triple rve468 mutants. Here, we further examined light quality-specific phenotypes of rve mutants and report that rve468 mutants lack the blue light-specific increase in expression of some circadian clock genes observed in wild type. To investigate the basis of these blue light-specific circadian phenotypes, we examined RVE protein abundances and degradation rates in blue and red light and found no significant differences between these conditions. We next examined genetic interactions between RVE genes and ZEITLUPE and ELONGATED HYPOCOTYL5, two factors with blue light-specific functions in the clock. We found that the RVEs interact additively with both ZEITLUPE and ELONGATED HYPOCOTYL5 to regulate circadian period, which suggests that neither of these factors are required for the blue light-specific differences that we observed. Overall, our results suggest that the RVEs have separable functions in plant growth and circadian regulation and that they are involved in blue light-specific circadian signaling via a novel mechanism.

A Small-Molecule Modulator Affecting the Clock-Associated PSEUDO-RESPONSE REGULATOR 7 Amount

Circadian clocks are biological timekeeping systems that coordinate genetic, metabolic and physiological behaviors with the external day-night cycle. The clock in plants relies on the transcriptional-translational feedback loops transcription-translation feedback loop (TTFL), consisting of transcription factors including PSUEDO-RESPONSE REGULATOR (PRR) proteins, plant lineage-specific transcriptional repressors. Here, we report that a novel synthetic small-molecule modulator, 5-(3,4-dichlorophenyl)-1-phenyl-1,7-dihydro-4H-pyrazolo[3,4-d] pyrimidine-4,6(5H)-dione (TU-892), affects the PRR7 protein amount. A clock reporter line of Arabidopsis was screened against the 10,000 small molecules in the Maybridge Hitfinder 10K chemical library. This screening identified TU-892 as a period-lengthening molecule. Gene expression analyses showed that TU-892 treatment upregulates CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) mRNA expression. TU-892 treatment reduced the amount of PRR7 protein, a transcriptional repressor of CCA1. Other PRR proteins including TIMING OF CAB EXPRESSION 1 were altered less by TU-892 treatment. TU-892-dependent CCA1 upregulation was attenuated in mutants impaired in PRR7. Collectively, TU-892 is a novel type of clock modulator that reduces the levels of PRR7 protein.

The Roles of the PSEUDO-RESPONSE REGULATORs in Circadian Clock and Flowering Time in Medicago truncatula

PSEUDO-RESPONSE REGULATORs (PRRs) play key roles in the circadian rhythms and flowering in plants. Here, we identified the four members of the PRR family in Medicago truncatula, including MtPRR9a, MtPRR9b, MtPRR7 and MtPRR5, and isolated their Tnt1 retrotransposon-tagged mutants. They were expressed in different organs and were nuclear-localized. The four MtPRRs genes played important roles in normal clock rhythmicity maintenance by negatively regulating the expression of MtGI and MtLHY. Surprisingly, the four MtPRRs functioned redundantly in regulating flowering time under long-day conditions, and the quadruple mutant flowered earlier. Moreover, MtPRR can recruit the MtTPL/MtTPR corepressors and the other MtPRRs to form heterodimers to constitute the core mechanism of the circadian oscillator.

The Triticeae CBF Gene Cluster-To Frost Resistance and Beyond

The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.

Diurnal gene oscillations modulated by RNA metabolism in tomato

Diurnal rhythms are known to regulate the expression of a large number of genes, coordinating plant growth and development with diel changes in light and temperature. However, the impact of RNA metabolism on rhythmic gene oscillations in plant is not yet fully understood. To address this question, we performed transcriptome and degradome profiling on tomato leaves at 6 time points during one 24 h cycle, using RNA-seq and genome-wide mapping of uncapped and cleavage transcripts (GMUCT). Time-series profiling of RNA-seq revealed 9342 diurnal-oscillated genes, which were enriched in various metabolic processes. To quantify the general level of RNA degradation for each gene, we utilized the Proportion Uncapped (PU) metric, which represents the GMUCT/RNA-seq ratio. Oscillated PU analysis revealed that 3885 genes were regulated by rhythmic RNA degradation. The RNA decay of these diurnal genes was highly coordinated with mRNA downregulation during oscillation, highlighting the critical role of internal transcription-degradation balance in rhythmic gene oscillation. Furthermore, we identified 2190 genes undergoing co-translational RNA decay (CTRD) with 5' phosphate read ends enriched at the boundary of ribosomes stalling at translational termination sites. Interestingly, diurnal-changed mRNAs with large amplitudes tended to be co-translationally decay, suggesting that CTRD contributed to the rapid turnover of diurnal mRNAs. Finally, we also identified several genes, whose miRNA cleavage efficiency oscillated in a diurnal manner. Taken together, these findings uncovered the vital functions of RNA metabolism, including rhythmic RNA degradation, CTRD, and miRNA cleavage, in modulating the diurnal mRNA oscillations during diel change at post-transcriptional level in tomato.

Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice

The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.

Myb-like transcription factors have epistatic effects on circadian clock function but additive effects on plant growth

The functions of closely related Myb-like repressor and Myb-like activator proteins within the plant circadian oscillator have been well-studied as separate groups, but the genetic interactions between them are less clear. We hypothesized that these repressors and activators would interact additively to regulate both circadian and growth phenotypes. We used CRISPR-Cas9 to generate new mutant alleles and performed physiological and molecular characterization of plant mutants for five of these core Myb-like clock factors compared with a repressor mutant and an activator mutant. We first examined circadian clock function in plants likely null for both the repressor proteins, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and the activator proteins, REVEILLE 4 (RVE4), REVEILLE (RVE6), and REVEILLE (RVE8). The rve468 triple mutant has a long period and flowers late, while cca1 lhy rve468 quintuple mutants, similarly to cca1 lhy mutants, have poor circadian rhythms and flower early. This suggests that CCA1 and LHY are epistatic to RVE4, RVE6, and RVE8 for circadian clock and flowering time function. We next examined hypocotyl elongation and rosette leaf size in these mutants. The cca1 lhy rve468 mutants have growth phenotypes intermediate between cca1 lhy and rve468 mutants, suggesting that CCA1, LHY, RVE4, RVE6, and RVE8 interact additively to regulate growth. Together, our data suggest that these five Myb-like factors interact differently in regulation of the circadian clock versus growth. More generally, the near-norm al seedling phenotypes observed in the largely arrhythmic quintuple mutant demonstrate that circadian-regulated output processes, like control of hypocotyl elongation, do not always depend upon rhythmic oscillator function.

Crops under past diversification and ongoing climate change: more than just selection of nuclear genes for flowering

Diversification and breeding following domestication and under current climate change across the globe are the two most significant evolutionary events experienced by major crops. Diversification of crops from their wild ancestors has favored dramatic changes in the sensitivity of the plants to the environment, particularly significantly in transducing light inputs to the circadian clock, which has allowed the growth of major crops in the relatively short growing season experienced in the Northern Hemisphere. Historically, mutants and the mapping of quantitative trait loci (QTL) have facilitated the identification and the cloning of genes that underlie major changes of the clock and the regulation of flowering. Recent studies have suggested that the thermal plasticity of the circadian clock output, and not just the core genes that follow temperature compensation, has also been under selection during diversification and breeding. Wild alleles that accelerate output rhythmicity could be beneficial for crop resilience. Furthermore, wild alleles with beneficial and flowering-independent effects under stress indicate their possible role in maintaining a balanced source-sink relationship, thereby allowing productivity under climatic change. Because the chloroplast genome also regulates the plasticity of the clock output, mapping populations including cytonuclear interactions should be utilized within an integrated field and clock phenomics framework. In this review, we highlight the need to integrate physiological and developmental approaches (physio-devo) to gain a better understanding when re-domesticating wild gene alleles into modern cultivars to increase their robustness under abiotic heat and drought stresses.

Fitness and Rhizobacteria of F2, F3 Hybrids of Herbicide-Tolerant Transgenic Soybean and Wild Soybean

The introduction of herbicide-tolerant (HT) transgenic soybeans (Glycine max (L.) Merr.) into farming systems raises great concern that transgenes may flow to endemic wild soybeans (Glycine soja Sieb. et Zucc.) via pollen, which may increase the ecological risks by increasing the fitness of hybrids under certain conditions and threaten the genetic diversity of wild soybean populations. In order to demonstrate the potential risk of gene flow from the HT soybean to the wild soybean, the fitness of F2 and F3 hybrids obtained from two wild soybean populations (HLJHRB-1, JSCZ) collected from China and the HT soybean was measured under farmland and wasteland soil conditions, as well as with or without weed competition. Compared with their wild progenitors, the F2 and F3 hybrids of HLJHRB-1 displayed a higher emergence rate, higher aboveground dry biomass, more pods and filled-seed plants, as well as better composite fitness under four planting conditions. The F2 and F3 hybrids of JSCZ also displayed a higher emergence rate, higher aboveground dry biomass, more pods, and more filled seeds per plant under mixed planting, whereas these characteristics were lower under pure planting conditions in wasteland and farmland soil. Therefore, the composite fitness of JSCZ hybrids was higher or lower depending on the planting conditions. Furthermore, the soil microbial communities of the F3 of HLJHRB-1, JSCZ, and the wild soybean were investigated with 16S rDNA sequencing, which showed that low alpha diversity of rhizobacteria was relative to high fitness, and Rhizobium played an important role in promoting F3 plant growth.

Transcriptome analysis of floral bud development and function analysis of a novel CO gene in Paeonia × lemoinei 'High Noon'

Paeonia × lemoinei 'High Noon' is one of the most important cultivars in tree peony (Paeonia sect. Moutan), a traditional horticultural plant in China, with a re-blooming characteristic which was quite different from other cultivars. So, the genetic resources in 'High Noon' were incredibly valuable in flowering-time-modified molecular breeding in tree peony. However, the molecular mechanism underlying the floral bud formation of 'High Noon' was not clear yet. To explore the molecular mechanism in this process, the transcriptomes of three stages during floral bud development were deeply analyzed in this study. As a result, a total of 5816 differentially expressed genes (DEGs) were identified between the three developmental stages, and pathways including ''DNA replication'', ''metabolic pathways'', ''circadian rhythm'', and ''plant hormone signal transduction'' were mostly enriched in the functional enrichment and expression pattern analysis. Furthermore, a total of 584 genes related to the photoperiod pathway were further identified and a novel CO homolog gene PlCO was identified to be a stable hydrophilic protein, which contained both CCT domain and B-box domain. Over-expression of PlCO in Arabidopsis resulted in early flowering, which suggested a promotion role of flowering. The PlCO protein localized in nucleus and possessed a transcription activity ability, which implied that PlCO might function as a transcription factor. The transcriptome analysis revealed pathways involved in floral bud development in tree peony and provided new insight into the regulatory network underlying the floral bud development. The gene identification in 'High Noon' provided new valuable candidate genes for flowering-time-modified molecular breeding in tree peony.

Potato virus X-delivered CRISPR activation programs lead to strong endogenous gene induction and transient metabolic reprogramming in Nicotiana benthamiana

Programmable transcriptional regulators based on CRISPR architecture are promising tools for the induction of plant gene expression. In plants, CRISPR gene activation is effective with respect to modulating development processes, such as the flowering time or customizing biochemical composition. The most widely used method for delivering CRISPR components into the plant is Agrobacterium tumefaciens-mediated genetic transformation, either transient or stable. However, as a result of their versatility and their ability to move, virus-derived systems have emerged as an interesting alternative for supplying the CRISPR components to the plant, in particular guide RNA (gRNA), which represents the variable component in CRISPR strategies. In the present study, we describe a Potato virus X-derived vector that, upon agroinfection in Nicotiana benthamiana, serves as a vehicle for delivery of gRNAs, producing highly specific virus-induced gene activation. The system works in combination with a N. benthamiana transgenic line carrying the remaining complementary CRISPR gene activation components, specifically the dCasEV2.1 cassette, which has been shown previously to mediate strong programmable transcriptional activation in plants. Using an easily scalable, non-invasive spraying method, we show that gRNA-mediated activation programs move locally and systemically, generating a strong activation response in different target genes. Furthermore, by activating three different endogenous MYB transcription factors, we demonstrate that this Potato virus X-based virus-induced gene reprogramming strategy results in program-specific metabolic fingerprints in N. benthamiana leaves characterized by distinctive phenylpropanoid-enriched metabolite profiles.