Molecular control of seasonal flowering in rice,arabidopsis and temperate cereals

Background

Rice (Oryza sativa) and Arabidopsis thaliana have been widely used as model systems to understand how plants control flowering time in response to photoperiod and cold exposure. Extensive research has resulted in the isolation of several regulatory genes involved in flowering and for them to be organized into a molecular network responsive to environmental cues. When plants are exposed to favourable conditions, the network activates expression of florigenic proteins that are transported to the shoot apical meristem where they drive developmental reprogramming of a population of meristematic cells. Several regulatory factors are evolutionarily conserved between rice and arabidopsis. However, other pathways have evolved independently and confer specific characteristics to flowering responses.

Scope

This review summarizes recent knowledge on the molecular mechanisms regulating daylength perception and flowering time control in arabidopsis and rice. Similarities and differences are discussed between the regulatory networks of the two species and they are compared with the regulatory networks of temperate cereals, which are evolutionarily more similar to rice but have evolved in regions where exposure to low temperatures is crucial to confer competence to flower. Finally, the role of flowering time genes in expansion of rice cultivation to Northern latitudes is discussed.

Conclusions

Understanding the mechanisms involved in photoperiodic flowering and comparing the regulatory networks of dicots and monocots has revealed how plants respond to environmental cues and adapt to seasonal changes. The molecular architecture of such regulation shows striking similarities across diverse species. However, integration of specific pathways on a basal scheme is essential for adaptation to different environments. Artificial manipulation of flowering time by means of natural genetic resources is essential for expanding the cultivation of cereals across different environments.     

Induction of flowering by seasonal changes in photoperiod

In many plants, major developmental transitions such as the initiation of flowering are synchronized to the changing seasons. Day length provides one of the environmental cues used to achieve this. We describe the molecular mechanisms that measure day length and control flowering in Arabidopsis. Also, we compare these mechanisms with those that control flowering time in rice. This comparison suggests that components of the Arabidopsis regulatory network are conserved in other species, but that their regulation can be altered to generate different phenotypic responses.     

How to be early flowering: an evolutionary perspective

In wild and cultivated annual plant species, flowering time is an important life-history trait that coordinates the life cycle with local environmental conditions. Extensive studies on the genetic basis of flowering time in the model species Arabidopsis thaliana have revealed a complex genetic network that can detect environmental and internal signals. Based on this knowledge and on known pleiotropic effects associated with flowering time genes, we suggest that a natural shift towards an early-flowering life cycle might involve only particular functional regions in a limited number of genes. Our predictions are supported by genetic theories of adaptation and by recent data about genes associated with natural variation. We analyse the extent to which these predictions can also apply to crop species.     

Genome-wide identification of flowering time genes associated with vernalization and the regulatory flowering networks in Chinese cabbage

Flowering time (Ft) is the most important characteristic of Chinese cabbage with high leaf yields and late-flowering are favorable traits, while little knowledge on genes involved in Ft and the flowering mechanism in this crop. In this study, we conducted genome-wide RNA-seq analysis using an inbred Chinese cabbage ‘4004’ line in response to vernalization and compared the Ft gene expression with radish crop. A number of Ft genes which play roles in flowering pathways were performed quantitative RT-PCR analysis to verify the regulatory flowering gene network in Chinese cabbage. We found that a total of 223 Ft genes in Chinese cabbage, and 50 of these genes responded to vernalization. The majority of flowering enhancers were upregulated, whereas most flowering repressors were downregulated in response to vernalization as confirmed by RT-qPCR. Among the major Ft genes, the expression of BrCOL1-2, BrFT1/2, BrSOC1/2/3, BrFLC1/2/3/5, and BrMAF was strongly affected by vernalization. In reference to comparative RNA-seq profiling of Ft genes, Chinese cabbage and radish revealed substantially different vernalization response in particular GA flowering pathway. Thus, this study provides new insight into functional divergence in flowering pathways and the regulatory mechanisms in Brassicaceae crops. Further analysis of the major integrator genes between early and late-flowering inbred lines facilitates understanding flowering trait variation and molecular basis of flowering in Chinese cabbage.     

Heat shock protein 101 (HSP101) promotes flowering under nonstress conditions

Heat shock proteins (HSPs) are stress-responsive proteins that are conserved across all organisms. Heat shock protein 101 (HSP101) has an important role in thermotolerance owing to its chaperone activity. However, if and how it functions in development under nonstress conditions is not yet known. By using physiological, molecular, and genetic methods, we investigated the role of HSP101 in the control of flowering in Arabidopsis (Arabidopsis thaliana (L.) Heynh.) under nonstress conditions. Knockout and overexpression of HSP101 cause late and early flowering, respectively. Late flowering can be restored by rescue of HSP101. HSP101 regulates the expression of genes involved in the six known flowering pathways; the most negatively regulated genes are FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP); downstream integrators of the flowering pathways are positively regulated. The late-flowering phenotype of loss-of-HSP101 mutants is suppressed by both the mutations of FLC and SVP. The responses of flowering time to exogenous signals do not change in HSP101 mutants. HSP101 is also found in nonspecific regions according to subcellular localization. We found that HSP101 promotes flowering under nonstress conditions and that this promotion depends on FLC and SVP. Our data suggest that this promotion could occur through a multiple gene regulation mechanism.

Heat shock protein 101 promotes flowering under nonstress conditions in Arabidopsis (Arabidopsis thaliana (L.) Heynh.).     

Can a late bloomer become an early bird? Tools for flowering time adjustment

The transition from the vegetative to reproductive stage followed by inflorescence is a critical step in plant life; therefore, studies of the genes that influence flowering time have always been of great interest to scientists. Flowering is a process controlled by many genes interacting mutually in a genetic network, and several hypothesis and models of flowering have been suggested so far. Plants in temperate climatic conditions must respond mainly to changes in the day length (photoperiod) and unfavourable winter temperatures. To avoid flowering before winter, some plants exploit a specific mechanism called vernalization. This review summarises current achievements in the study of genes controlling flowering in the dicot model species thale cress (Arabidopsis thaliana), as well as in monocot model species rice (Oryza sativa) and temperate cereals such as barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). The control of flowering in crops is an attractive target for modern plant breeding efforts aiming to prepare locally well-adapted cultivars. The recent progress in genomics revealed the importance of minor-effect genes (QTLs) and natural allelic variation of genes for fine-tuning flowering and better cultivar adaptation. We briefly describe the up-to-date technologies and approaches that scientists may employ and we also indicate how these modern biotechnological tools and “-omics” can expand our knowledge of flowering in agronomically important crops.     

Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes

There is currently tremendous interest in the possibility of using genome-wide association mapping to identify genes responsible for natural variation, particularly for human disease susceptibility. The model plant Arabidopsis thaliana is in many ways an ideal candidate for such studies, because it is a highly selfing hermaphrodite. As a result, the species largely exists as a collection of naturally occurring inbred lines, or accessions, which can be genotyped once and phenotyped repeatedly. Furthermore, linkage disequilibrium in such a species will be much more extensive than in a comparable outcrossing species. We tested the feasibility of genome-wide association mapping in A. thaliana by searching for associations with flowering time and pathogen resistance in a sample of 95 accessions for which genome-wide polymorphism data were available. In spite of an extremely high rate of false positives due to population structure, we were able to identify known major genes for all phenotypes tested, thus demonstrating the potential of genome-wide association mapping in A. thaliana and other species with similar patterns of variation. The rate of false positives differed strongly between traits, with more clinal traits showing the highest rate. However, the false positive rates were always substantial regardless of the trait, highlighting the necessity of an appropriate genomic control in association studies.     

Arabidopsis thaliana and its wild relatives: a model system for ecology and evolution

The postgenomics era will bring many changes to ecology and evolution. Information about genomic sequence and function provides a new foundation for organismal biology. The crucifer Arabidopsis thaliana and its wild relatives will play an important role in this synthesis of genomics and ecology. We discuss the need for model systems in ecology, the biology and relationships of crucifers, and the molecular resources available for these experiments. The scientific potential of this model system is illustrated by several recent studies in plant–insect interactions, developmental plasticity, comparative genomics and molecular evolution.     

Environmental regulation of flowering

The timing of flower initiation is a highly plastic developmental process. To achieve reproductive success, plants must select the most favourable season to initiate reproductive development; this in turn requires continuous monitoring of environmental factors and a properly response. Environmental factors which change in a predictable fashion along the year, such as light and temperature, are the most relevant in terms of selection of the flowering season. In Arabidopsis and more recently in a few other species, molecular genetic analyses are providing a way to identify the genes involved in the regulation of flowering time. From gene sequences it is possible to develop hypotheses regarding molecular function and to infer some of the molecular mechanisms involved in the environmental regulation of flowering time. In this paper, we summarize recent discoveries concerning the mechanisms which plants use to perceive and respond to major environmental factors (light and temperature) and their different components. We focus mainly on annual plants and especially on Arabidopsis because most of the available molecular and functional data come from this species. However, additional information arising from other plant systems is also considered.     

植物开花调控途径

开花是植物从营养生长转换为生殖生长的生理发育过程,受光周期、温度、激素、年龄等多个因素诱导,在植物生长和物种进化中处于核心地位。综合不断更新的开花分子遗传结果,将植物响应各种内源和外源信号启动开花的途径归纳为:经典的光周期途径、春化途径、自主途径、赤霉素途径和较新的年龄途径共5条。旨在描绘出这些不同途径间既独立又相互影响的复杂网络关系,为进一步探索和阐述更多植物的开花分子机理提供借鉴与参考。     

Mutations in AP22.65 accelerate flowering in Arabidopsis thaliana

Identification of the gene(s) responsible for flowering time in Arabidopsis has significant implications. We used the T-DNA insertion library of Arabidopsis thaliana to screen an early-flowering mutant that exhibits accelerated flowering under short-day conditions. AP22.65, a novel flowering-time gene in that species, was isolated and identified via genome-walking and bioinformatics analysis. The flowering time of AP22.65-complementing plants was similar to that of the Col-0 wild type (WT). Conversely, its overexpression delayed flowering. Consistent with this phenotype, expression of AP22.65 was decreased in the ap22.65-1 mutant, recovered in AP22.65-complementing plants, and increased in AP22.65-overexpressing plants. Compared with the WT, expression levels of critical genes in different flowering pathways, i.e., SPY, FLC, GI, CO, FT, and LFY, were down-regulated in loss-of-function mutants. Expression of AP22.65 was distributed in flowers, siliques, rosette leaves, and whole seedlings. Therefore, this gene may be a negative regulator of Arabidopsis flowering.     

Photoperiodic flowering of Arabidopsis: integrating genetic and physiological approaches to characterization of the floral stimulus

In many plants the transition from vegetative growth to flowering is controlled by environmental cues. One of these cues is day length or photoperiod, which synchronizes flowering of many species with the changing seasons. Recently, advances have been made in understanding the molecular mechanisms that confer photoperiodic control of flowering and, in particular, how inductive events occurring in the leaf, where photoperiod is perceived, are linked to floral evocation that takes place at the shoot apical meristem. We discuss recent data obtained using molecular genetic approaches on the function of regulatory proteins that control flowering time in Arabidopsis thaliana. These data are compared with the results of physiological analyses of the floral transition, which were performed in a range of species and directed towards identification of the transmitted floral singals.     

Conservation of Arabidopsis flowering genes in model legumes

The model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have provided a wealth of information about genes and genetic pathways controlling the flowering process, but little is known about the corresponding pathways in legumes. The garden pea (Pisum sativum) has been used for several decades as a model system for physiological genetics of flowering, but the lack of molecular information about pea flowering genes has prevented direct comparison with other systems. To address this problem, we have searched expressed sequence tag and genome sequence databases to identify flowering-gene-related sequences from Medicago truncatula, soybean (Glycine max), and Lotus japonicus, and isolated corresponding sequences from pea by degenerate-primer polymerase chain reaction and library screening. We found that the majority of Arabidopsis flowering genes are represented in pea and in legume sequence databases, although several gene families, including the MADS-box, CONSTANS, and FLOWERING LOCUS T/TERMINAL FLOWER1 families, appear to have undergone differential expansion, and several important Arabidopsis genes, including FRIGIDA and members of the FLOWERING LOCUS C clade, are conspicuously absent. In several cases, pea and Medicago orthologs are shown to map to conserved map positions, emphasizing the closely syntenic relationship between these two species. These results demonstrate the potential benefit of parallel model systems for an understanding of flowering phenology in crop and model legume species.     

Divergence of flowering genes in soybean

Soybean genome sequences were blasted with Arabidopsis thaliana regulatory genes involved in photoperiod-dependent flowering. This approach enabled the identification of 118 genes involved in the flowering pathway. Two genome sequences of cultivated (Williams 82) and wild (IT182932) soybeans were employed to survey functional DNA variations in the flowering-related homologs. Forty genes exhibiting nonsynonymous substitutions between G. max and G. soja were catalogued. In addition, 22 genes were found to co-localize with QTLs for six traits including flowering time, first flower, pod maturity, beginning of pod, reproductive period, and seed filling period. Among the genes overlapping the QTL regions, two LHY/CCA1 genes, GI and SFR6 contained amino acid changes. The recently duplicated sequence regions of the soybean genome were used as additional criteria for the speculation of the putative function of the homologs. Two duplicated regions showed redundancy of both flowering-related genes and QTLs. ID 12398025, which contains the homeologous regions between chr 7 and chr 16, was redundant for the LHY/CCA1 and SPA1 homologs and the QTLs. Retaining of the CRY1 gene and the pod maturity QTLs were observed in the duplicated region of ID 23546507 on chr 4 and chr 6. Functional DNA variation of the LHY/CCA1 gene (Glyma07g05410) was present in a counterpart of the duplicated region on chr 7, while the gene (Glyma16g01980) present in the other portion of the duplicated region on chr 16 did not show a functional sequence change. The gene list catalogued in this study provides primary insight for understanding the regulation of flowering time and maturity in soybean.     

Role of VIN3-LIKE 2 in facultative photoperiodic flowering response in Arabidopsis

In Arabidopsis, expression of FLC and FLC-related genes (collectively called FLC clade) contributes to flowering time in response to environmental changes, such as day length and temperature, by acting as floral repressors. VIN3 is required for vernalization-mediated FLC repression and a VIN3 related protein, VIN3-LIKE 1/VERNALIZATION 5 (VIL1/VRN5), acts to regulate FLC and FLM in response to vernalization.^1–3 VIN3 also exists as a small family of PHD finger proteins in Arabidopsis, including VIL1/VRN5, VIL2/VEL1, VIL3/VEL2 and VIL4/VEL3. We showed that the PHD finger protein, VIL2, is required for proper repression of MAF5, an FLC clade member, to accelerate flowering under non-inductive photoperiods. VIL2 acts together with POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) to repress MAF5 in a photoperiod dependent manner.Key words: photoperiod, chromatin, floweringThe decision to flower is critical to the survival of flowering plants. Thus, plants sense environmental cues to initiate floral transition at a time that both ensures and optimizes their own reproductive fitness. Using a model plant, Arabidopsis thaliana, genetic studies have shown that the regulation of floral transition mainly consists of four genetic pathways: the inductive photoperiod pathway, the autonomous pathway, the vernalization pathway and the gibberellin pathway.⁴ In Arabidopsis, these four flowering pathways eventually merge into a group of genes called floral integrators, including FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and LEAFY (LFY). Based on the response to specific photoperiod conditions, the flowering behaviors of plants can be classified into three groups: long day (LD), short day (SD) and day neutral response.^5,6 Depending on the requirement of day length, plants show either obligate or facultative responses. For example, henbane, carnation and ryegrass are obligate long day (LD) flowering plants which flower under increasing inductive photoperiod but do not flower at all under non-inductive photoperiod.⁵ On the other hand, plants including Arabidopsis, wheat, lettuce and barley, are considered to be facultative flowering plants. Thus, these plants exhibit early flowering under LD and late-flowering under non-inductive short days (SD). Studies on photoperiodic flowering time mainly focus on the inductive LD-photoperiod pathway in Arabidopsis.