Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals

Photoperiod and temperature synergistically regulate heading date and regional adaptation in rice

Plants must accurately integrate external environmental signals with their own development to initiate flowering at the appropriate time for reproductive success. Photoperiod and temperature are key external signals that determine flowering time; both are cyclical and periodic, and they are closely related. In this review, we describe photoperiod-sensitive genes that simultaneously respond to temperature signals in rice (Oryza sativa). We introduce the mechanisms by which photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. We also discuss the prospects for designing different combinations of heading date genes and other cold tolerance or thermo-tolerance genes to help rice better adapt to changes in light and temperature via molecular breeding to enhance yield in the future.

A FLOWERING LOCUS T ortholog is associated with photoperiod-insensitive flowering in hemp (Cannabis sativa L.)

Hemp (Cannabis sativa L.) is an extraordinarily versatile crop, with applications ranging from medicinal compounds to seed oil and fibre products. Cannabis sativa is a short-day plant, and its flowering is highly controlled by photoperiod. However, substantial genetic variation exists for photoperiod sensitivity in C. sativa, and photoperiod-insensitive ("autoflower") cultivars are available. Using a bi-parental mapping population and bulked segregant analysis, we identified Autoflower2, a 0.5 Mbp locus significantly associated with photoperiod-insensitive flowering in hemp. Autoflower2 contains an ortholog of the central flowering time regulator FLOWERING LOCUS T (FT) from Arabidopsis thaliana which we termed CsFT1. We identified extensive sequence divergence between alleles of CsFT1 from photoperiod-sensitive and insensitive cultivars of C. sativa, including a duplication of CsFT1 and sequence differences, especially in introns. Furthermore, we observed higher expression of one of the CsFT1 copies found in the photoperiod-insensitive cultivar. Genotyping of several mapping populations and a diversity panel confirmed a correlation between CsFT1 alleles and photoperiod response, affirming that at least two independent loci involved in the photoperiodic control of flowering, Autoflower1 and Autoflower2, exist in the C. sativa gene pool. This study reveals the multiple independent origins of photoperiod insensitivity in C. sativa, supporting the likelihood of a complex domestication history in this species. By integrating the genetic relaxation of photoperiod sensitivity into novel C. sativa cultivars, expansion to higher latitudes will be permitted, thus allowing the full potential of this versatile crop to be reached.

Revisiting the role and mechanism of ELF3 in circadian clock modulation

The gene encoding EARLY FLOWERING3 (ELF3) is necessary for photoperiodic flowering and the normal regulation of circadian rhythms. It provides important information at the cellular level to uncover the biological mechanisms that improve plant growth and development. ELF3 interactions with transcription factors such as BROTHER OF LUX ARRHYTHMO (BOA), LIGHT-REGULATED WD1 (LWD1), PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), PHYTOCHROME-INTERACTING FACTOR 7 (PIF7), and LUX ARRHYTHMO (LUX) suggest a role in evening complex (EC) independent pathways, demanding further investigation to elucidate the EC-dependent versus EC-independent mechanisms. The ELF3 regulation of flowering time about photoperiod and temperature variations can also optimize crop cultivation across diverse latitudes. In this review paper, we summarize how ELF3's role in the circadian clock and light-responsive flowering control in crops offers substantial potential for scientific advancement and practical applications in biotechnology and agriculture. Despite its essential role in crop adaptation, very little is known in many important crops. Consequently, comprehensive and targeted research is essential for extrapolating ELF3-related insights from Arabidopsis to other crops, utilizing both computational and experimental methodologies. This research should prioritize investigations into ELF3's protein-protein interactions, post-translational modifications, and genomic targets to elucidate its contribution to accurate circadian clock regulation.

OsCOL5 suppresses heading through modulation of Ghd7 and Ehd2, enhancing rice yield

KEY MESSAGE

OsCOL5, an ortholog of Arabidopsis COL5, is involved in photoperiodic flowering and enhances rice yield through modulation of Ghd7 and Ehd2 and interactions with OsELF3-1 and OsELF3-2. Heading date, also known as flowering time, plays a crucial role in determining the adaptability and yield potential of rice (Oryza sativa L.). CONSTANS (CO)-like is one of the most critical flowering-associated gene families, members of which are evolutionarily conserved. Here, we report the molecular functional characterization of OsCOL5, an ortholog of Arabidopsis COL5, which is involved in photoperiodic flowering and influences rice yield. Structural analysis revealed that OsCOL5 is a typical member of CO-like family, containing two B-box domains and one CCT domain. Rice plants overexpressing OsCOL5 showed delayed heading and increases in plant height, main spike number, total grain number per plant, and yield per plant under both long-day (LD) and short-day (SD) conditions. Gene expression analysis indicated that OsCOL5 was primarily expressed in the leaves and stems with a diurnal rhythm expression pattern. RT-qPCR analysis of heading date genes showed that OsCOL5 suppressed flowering by up-regulating Ghd7 and down-regulating Ehd2, consequently reducing the expression of Ehd1, Hd3a, RFT1, OsMADS14, and OsMADS15. Yeast two-hybrid experiments showed direct interactions of OsCOL5 with OsELF3-1 and OsELF3-2. Further verification showed specific interactions between the zinc finger/B-box domain of OsCOL5 and the middle region of OsELF3-1 and OsELF3-2. Yeast one-hybrid assays revealed that OsCOL5 may bind to the CCACA motif. The results suggest that OsCOL5 functions as a floral repressor, playing a vital role in rice's photoperiodic flowering regulation. This gene shows potential in breeding programs aimed at improving rice yield by influencing the timing of flowering, which directly impacts crop productivity.

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.

SULTR2;1 Adjusts the Bolting Timing by Transporting Sulfate from Rosette Leaves to the Primary Stem

Sulfur (S) is an essential macronutrient for plant growth and metabolism. SULTR2;1 is a low-affinity sulfate transporter facilitating the long-distance transport of sulfate in Arabidopsis. The physiological function of SULTR2;1 in the plant life cycle still needs to be determined. Therefore, we analyzed the sulfate transport, S-containing metabolite accumulation and plant growth using Arabidopsis SULTR2;1 disruption lines, sultr2;1-1 and sultr2;1-2, from seedling to mature growth stages to clarify the metabolic and physiological roles of SULTR2;1. We observed that sulfate distribution to the stems was affected in sultr2;1 mutants, resulting in decreased levels of sulfate, cysteine, glutathione (GSH) and total S in the stems, flowers and siliques; however, the GSH levels increased in the rosette leaves. This suggested the essential role of SULTR2;1 in sulfate transport from rosette leaves to the primary stem. In addition, sultr2;1 mutants unexpectedly bolted earlier than the wild-type without affecting the plant biomass. Correlation between GSH levels in rosette leaves and the bolting timing suggested that the rosette leaf GSH levels or limited sulfate transport to the early stem can trigger bolting. Overall, this study demonstrated the critical roles of SULTR2;1 in maintaining the S metabolite levels in the aerial part and transitioning from the vegetative to the reproductive growth phase.

CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits

How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.

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.

Florigen-producing cells express FPF1-LIKE PROTEIN 1 that accelerates flowering and stem growth in long days with sunlight red/far-red ratio in Arabidopsis

Seasonal changes in spring induce flowering by expressing the florigen, FLOWERING LOCUS T (FT), in Arabidopsis. FT is expressed in unique phloem companion cells with unknown characteristics. The question of which genes are co-expressed with FT and whether they have roles in flowering remains elusive. Through tissue-specific translatome analysis, we discovered that under long-day conditions with the natural sunlight red/far-red ratio, the FT-producing cells express a gene encoding FPF1-LIKE PROTEIN 1 (FLP1). The master FT regulator, CONSTANS (CO), controls FLP1 expression, suggesting FLP1's involvement in the photoperiod pathway. FLP1 promotes early flowering independently of FT, is active in the shoot apical meristem, and induces the expression of SEPALLATA 3 (SEP3), a key E-class homeotic gene. Unlike FT, FLP1 facilitates inflorescence stem elongation. Our cumulative evidence indicates that FLP1 may act as a mobile signal. Thus, FLP1 orchestrates floral initiation together with FT and promotes inflorescence stem elongation during reproductive transitions.

Genomic and phenotypic signatures provide insights into the wide adaptation of a global plant invader

Invasive alien species are primary drivers of biodiversity loss and species extinction. Smooth cordgrass (Spartina alterniflora) is one of the most aggressive invasive plants in coastal ecosystems around the world. However, the genomic bases and evolutionary mechanisms underlying its invasion success have remained largely unknown. Here, we assembled a chromosome-level reference genome and performed phenotypic and population genomic analyses between native US and introduced Chinese populations. Our phenotypic comparisons showed that introduced Chinese populations have evolved competitive traits, such as early flowering time and greater plant biomass, during secondary introductions along China's coast. Population genomic and transcriptomic inferences revealed distinct evolutionary trajectories of low- and high-latitude Chinese populations. In particular, genetic mixture among different source populations, together with independent natural selection acting on distinct target genes, may have resulted in high genome dynamics of the introduced Chinese populations. Our study provides novel phenotypic and genomic evidence showing how smooth cordgrass rapidly adapts to variable environmental conditions in its introduced ranges. Moreover, candidate genes related to flowering time, fast growth, and stress tolerance (i.e., salinity and submergence) provide valuable genetic resources for future improvement of cereal crops.

The TaSOC1-TaVRN1 module integrates photoperiod and vernalization signals to regulate wheat flowering

Wheat needs different durations of vernalization, which accelerates flowering by exposure to cold temperature, to ensure reproductive development at the optimum time, as that is critical for adaptability and high yield. TaVRN1 is the central flowering regulator in the vernalization pathway and encodes a MADS-box transcription factor (TF) that usually works by forming hetero- or homo-dimers. We previously identified that TaVRN1 bound to an MADS-box TF TaSOC1 whose orthologues are flowering activators in other plants. The specific function of TaSOC1 and the biological implication of its interaction with TaVRN1 remained unknown. Here, we demonstrated that TaSOC1 was a flowering repressor in the vernalization and photoperiod pathways by overexpression and knockout assays. We confirmed the physical interaction between TaSOC1 and TaVRN1 in wheat protoplasts and in planta, and further validated their genetic interplay. A Flowering Promoting Factor 1-like gene TaFPF1-2B was identified as a common downstream target of TaSOC1 and TaVRN1 through transcriptome and chromatin immunoprecipitation analyses. TaSOC1 competed with TaVRT2, another MADS-box flowering regulator, to bind to TaVRN1; their coding genes synergistically control TaFPF1-2B expression and flowering initiation in response to photoperiod and low temperature. We identified major haplotypes of TaSOC1 and found that TaSOC1-Hap1 conferred earlier flowering than TaSOC1-Hap2 and had been subjected to positive selection in wheat breeding. We also revealed that wheat SOC1 family members were important domestication loci and expanded by tandem and segmental duplication events. These findings offer new insights into the regulatory mechanism underlying flowering control along with useful genetic resources for wheat improvement.

Hybrid Rice Production: A Worldwide Review of Floral Traits and Breeding Technology, with Special Emphasis on China

Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field.

Phytohormone biosynthesis and transcriptional analyses provide insight into the main growth stage of male and female cones Pinus koraiensis

The cone is a crucial component of the whole life cycle of gymnosperm and an organ for sexual reproduction of gymnosperms. In Pinus koraiensis, the quantity and development process of male and female cones directly influence seed production, which in turn influences the tree's economic value. There are, however, due to the lack of genetic information and genomic data, the morphological development and molecular mechanism of female and male cones of P. koraiensis have not been analyzed. Long-term phenological observations were used in this study to document the main process of the growth of both male and female cones. Transcriptome sequencing and endogenous hormone levels at three critical developmental stages were then analyzed to identify the regulatory networks that control these stages of cones development. The most significant plant hormones influencing male and female cones growth were discovered to be gibberellin and brassinosteroids, according to measurements of endogenous hormone content. Additionally, transcriptome sequencing allowed the identification of 71,097 and 31,195 DEGs in male and female cones. The synthesis and control of plant hormones during cones growth were discovered via enrichment analysis of key enrichment pathways. FT and other flowering-related genes were discovered in the coexpression network of flower growth development, which contributed to the growth development of male and female cones of P. koraiensis. The findings of this work offer a cutting-edge foundation for understanding reproductive biology and the molecular mechanisms that control the growth development of male and female cones in P. koraiensis.

Synergistic optimization of crops by combining early maturation with other agronomic traits

Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.

Phosphorylation mediated regulation of RNA splicing in plants

For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.

Transcriptome analysis during vernalization in wheat (Triticum aestivum L.)

BACKGROUND

Vernalization, as a vital process in the life cycle of winter cereal, has important effects on floral organ formation and flowering time. Many morphological changes together with molecular changes occur during the vernalization period. Here, we used transcriptome sequencing to analyze the transcriptomic changes in wheat leaves before, during and after vernalization using the winter wheat cultivar 'Shiluan02-1'.

RESULTS

A total of 16,370 differentially expressed genes were obtained across different vernalization periods. Gene Ontology enrichment analysis revealed that photoperiodism, photoprotection, photosynthesis, lipid transport and biosynthetic process, and chlorophyll metabolic process were closely related to vernalization. In addition, AP2/ERF, C2H2, bHLH, WRKY, MYB, MYB-related, and NAC transcription factors were significantly enriched during vernalization, and the transcription factor expression patterns suggested the intricate regulation of transcription factor modules in plant vernalization pathways. Analysis of gene expression patterns of the MADS-box transcription factor genes showed different expression patterns during vernalization phases, among which VERNALIZATION1 (VRN1) genes were found to gradually increase during vernalization periods from V0 to V35, while decline in the V42 phase, then increase after vernalization. The Tavrt-2 gene cooperated with Tavrn1 to regulate flowering induced by vernalization, and its expression level was rapidly increased by vernalization but declined in the V42 phase and then increased after vernalization. Some genes from the ICE-CBF-COR pathway were also identified, and additional analysis indicated that some key genes related to phytohormone biosynthesis and signal transduction were enriched during the vernalization period, such as gibberellic acid, ethylene, abscisic acid and jasmonic acid biosynthesis and signaling pathway genes.

CONCLUSIONS

Our study provides valuable molecular information for future studies on wheat vernalization regulation and also serves as an excellent reference for future wheat breeding.

An integrated transcriptome and metabolome analysis reveals the gene network regulating flower development in Pogostemon cablin

Pogostemon cablin is a well-known protected species widely used in medicine and spices, however the underlying molecular mechanisms and metabolite dynamics of P. cablin flower development remain unclear due to the difficulty in achieving flowering in this species. A comparison of the transcriptome and widely targeted metabolome during P. cablin flower development was first performed in this study. Results showed that a total of 13,469 differentially expressed unigenes (DEGs) and 371 differentially accumulated metabolites (DAMs) were identified. Transcriptomic analysis revealed that the DEGs were associated with starch and sucrose metabolism, terpenoid biosynthesis and phenylpropanoid biosynthesis. Among these DEGs, 75 MIKC-MADS unigenes were associated with the development of floral organs. Gibberellins (GAs), auxin, and aging signaling might form a cross-regulatory network to regulate flower development in P. cablin. According to the metabolic profile, the predominant DAMs were amino acids, flavonoids, terpenes, phenols, and their derivatives. The accumulation patterns of these predominant DAMs were closely associated with the flower developmental stage. The integration analysis of DEGs and DAMs indicated that phenylpropanoids, flavonoids, and amino acids might be accumulated due to the activation of starch and sucrose metabolism. Our results provide some important insights for elucidating the reproductive process, floral organ, and color formation of P. cablin flowers at the molecular level. These results will improve our understanding of the molecular and genetic mechanisms involved in the floral development of P. cablin.

Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time

KEY MESSAGE

We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.

Photoperiodic flowering in Arabidopsis: Multilayered regulatory mechanisms of CONSTANS and the florigen FLOWERING LOCUS T

The timing of flowering affects the success of sexual reproduction. This developmental event also determines crop yield, biomass, and longevity. Therefore, this mechanism has been targeted for improvement along with crop domestication. The underlying mechanisms of flowering are highly conserved in angiosperms. Central to these mechanisms is how environmental and endogenous conditions control transcriptional regulation of the FLOWERING LOCUS T (FT) gene, which initiates floral development under long-day conditions in Arabidopsis. Since the identification of FT as florigen, efforts have been made to understand the regulatory mechanisms of FT expression. Although many transcriptional regulators have been shown to directly influence FT, the question of how they coordinately control the spatiotemporal expression patterns of FT still requires further investigation. Among FT regulators, CONSTANS (CO) is the primary one whose protein stability is tightly controlled by phosphorylation and ubiquitination/proteasome-mediated mechanisms. In addition, various CO interaction partners, some of them previously identified as FT transcriptional regulators, positively or negatively modulate CO protein activity. The FT promoter possesses several transcriptional regulatory "blocks," highly conserved regions among Brassicaceae plants. Different transcription factors bind to specific blocks and affect FT expression, often causing topological changes in FT chromatin structure, such as the formation of DNA loops. We discuss the current understanding of the regulation of FT expression mainly in Arabidopsis and propose future directions related to this topic.

OsCRY2 and OsFBO10 co-regulate photomorphogenesis and photoperiodic flowering in indica rice

Cryptochromes (CRYs) are a class of photoreceptors that perceive blue/ultraviolet-A light of the visible spectrum to mediate a vast number of physiological responses in bacteria, fungi, animals and plants. In the present study, we have characterized OsCRY2 in a photoperiod sensitive indica variety, Basmati 370, by generating and analyzing overexpression (OE) and knock-down (KD) transgenic lines. The OsCRY2^OE lines displayed dwarfism as shown in their reduced plant height and leaf length, attributed largely by an overall reduction in their cell size. The OsCRY2^OE lines flowered significantly earlier and showed shorter and broader seeds with an overall reduced seed weight. The OsCRY2^KD lines showed contrasting phenotypes, such as increased plant height and delayed flowering, however, decreased seed size and weight were also observed in the KD lines, along with reduced spikelet fertility and high seed shattering rate in mature panicles. Novel interactions were confirmed between OsCRY2 and members of ZEITLUPE family of blue/ultraviolet-A light photoreceptors, encoded by OsFBO8, OsFBO9 and OsFBO10 which are orthologous to ZEITLUPE (ZTL), LOV KELCH PROTEIN2 (LKP2) and FLAVIN BINDING, KELCH REPEAT F-BOX1 (FKF1), respectively, of Arabidopsis thaliana. Since FKF1 is known to play a role in regulating photoperiodic flowering, OsFBO10 was chosen for further studies. OsCRY2 and OsFBO10 interacted in the nucleus and cytoplasm of the cell and cross-regulated the expression of each other. They were also found to regulate the expression of several genes involved in photoperiodic flowering in rice. Both OsCRY2 and OsFBO10 played a positive role in photomorphogenic responses in different light conditions. The physical interaction of OsCRY2 with OsFBO10, their involvement in common physiological and developmental pathways and their cross-regulation of each other suggest that the two photoreceptors may regulate common developmental pathways in plants, either jointly or redundantly.

The amino acid residue E96 of Ghd8 is crucial for the formation of the flowering repression complex Ghd7-Ghd8-OsHAP5C in rice

Ghd7 is an important gene involved in the photoperiod flowering pathway in rice. A Ghd7-involved transcriptional regulatory network has been established, but its translational regulatory pathway is poorly understood. The mutant suppressor of overexpression of Ghd7 (sog7) was identified from EMS-induced mutagenesis on the background of ZH11 overexpressing Ghd7. MutMap analysis revealed that SOG7 is allelic to Ghd8 and delayed flowering under long-day (LD) conditions. Biochemical assays showed that Ghd8 interacts with OsHAP5C and Ghd7 both in vivo and in vitro. Surprisingly, a point mutation E96K in the α2 helix of the Ghd8 histone fold domain (HFD) destroyed its ability to interact with Ghd7. The prediction of the structure shows that mutated amino acid is located in the interaction region of CCT/NF-YB/YC complexes, which alter the structure of α4 of Ghd8. This structural difference prevents the formation of complex NF-YB/YC. The triple complex of Ghd8-OsHAP5C-Ghd7 directly bound to the promotor of Hd3a and downregulated the expression of Ehd1, Hd3a and RFT1, and finally resulted in a delayed heading. These findings are helpful in deeply understanding the Ghd7-involved photoperiod flowering pathway and promote the elucidation of rice heading.

Prospects for rice in 2050

A key to achieve the goals put forward in the UN's 2030 Agenda for Sustainable Development, it will need transformative change to our agrifood systems. We must mount to the global challenge to achieve food security in a sustainable manner in the context of climate change, population growth, urbanization, and depletion of natural resources. Rice is one of the major staple cereal crops that has contributed, is contributing, and will still contribute to the global food security. To date, rice yield has held pace with increasing demands, due to advances in both fundamental and biological studies, as well as genomic and molecular breeding practices. However, future rice production depends largely on the planting of resilient cultivars that can acclimate and adapt to changing environmental conditions. This Special Issue highlight with reviews and original research articles the exciting and growing field of rice-environment interactions that could benefit future rice breeding. We also outline open questions and propose future directions of 2050 rice research, calling for more attentions to develop environment-resilient rice especially hybrid rice, upland rice and perennial rice.

How ambient temperature affects the heading date of foxtail millet (Setaria italica)

Foxtail millet (Setaria italica), a short-day plant, is one of the important crops for food security encountering climate change, particularly in regions where it is a staple food. Under the short-day condition in Taiwan, the heading dates (HDs) of foxtail millet accessions varied by genotypes and ambient temperature (AT). The allelic polymorphisms in flowering time (FT)-related genes were associated with HD variations. AT, in the range of 13°C-30°C that was based on field studies at three different latitudes in Taiwan and observations in the phytotron at four different AT regimes, was positively correlated with growth rate, and high AT promoted HD. To elucidate the molecular mechanism of foxtail millet HD, the expression of 14 key FT-related genes in four accessions at different ATs was assessed. We found that the expression levels of SiPRR95, SiPRR1, SiPRR59, SiGhd7-2, SiPHYB, and SiGhd7 were negatively correlated with AT, whereas the expression levels of SiEhd1, SiFT11, and SiCO4 were positively correlated with AT. Furthermore, the expression levels of SiGhd7-2, SiEhd1, SiFT, and SiFT11 were significantly associated with HD. A coexpression regulatory network was identified that shown genes involved in the circadian clock, light and temperature signaling, and regulation of flowering, but not those involved in photoperiod pathway, interacted and were influenced by AT. The results reveal how gene × temperature and gene × gene interactions affect the HD in foxtail millet and could serve as a foundation for breeding foxtail millet cultivars for shift production to increase yield in response to global warming.

Transcriptomic Analysis of Flowering Time Genes in Cultivated Chickpea and Wild Cicer

Chickpea (Cicer arietinum L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in Cicer is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 96029, later flowering C. arietinum accessions, and two wild species, C. reticulatum and C. echinospermum. We identify Cicer orthologs of A. thaliana flowering time genes and analyze differential expression of 278 genes between four species/accessions, three tissue types, and two conditions. Our results show that the differences in gene expression between ICCV 96029 and other cultivated chickpea accessions are vernalization-dependent. In addition, we highlight the role of FTa3, an ortholog of FLOWERING LOCUS T in Arabidopsis, in the vernalization response of cultivated chickpea. A common set of differentially expressed genes was found for all comparisons between wild species and cultivars. The direction of expression change for different copies of the FT-INTERACTING PROTEIN 1 gene was variable in different comparisons, which suggests complex mechanisms of FT protein transport. Our study makes a contribution to the understanding of flowering time control in Cicer, and can provide genetic strategies to further improve this important agronomic trait.

Analysis of the Utilization and Prospects of CRISPR-Cas Technology in the Annotation of Gene Function and Creation New Germplasm in Maize Based on Patent Data

Maize (Zea mays L.) is a food crop with the largest planting area and the highest yield in the world, and it plays a vital role in ensuring global food security. Conventional breeding methods are costly, time-consuming, and ineffective in maize breeding. In recent years, CRISPR-Cas editing technology has been used to quickly generate new varieties with high yield and improved grain quality and stress resistance by precisely modifying key genes involved in specific traits, thus becoming a new engine for promoting crop breeding and the competitiveness of seed industries. Using CRISPR-Cas, a range of new maize materials with high yield, improved grain quality, ideal plant type and flowering period, male sterility, and stress resistance have been created. Moreover, many patents have been filed worldwide, reflecting the huge practical application prospects and commercial value. Based on the existing patent data, we analyzed the development process, current status, and prospects of CRISPR-Cas technology in dissecting gene function and creating new germplasm in maize, providing information for future basic research and commercial production.

Temperature-mediated flower size plasticity in Arabidopsis

Organisms can rapidly mitigate the effects of environmental changes by changing their phenotypes, known as phenotypic plasticity. Yet, little is known about the temperature-mediated plasticity of traits that are directly linked to plant fitness such as flower size. We discovered substantial genetic variation in flower size plasticity to temperature both among selfing Arabidopsis thaliana and outcrossing A. arenosa individuals collected from a natural growth habitat. Genetic analysis using a panel of 290 A. thaliana accession and mutant lines revealed that MADS AFFECTING FLOWERING (MAF) 2-5 gene cluster, previously shown to regulate temperature-mediated flowering time, was associated to the flower size plasticity to temperature. Furthermore, our findings pointed that the control of plasticity differs from control of the trait itself. Altogether, our study advances the understanding of genetic and molecular factors underlying plasticity on fundamental fitness traits, such as flower size, in response to future climate scenarios.

Role of metabolites in flower development and discovery of compounds controlling flowering time

Flowering is one of the most important physiological processes of plants that ensures continuity of genetic flow from one generation to the next and also maintains food security. Therefore, impact of various climate-related abiotic stresses on flowering have been assessed to evaluate the long-term impact of global climate change. In contrast to the enormous volume of research that has been conducted at the genetic, transcriptional, post-transcriptional, and protein level, much less attention has been paid to understand the role of various metabolites in flower induction and floral organ development during normal growth or in stressed environmental condition. This review article aims at summarizing information on various primary (e.g., carbohydrates, lipids, fatty acid derivatives, protein and amino acids) and secondary metabolites (e.g., polyamines, phenolics, neuro-indoles, phenylpropanoid, flavonoids and terpenes) that have so far been identified either during flower induction or in individual floral organs implying their possible role in organ development. Specialized metabolites responsible for flower colour, scent and shape to support plant-pollinator interaction have been extensively reviewed by many research groups and hence are not considered in this article. Many of the metabolites discussed here may be used as metabolomarkers to identify tolerant crop genotypes. Several agrochemicals have been successfully used to release endodormancy in temperate trees. Along the same line, a strategy that combines metabolite profiling, screening of small-molecule libraries, and structural alteration of selected compounds has been proposed in order to identify novel lead compounds that can regulate flowering time when applied exogenously.

Bifunctional regulators of photoperiodic flowering in short day plant rice

Photoperiod is acknowledged as a crucial environmental factor for plant flowering. According to different responses to photoperiod, plants were divided into short-day plants (SDPs), long-day plants (LDPs), and day-neutral plants (DNPs). The day length measurement system of SDPs is different from LDPs. Many SDPs, such as rice, have a critical threshold for day length (CDL) and can even detect changes of 15 minutes for flowering decisions. Over the last 20 years, molecular mechanisms of flowering time in SDP rice and LDP Arabidopsis have gradually clarified, which offers a chance to elucidate the differences in day length measurement between the two types of plants. In Arabidopsis, CO is a pivotal hub in integrating numerous internal and external signals for inducing photoperiodic flowering. By contrast, Hd1 in rice, the homolog of CO, promotes and prevents flowering under SD and LD, respectively. Subsequently, numerous dual function regulators, such as phytochromes, Ghd7, DHT8, OsPRR37, OsGI, OsLHY, and OsELF3, were gradually identified. This review assesses the relationship among these regulators and a proposed regulatory framework for the reversible mechanism, which will deepen our understanding of the CDL regulation mechanism and the negative response to photoperiod between SDPs and LDPs.

SELF PRUNING 3C is a flowering repressor that modulates seed germination, root architecture, and drought responses

Allelic variation in the CETS (CENTRORADIALIS, TERMINAL FLOWER 1, SELF PRUNING) gene family controls agronomically important traits in many crops. CETS genes encode phosphatidylethanolamine-binding proteins that have a central role in the timing of flowering as florigenic and anti-florigenic signals. The great expansion of CETS genes in many species suggests that the functions of this family go beyond flowering induction and repression. Here, we characterized the tomato SELF PRUNING 3C (SP3C) gene, and show that besides acting as a flowering repressor it also regulates seed germination and modulates root architecture. We show that loss of SP3C function in CRISPR/Cas9-generated mutant lines increases root length and reduces root side branching relative to the wild type. Higher SP3C expression in transgenic lines promotes the opposite effects in roots, represses seed germination, and also improves tolerance to water stress in seedlings. These discoveries provide new insights into the role of SP paralogs in agronomically relevant traits, and support future exploration of the involvement of CETS genes in abiotic stress responses.

The adaptive nature of the plant circadian clock in natural environments

The plant circadian clock coordinates developmental, physiological, and metabolic processes with diel changes in light and temperature throughout the year. The balance between the persistence and plasticity of the clock in response to predictable and unpredictable environmental changes may be key to the clock's adaptive nature across temporal and spatial scales. Studies under controlled conditions have uncovered critical signaling pathways involved in light and temperature perception by the clock; however, they don't account for the natural lag of temperature behind photoperiod. Studies in natural environments provide key insights into the clock's adaptive advantage under more complex natural settings. Here, we discuss the role of the circadian clock in light and temperature perception and signaling, how the clock integrates these signals for a coordinated and adaptive response, and the adaptive advantage conferred by the clock across time and space in natural environments.

Flowering time runs hot and cold

Evidence suggests that anthropogenically-mediated global warming results in accelerated flowering for many plant populations. However, the fact that some plants are late flowering or unaffected by warming, underscores the complex relationship between phase change, temperature, and phylogeny. In this review, we present an emerging picture of how plants sense temperature changes, and then discuss the independent recruitment of ancient flowering pathway genes for the evolution of ambient, low, and high temperature-regulated reproductive development. As well as revealing areas of research required for a better understanding of how past thermal climates have shaped global patterns of plasticity in plant phase change, we consider the implications for these phenological thermal responses in light of climate change.

Regulatory network for FOREVER YOUNG FLOWER-like genes in regulating Arabidopsis flower senescence and abscission

FOREVER YOUNG FLOWER (FYF) has been reported to play an important role in regulating flower senescence/abscission. Here, we functionally analyzed five Arabidopsis FYF-like genes, two in the FYF subgroup (FYL1/AGL71 and FYL2/AGL72) and three in the SOC1 subgroup (SOC1/AGL20, AGL19, and AGL14/XAL2), and showed their involvement in the regulation of flower senescence and/or abscission. We demonstrated that in FYF subgroup, FYF has both functions in suppressing flower senescence and abscission, FYL1 only suppresses flower abscission and FYL2 has been converted as an activator to promote flower senescence. In SOC1 subgroup, AGL19/AGL14/SOC1 have only one function in suppressing flower senescence. We also found that FYF-like proteins can form heterotetrameric complexes with different combinations of A/E functional proteins (such as AGL6 and SEP1) and AGL15/18-like proteins to perform their functions. These findings greatly expand the current knowledge behind the multifunctional evolution of FYF-like genes and uncover their regulatory network in plants.

Transcriptome Analysis of Lycoris chinensis Bulbs Reveals Flowering in the Age-Mediated Pathway

Lycoris is a summer bulbous flower that commonly needs to go through a long period of vegetative growth for 3 to 5 years before flowering. Plant flowering is regulated by a complex genetic network. Compared with most perennial flowers, knowledge on the molecular mechanism responsible for floral transition in bulbous flowers is lacking, and only a few genes that regulate flowering have been identified with few reports on the floral transition in Lycoris. In this study, we identified many differentially expressed genes (DEGs) and transcription factors (TFs) by RNA-Seq in L. chinensis bulbs of different ages, including one- to four-year-old nonflowering bulbs and four-year-old flowering bulbs. Some DEGs were enriched in Gene Ontology (GO) terms between the three- and four-year-old bulbs, and there most genes were enriched in terms of metabolic process and catalytic activity. In the four-year old bulbs, most of the DEGs that may be involved in flowering were classified under the GO term biological process, which was a totally different result from the vegetative bulbs. Some DEGs between flowering and nonflowering bulbs were enriched in plant hormone signal transduction, including the hormones auxin, cytokinin, abscisic acid, and ethylene, but no DEGs were enriched in the gibberellin pathway. Auxin is the main endogenous phytohormone involved in bulb growth and development, but cytokinin, abscisic acid, and ethylene were shown to increase in flowering bulbs. In addition, energy-metabolism-related genes maintain a high expression level in large bulbs, and some positive regulators (SPL, COL, and AP1) and early flowering genes were also shown to be highly expressed in the meristems of flowering bulbs. It suggested that sugar molecules may be the energy source that regulates the signal transduction of flowering by connecting with phytohormone signaling in Lycoris. A total of 1911 TFs were identified and classified into 89 categories, where the top six families with the largest gene numbers were C2H2, NAC, AP2/ERF-ERF, C3H, MYB-related, and WRKY. Most DEGs were in the AP2/ERF-ERF family, and most of them were downregulated in 4-year-old flowering bulbs. A number of families were reported to be involved in plant flowering, including NAC, AP2/ERF, MYB, WRKY, bZIP, MADS, and NF-Y. These results can act as a genetic resource to aid in the explanation of the genetic mechanism responsible for the flowering of Lycoris and other bulbous flowers.

Over-Expression of Larch DAL1 Accelerates Life-Cycle Progression in Arabidopsis

Homologs of Larix kaempferiDEFICIENS-AGAMOUS-LIKE 1 (LaDAL1) promote flowering in Arabidopsis. However, their functional role in the whole life-cycle is limited. Here, we analyzed the phenotypes and transcriptomes of Arabidopsis plants over-expressing LaDAL1. With respect to the defined life-cycle stage of Arabidopsis based on the meristem state, the results showed that LaDAL1 promoted seed germination, bolting, flower initiation, and global proliferative arrest, indicating that LaDAL1 accelerates the meristem reactivation, the transitions of vegetative meristem to inflorescence and flower meristem, and meristem arrest. As a marker gene of meristem, TERMINAL FLOWER 1 was down-regulated after LaDAL1 over-expression. These results reveal that LaDAL1 accelerates the life-cycle progression in Arabidopsis by promoting the transition of meristem fate, providing more and novel functional information about the conifer age-related gene DAL1.

Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut (Juglans mandshurica Maxim.)

Flowers are imperative reproductive organs and play a key role in the propagation of offspring, along with the generation of several metabolic products in flowering plants. In Juglans mandshurica, the number and development of flowers directly affect the fruit yield and subsequently its commercial value. However, owing to the lack of genetic information, there are few studies on the reproductive biology of Juglans mandshurica, and the molecular regulatory mechanisms underlying the development of female and male inflorescence remain unclear. In this study, phytohormones and transcriptomic sequencing analyses at the three stages of female and male inflorescence growth were performed to understand the regulatory functions underlying flower development. Gibberellin is the most dominant phytohormone that regulates flower development. In total, 14,579 and 7188 differentially expressed genes were identified after analyzing the development of male and female flowers, respectively, wherein, 3241 were commonly expressed. Enrichment analysis for significantly enriched pathways suggested the roles of MAPK signaling, phytohormone signal transduction, and sugar metabolism. Genes involved in floral organ transition and flowering were obtained and analyzed; these mainly belonged to the M-type MADS-box gene family. Three flowering-related genes (SOC1/AGL20, ANT, and SVP) strongly interacted with transcription factors in the co-expression network. Two key CO genes (CO3 and CO1) were identified in the photoperiod pathway. We also identified two GA20xs genes, one SVP gene, and five AGL genes (AGL8, AGL9, AGL15, AGL19, and AGL42) that contributed to flower development. The findings are expected to provide a genetic basis for the studies on the regulatory networks and reproductive biology in inflorescence development for J. mandshurica.

Transcriptome landscape of early inflorescence developmental stages identifies key flowering time regulators in chickpea

Transcriptome landscape during early inflorescence developmental stages identified candidate flowering time regulators including Early Flowering 3a. Further genomics approaches validated the role of this gene in flowering time regulation. The early stages of inflorescence development in plants are as crucial as the later floral developmental stages. Several traits, such as inflorescence architecture and flower developmental timings, are determined during those early stages. In chickpea, diverse forms of inflorescence architectures regarding meristem determinacy and the number of flowers per node are observed within the germplasm. Transcriptome analysis in four desi chickpea accessions with such unique inflorescence characteristics identifies the underlying shared regulatory events leading to inflorescence development. The vegetative to reproductive stage transition brings about major changes in the transcriptome landscape. The inflorescence development progression associated genes identified through co-expression network analysis includes both protein-coding genes and long non-coding RNAs (lncRNAs). Few lncRNAs identified in our study positively regulate flowering-related mRNA stability by acting competitively with miRNAs. Bulk segregrant analysis and association mapping narrowed down an InDel marker regulating flowering time in chickpea. Deletion of 11 bp in first exon of a negative flowering time regulator, Early Flowering 3a gene, leads to early flowering phenotype in chickpea. Understanding the key players involved in vegetative to reproductive stage transition and floral meristem development will be useful in manipulating flowering time and inflorescence architecture in chickpea and other legumes.

MiR172-APETALA2-like genes integrate vernalization and plant age to control flowering time in wheat

Plants possess regulatory mechanisms that allow them to flower under conditions that maximize reproductive success. Selection of natural variants affecting those mechanisms has been critical in agriculture to modulate the flowering response of crops to specific environments and to increase yield. In the temperate cereals, wheat and barley, the photoperiod and vernalization pathways explain most of the natural variation in flowering time. However, other pathways also participate in fine-tuning the flowering response. In this work, we integrate the conserved microRNA miR172 and its targets APETALA2-like (AP2L) genes into the temperate grass flowering network involving VERNALIZATION 1 (VRN1), VRN2 and FLOWERING LOCUS T 1 (FT1 = VRN3) genes. Using mutants, transgenics and different growing conditions, we show that miR172 promotes flowering in wheat, while its target genes AP2L1 (TaTOE1) and AP2L5 (Q) act as flowering repressors. Moreover, we reveal that the miR172-AP2L pathway regulates FT1 expression in the leaves, and that this regulation is independent of VRN2 and VRN1. In addition, we show that the miR172-AP2L module and flowering are both controlled by plant age through miR156 in spring cultivars. However, in winter cultivars, flowering and the regulation of AP2L1 expression are decoupled from miR156 downregulation with age, and induction of VRN1 by vernalization is required to repress AP2L1 in the leaves and promote flowering. Interestingly, the levels of miR172 and both AP2L genes modulate the flowering response to different vernalization treatments in winter cultivars. In summary, our results show that conserved and grass specific gene networks interact to modulate the flowering response, and that natural or induced mutations in AP2L genes are useful tools for fine-tuning wheat flowering time in a changing environment.

Light and Plant Growth Regulators on In Vitro Proliferation

Plant tissue cultures depend entirely upon artificial light sources for illumination. The illumination should provide light in the appropriate regions of the electromagnetic spectrum for photomorphogenic responses and photosynthetic metabolism. Controlling light quality, irradiances and photoperiod enables the production of plants with desired characteristics. Moreover, significant money savings may be achieved using both more appropriate and less consuming energy lamps. In this review, the attention will be focused on the effects of light characteristics and plant growth regulators on shoot proliferation, the main process in in vitro propagation. The effects of the light spectrum on the balance of endogenous growth regulators will also be presented. For each light spectrum, the effects on proliferation but also on plantlet quality, i.e., shoot length, fresh and dry weight and photosynthesis, have been also analyzed. Even if a huge amount of literature is available on the effects of light on in vitro proliferation, the results are often conflicting. In fact, a lot of exogenous and endogenous factors, but also the lack of a common protocol, make it difficult to choose the most effective light spectrum for each of the large number of species. However, some general issues derived from the analysis of the literature are discussed.

Enhancing crop diversity for food security in the face of climate uncertainty

Global agriculture is dominated by a handful of species that currently supply a huge proportion of our food and feed. It additionally faces the massive challenge of providing food for 10 billion people by 2050, despite increasing environmental deterioration. One way to better plan production in the face of current and continuing climate change is to better understand how our domestication of these crops included their adaptation to environments that were highly distinct from those of their centre of origin. There are many prominent examples of this, including the development of temperate Zea mays (maize) and the alteration of day-length requirements in Solanum tuberosum (potato). Despite the pre-eminence of some 15 crops, more than 50 000 species are edible, with 7000 of these considered semi-cultivated. Opportunities afforded by next-generation sequencing technologies alongside other methods, including metabolomics and high-throughput phenotyping, are starting to contribute to a better characterization of a handful of these species. Moreover, the first examples of de novo domestication have appeared, whereby key target genes are modified in a wild species in order to confer predictable traits of agronomic value. Here, we review the scale of the challenge, drawing extensively on the characterization of past agriculture to suggest informed strategies upon which the breeding of future climate-resilient crops can be based.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

The Relationships between Plant Developmental Traits and Winter Field Survival in Rye (Secale cereale L.)

Overwintering cereals accumulate low temperature tolerance (LTT) during cold acclimation in the autumn. Simultaneously, the plants adjust to the colder season by making developmental changes at the shoot apical meristem. These processes lead to higher winter hardiness in winter rye varieties (Secale cereale L.) adapted to Northern latitudes as compared to other cereal crops. To dissect the winter-hardiness trait in rye, a panel of 96 genotypes of different origins and growth habits was assessed for winter field survival (WFS), LTT, and six developmental traits. Best Linear Unbiased Estimates for WFS determined from five field trials correlated strongly with LTT (r = 0.90, p < 0.001); thus, cold acclimation efficiency was the major contributor to WFS. WFS also correlated strongly (p < 0.001) with final leaf number (r = 0.80), prostrate growth habit (r = 0.61), plant height (r = 0.34), but showed weaker associations with top internode length (r = 0.30, p < 0.01) and days to anthesis (r = 0.25, p < 0.05). The heritability estimates (h²) for WFS-associated traits ranged from 0.45 (prostrate growth habit) to 0.81 (final leaf number) and were overall higher than for WFS (h² = 0.48). All developmental traits associated with WFS and LTT are postulated to be regulated by phytohormone levels at shoot apical meristem.

Functional Analysis of the "Green Revolution" Gene Photoperiod-1 and Its Selection Trends During Bread Wheat Breeding

Flowering is central to the transformation of plants from vegetative growth to reproductive growth. The circadian clock system enables plants to sense the changes in the external environment and to modify the growth and development process at an appropriate time. Photoperiod-1 (Ppd-1), which is controlled by the output signal of the circadian clock, has played an important role in the wheat "Green Revolution." In the current study, we systematically studied the relationship between Ppd-1 haplotypes and both wheat yield- and quality-related traits, using genome-wide association analysis and transgenic strategies, and found that highly appropriate haplotypes had been selected in the wheat breeding programs. Genome-wide association analysis showed that Ppd-1 is associated with significant differences in yield-related traits in wheat, including spike length (SL), heading date (HD), plant height (PH), and thousand-grain weight (TGW). Ppd-1-Hapl-A1 showed increased SL by 4.72-5.93%, whereas Ppd-1-Hapl-B1 and Ppd-1-Hapl-D1 displayed earlier HD by 0.58-0.75 and 1.24-2.93%, respectively, decreased PH by 5.64-13.08 and 13.62-27.30%, respectively, and increased TGW by 4.89-10.94 and 11.12-21.45%, respectively. Furthermore, the constitutive expression of the Ppd-D1 gene in rice significantly delayed heading date and resulted in reduced plant height, thousand-grain weight, grain width (GW), and total protein content. With reference to 40years of data from Chinese wheat breeding, it was found that the appropriate haplotypes Ppd-1-Hapl-A1, Ppd-1-Hapl-B1, and Ppd-1-Hapl-D1 had all been subjected to directional selection, and that their distribution frequencies had increased from 26.09, 60.00, and 52.00% in landraces to 42.55, 93.62, and 96.23% in wheat cultivars developed in the 2010s. A Ppd-B1 methylation molecular marker was also developed to assist molecular wheat breeding. This research is of significance for fully exploring the function of the Ppd-1 gene and its genetic resource diversity, to effectively use the most appropriate haplotypes and to improve crop yield and sustainability.

Energy as a seasonal signal for growth and reproduction

Plants measure photoperiod as a predictable signal for seasonal change. Recently, new connections between photoperiod measuring systems and metabolism in plants have been revealed. These studies explore historical observations of metabolism and photoperiod with modern tools and approaches, suggesting there is much more to learn about photoperiodism in plants.

ERF1 delays flowering through direct inhibition of FLOWERING LOCUS T expression in Arabidopsis

ETHYLENE RESPONSE FACTOR1 (ERF1) is a key component in ethylene signaling, playing crucial roles in both biotic and abiotic stress responses. Here, we demonstrate that ERF1 also has an important role during floral initiation in Arabidopsis thaliana. Knockdown or knockout of ERF1 accelerated floral initiation, whereas overexpression of ERF1 dramatically delayed floral transition. These contrasting phenotypes were correlated with opposite transcript levels of FLOWERING LOCUS T (FT). Chromatin immunoprecipitation (ChIP) assays revealed that ERF1 associates with genomic regions of the FT gene to repress its transcription. ft-10/ERF1RNAi plants showed a similar flowering phenotype to the ft-10 mutant, whereas the flowering of FTox/ERF1ox mimicked that of FTox plants, suggesting that ERF1 acts upstream of FT during floral initiation. Similarly, altered floral transition in ethylene-related mutants was also correlated with FT expression. Further analysis suggested that ERF1 also participates in delay in flowering-time control mediated by the ethylene precursor 1-aminocyclopropane-1-carboxylic acid. Thus, ERF1 may act as a negative modulator of flowering-time control by repressing FT transcription in Arabidopsis.

Microbial effects on plant phenology and fitness

Plant development and the timing of developmental events (phenology) are tightly coupled with plant fitness. A variety of internal and external factors determine the timing and fitness consequences of these life-history transitions. Microbes interact with plants throughout their life history and impact host phenology. This review summarizes current mechanistic and theoretical knowledge surrounding microbe-driven changes in plant phenology. Overall, there are examples of microbes impacting every phenological transition. While most studies have focused on flowering time, microbial effects remain important for host survival and fitness across all phenological phases. Microbe-mediated changes in nutrient acquisition and phytohormone signaling can release plants from stressful conditions and alter plant stress responses inducing shifts in developmental events. The frequency and direction of phenological effects appear to be partly determined by the lifestyle and the underlying nature of a plant-microbe interaction (i.e., mutualistic or pathogenic), in addition to the taxonomic group of the microbe (fungi vs. bacteria). Finally, we highlight biases, gaps in knowledge, and future directions. This biotic source of plasticity for plant adaptation will serve an important role in sustaining plant biodiversity and managing agriculture under the pressures of climate change.

Isoprenoid-Derived Metabolites and Sugars in the Regulation of Flowering Time: Does Day Length Matter?

In plants, a diverse set of pathways regulate the transition to flowering, leading to remarkable developmental flexibility. Although the importance of photoperiod in the regulation of flowering time is well known, increasing evidence suggests the existence of crosstalk among the flowering pathways regulated by photoperiod and metabolic pathways. For example, isoprenoid-derived phytohormones (abscisic acid, gibberellins, brassinosteroids, and cytokinins) play important roles in regulating flowering time. Moreover, emerging evidence reveals that other metabolites, such as chlorophylls and carotenoids, as well as sugar metabolism and sugar accumulation, also affect flowering time. In this review, we summarize recent findings on the roles of isoprenoid-derived metabolites and sugars in the regulation of flowering time and how day length affects these factors.