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

Global analysis of H3K4me3/H3K27me3 in Brachypodium distachyon reveals VRN3 as critical epigenetic regulation point in vernalization and provides insights into epigenetic memory

Vernalization, the requirement of plants for long-term exposure to low environmental temperature for flowering, is an epigenetic phenomenon. Histone modification regulation has been revealed in vernalization, but is limited to key genes. Now, we know that VRN1 is epigenetically critical for monocots. Genome-wide analysis is still unavailable, however. We performed chromatin immunoprecipitation-sequencing for H3K4me3/H3K27me3 in Brachypodium distachyon to obtain a global view of histone modifications in vernalization on a genome-wide scale and for different pathways/genes. Our data showed that H3K4me3 and H3K27me3 play distinct roles in vernalization. Unlike H3K4me3, H3K27me3 exhibited regional regulation, showed main regulation targets in vernalization and contributed to epigenetic memory. For genes in four flowering regulation pathways, only FT2 (functional ortholog of VRN3 in B. distachyon) and VRN1 showed coordinated changes in H3K4me3/H3K27me3. The epigenetic response at VRN3 was weaker under short-day than under long-day conditions. VRN3 was revealed as an epigenetic regulation point integrating vernalization and day length signals. We globally identified genes maintaining vernalization-induced epigenetic changes. Most of these genes showed dose-dependent vernalization responses, revealing a quantitative 'recording system' for vernalization. Our studies shed light on the epigenetic role of VRN3 and H3K4me3/H3K27me3 in vernalization and reveal genes underlying epigenetic memory, laying the foundation for further study.

Early flowering and rapid grain filling determine early maturity and escape from harvesting in weedy rice

BACKGROUND

Early maturity is an important trait that is essential to the survival of weedy rice. To explore the mechanism of early maturity in weedy rice, the reproductive development of a large sample of weedy rice accessions and cultivars was compared in a common garden study. A selected sample of both weedy and cultivated rice was sown at different dates in two years to study in more detail their flowering and grain-filling patterns.

RESULTS

The weedy rice from three major cropping regions matured 7-8 days earlier than their associated cultivars. Representative weedy rice accessions planted on conventional sowing dates flowered 3-26 days earlier than cultivars; delayed sowing caused divergence in the flowering regimes in weedy rice. However, regardless of the sowing date, weedy rice filled its grain 7-21 days faster than cultivars in both study years. Vegetative and reproductive traits of weedy and cultivated rice have different patterns of variation with delayed planting.

CONCLUSION

Early maturity is an essential factor determining the persistence of weedy rice by contributing to the escape of its seed from being harvested with the rice crop. Both early flowering and shorter grain-filling stages determine early maturity, and flowering is more plastic than grain filling. © 2017 Society of Chemical Industry.

Divergent Hd1, Ghd7, and DTH7 Alleles Control Heading Date and Yield Potential of Japonica Rice in Northeast China

The heading date is a vital factor in achieving a full rice yield. Cultivars with particular flowering behaviors have been artificially selected to survive in the long-day and low-temperature conditions of Northeast China. To dissect the genetic mechanism responsible for heading date in rice populations from Northeast China, association mapping was performed to identify major controlling loci. A genome-wide association study (GWAS) identified three genetic loci, Hd1, Ghd7, and DTH7, using general and mixed linear models. The three genes were sequenced to analyze natural variations and identify their functions. Loss-of-function alleles of these genes contributed to early rice heading dates in the northern regions of Northeast China, while functional alleles promoted late rice heading dates in the southern regions of Northeast China. Selecting environmentally appropriate allele combinations in new varieties is recommended during breeding. Introducing the early indica rice's genetic background into Northeast japonica rice is a reasonable strategy for improving genetic diversity.

The gymnastics of epigenomics in rice

Epigenomics is represented by the high-throughput investigations of genome-wide epigenetic alterations, which ultimately dictate genomic, transcriptomic, proteomic and metabolomic dynamism. Rice has been accepted as the global staple crop. As a result, this model crop deserves significant importance in the rapidly emerging field of plant epigenomics. A large number of recently available data reveal the immense flexibility and potential of variable epigenomic landscapes. Such epigenomic impacts and variability are determined by a number of epigenetic regulators and several crucial inheritable epialleles, respectively. This article highlights the correlation of the epigenomic landscape with growth, flowering, reproduction, non-coding RNA-mediated post-transcriptional regulation, transposon mobility and even heterosis in rice. We have also discussed the drastic epigenetic alterations which are reported in rice plants grown from seeds exposed to the extraterrestrial environment. Such abiotic conditions impose stress on the plants leading to epigenomic modifications in a genotype-specific manner. Some significant bioinformatic databases and in silico approaches have also been explained in this article. These softwares provide important interfaces for comparative epigenomics. The discussion concludes with a unified goal of developing epigenome editing to promote biological hacking of the rice epigenome. Such a cutting-edge technology if properly standardized, can integrate genomics and epigenomics together with the generation of high-yielding trait in several cultivars of rice.

Neural Net Classification Combined With Movement Analysis to Evaluate Setaria viridis as a Model System for Time of Day of Anther Appearance

In many plant species, the time of day at which flowers open to permit pollination is tightly regulated. Proper time of flower opening, or Time of Day of Anther Appearance (TAA), may coordinate flowering opening with pollinator activity or may shift temperature sensitive developmental processes to cooler times of the day. The genetic mechanisms that regulate the timing of this process in cereal crops are unknown. To address this knowledge gap, it is necessary to establish a monocot model system that exhibits variation in TAA. Here, we examine the suitability of Setaria viridis, the model for C4 photosynthesis, for such a role. We developed an imaging system to monitor the temporal regulation of growth, flower opening time, and other physiological characteristics in Setaria. This system enabled us to compare Setaria varieties Ames 32254, Ames 32276, and PI 669942 variation in growth and daily flower opening time. We observed that TAA occurs primarily at night in these three Setaria accessions. However, significant variation between the accessions was observed for both the ratio of flowers that open in the day vs. night and the specific time of day where the rate is maximal. Characterizing this physiological variation is a requisite step toward uncovering the molecular mechanisms regulating TAA. Leveraging the regulation of TAA could provide researchers with a genetic tool to improve crop productivity in new environments.

Differential Regulation of Starch-synthetic Gene Expression in Endosperm Between Indica and Japonica Rice Cultivars

BACKGROUND

Grain filling rates (GFRs) of indica rice cultivars are often higher than those of japonica cultivars. Although GFR is mainly determined by the starch accumulation rate (SAR) in endosperm, the genetic basis for SAR during the ripening period has not been well studied in rice. To elucidate the factors influencing the differing SARs between typical indica and japonica cultivars, we focused on differences in sink potentials, especially on starch synthesis in the endosperm.

RESULTS

SAR in indica rice cultivar IR36 was significantly higher than in japonica cultivar T65. Although enzymes for both amylose and amylopectin syntheses had higher activity in IR36, amylopectin synthesis was seemingly more important for accelerating SAR because an elevation of amylose synthesis ability alone in the T65 genetic background did not result in the same level of SAR as IR36. In IR36, most starch-synthetic genes (SSGs) in the endosperm were more highly expressed during ripening than in T65. In panicle culture experiments, the SSGs in rice endosperm were regulated in either sucrose-dependent or -independent manners, or both. All SSGs except SSI and BEIIa were responsive to sucrose in both cultivars, and GBSSI, AGPS2b and PUL were more responsive to sucrose in IR36. Interestingly, the GBSSI gene (Wx ^a ) in IR36 was highly activated by sucrose, but the GBSSI gene (Wx ^b ) in T65 was insensitive. In sucrose-independent regulation, AGPL2, SSIIIa, BEI, BEIIb and ISA1 genes in IR36 were upregulated 1.5 to 2 times more than those in T65. Additionally, at least SSI and BEIIa might be regulated by unknown signals; that regulation pathway should be more activated in IR36 than T65.

CONCLUSIONS

In this study, at least three regulatory pathways seem to be involved in SSG expression in rice endosperm, and all pathways were more active in IR36. One of the factors leading to the high SAR of IR36 seemed to be an increase in the sink potential.

Arabidopsis KHZ1 and KHZ2, two novel non-tandem CCCH zinc-finger and K-homolog domain proteins, have redundant roles in the regulation of flowering and senescence

The two novel CCCH zinc-finger and K-homolog (KH) proteins, KHZ1 and KHZ2, play important roles in regulating flowering and senescence redundantly in Arabidopsis. The CCCH zinc-finger proteins and K-homolog (KH) proteins play important roles in plant development and stress responses. However, the biological functions of many CCCH zinc-finger proteins and KH proteins remain uncharacterized. In Arabidopsis, KHZ1 and KHZ2 are characterized as two novel CCCH zinc-finger and KH domain proteins which belong to subfamily VII in CCCH family. We obtained khz1, khz2 mutants and khz1 khz2 double mutants, as well as overexpression (OE) lines of KHZ1 and KHZ2. Compared with the wild type (WT), the khz2 mutants displayed no defects in growth and development, and the khz1 mutants were slightly late flowering, whereas the khz1 khz2 double mutants showed a pronounced late flowering phenotype. In contrast, artificially overexpressing KHZ1 and KHZ2 led to the early flowering. Consistent with the late flowering phenotype, the expression of flowering repressor gene FLC was up-regulated, while the expression of flowering integrator and floral meristem identity (FMI) genes were down-regulated significantly in khz1 khz2. In addition, we also observed that the OE plants of KHZ1 and KHZ2 showed early leaf senescence significantly, whereas the khz1 khz2 double mutants showed delayed senescence of leaf and the whole plant. Both KHZ1 and KHZ2 were ubiquitously expressed throughout the tissues of Arabidopsis. KHZ1 and KHZ2 were localized to the nucleus, and possessed both transactivation activities and RNA-binding abilities. Taken together, we conclude that KHZ1 and KHZ2 have redundant roles in the regulation of flowering and senescence in Arabidopsis.

The rice CONSTANS-like protein OsCOL15 suppresses flowering by promoting Ghd7 and repressing RID1

The photoperiodic flowering pathway is one of the most important regulatory networks controlling flowering time in rice (Oryza sativa L.). Rice is a facultative short-day (SD) plant; flowering is promoted under inductive SD conditions and delayed under non-inductive long-day (LD) conditions. In rice, flowering inhibitor genes play an important role in maintaining the trade-off between reproduction and yield. In this study, we identified a novel floral inhibitor, OsCOL15, which encodes a CONSTANS-like transcription factor. Consistent with a function in transcriptional regulation, OsCOL15 localized to the nucleus. Moreover, OsCOL15 had transcriptional activation activity, and the central region of the protein between the B-box and CCT domains was required for this activity. We determined that OsCOL15 is most highly expressed in young organs and exhibits a diurnal expression pattern typical of other floral regulators. Overexpression of OsCOL15 resulted in a delayed flowering phenotype under both SD and LD conditions. Real-time quantitative RT-PCR analysis of flowering regulator gene expression suggested that OsCOL15 suppresses flowering by up-regulating the flowering repressor Grain number, plant height and heading date 7 (Ghd7) and down-regulating the flowering activator Rice Indeterminate 1 (RID1), thus leading to the down-regulation of the flowering activators Early heading date 1, Heading date 3a, and RICE FLOWERING LOCUS T1. These results demonstrate that OsCOL15 is an important floral regulator acting upstream of Ghd7 and RID1 in the rice photoperiodic flowering-time regulatory network.

The identification of new candidate genes Triticum aestivum FLOWERING LOCUS T3-B1 (TaFT3-B1) and TARGET OF EAT1 (TaTOE1-B1) controlling the short-day photoperiod response in bread wheat

Perception of photoperiod changes enables plants to flower under optimum conditions for survival. We used doubled haploid populations of crosses among Avalon × Cadenza, Charger × Badger and Spark × Rialto and identified short-day flowering time response quantitative trait loci (QTL) on wheat chromosomes 1BS and 1BL. We used synteny between Brachypodium distachyon and wheat to identify potential candidates for both QTL. The 1BL QTL peak coincided with TaFT3-B1, a homologue of the barley gene HvFT3, the most likely candidate gene. The 1BS QTL peak coincided with homologues of Arabidopsis thaliana SENSITIVITY TO RED LIGHT REDUCED 1, WUSCHEL-like and RAP2.7, which is also known as Zea mays TARGET OF EAT1, named TaSRR1-B1, TaWUSCHELL-B1 and TaTOE1-B1, respectively. Gene expression assays suggest that TaTOE1-B1 and TaFT3-B1 are expressed more during short days. We identified four alleles of TaFT3-B1 and three alleles of TaTOE1-B1. We studied the effect of these alleles in the Watkins and GEDIFLUX diversity panels by using 936 and 431 accessions, respectively. Loss of TaFT3-B1 by deletion was associated with late flowering. Increased TaFT3-B1 copy number was associated with early flowering, suggesting that TaFT3-B1 promotes flowering. Significant association was observed in the GEDIFLUX collection for TaTOE1-B1, a putative flowering repressor.

Divergence in How Genetic Pathways Respond to Environments

An upstream gene in the pathway that induces flowering in response to cold has been identified. The gene, RVR1, occurs in several plant lineages and operates in a pathway that exhibits functional divergence across development and across taxa. Such divergence can provide insight into how genetic pathways evolve.

Diverse Roles of Ethylene in Regulating Agronomic Traits in Rice

Gaseous hormone ethylene has diverse effects in various plant processes. These processes include seed germination, plant growth, senescence, fruit ripening, biotic and abiotic stresses responses, and many other aspects. The biosynthesis and signaling of ethylene have been extensively studied in model Arabidopsis in the past two decades. However, knowledge about the ethylene signaling mechanism in crops and roles of ethylene in regulation of crop agronomic traits are still limited. Our recent findings demonstrate that rice possesses both conserved and diverged mechanism for ethylene signaling compared with Arabidopsis. Here, we mainly focused on the recent advances in ethylene regulation of important agronomic traits. Of special emphasis is its impact on rice growth, flowering, grain filling, and grain size control. Similarly, the influence of ethylene on other relevant crops will be compared. Additionally, interactions of ethylene with other hormones will also be discussed in terms of crop growth and development. Increasing insights into the roles and mechanisms of ethylene in regulating agronomic traits will contribute to improvement of crop production through precise manipulation of ethylene actions in crops.

Alternative functions of Hd1 in repressing or promoting heading are determined by Ghd7 status under long-day conditions

Previous studies suggested that Hd1 promoted heading under short-day conditions (SD) and delayed heading under long-day conditions (LD). However in this study, Hd1 was demonstrated to consistently promote heading date in Zhenshan 97 (ZS97) background by upregulating Ehd1, Hd3a and RFT1 expression under both SD and LD. While the high photoperiod sensitivity of Hd1 was observed in Minghui 63 (MH63) background, with heading being suppressed in LD but promoted in SD. Comparative analysis of two sets of near isogenic lines of Hd1 in MH63 and ZS97 backgrounds indicated that the alternative functions of Hd1 in promoting or suppressing heading under LD are dependent on the previously cloned flowering repressor gene Ghd7. The interaction between proteins Ghd7 and Hd1 occurred through binding of the CCT domain of Ghd7 to the transcription-activating domain of Hd1, resulting in suppression of Ehd1 and florigen gene expression. The involvement of the transcription-activating domain of Hd1 in this protein-protein interaction probably blocked or weakened its transcriptional activity. These findings suggest that Hd1 alone essentially acts as a promoter of heading date, and the protein interaction between Ghd7 and Hd1 determines photoperiod sensitivity and integrated Hd1-mediated and Ehd1-mediated flowering pathways in rice.

Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. Thermal stress and spikelet sterility

Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology. The objectives were to improve the RIDEV model of rice thermal sterility, to estimate response traits by fitting model parameters, and to link the response traits to genomic regions through genome-wide association studies (GWAS). RIDEV captured 64% of variation of sterility when cold acclimation during vegetative stage was simulated, but only 38% when it was not. The RIDEV parameters gave more and stronger quantitative trait loci (QTLs) than index variables derived more directly from observation. The 15 QTLs identified at P<1 × 10-5 (33 at P<1 × 10-4) were related to sterility effects of heat, cold, cold acclimation, or unexplained causes (baseline sterility). Nine annotated genes were found on average within the 50% linkage disequilibrium (LD) region. Among them, one to five plausible candidate genes per QTL were identified based on known expression profiles (organ, stage, stress factors) and function. Meiosis-, development- and flowering-related genes were frequent, as well a stress signaling kinases and transcription factors. Putative epigenetic factors such as DNA methylases or histone-related genes were frequent in cold-acclimation QTLs, and positive-effect alleles were frequent in cold-tolerant highland rice from Madagascar. The results indicate that epigenetic control of acclimation may be important in indica rice genotypes adapted to cool environments.

Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 1. Phenology

Phenology and time of flowering are crucial determinants of rice adaptation to climate variation. A previous study characterized flowering responses of 203 diverse indica rices (the ORYTAGE panel) to ten environments in Senegal (six sowing dates) and Madagascar (two years and two altitudes) under irrigation in the field. This study used the physiological phenology model RIDEV V2 to heuristically estimate component traits of flowering such as cardinal temperatures (base temperature (Tbase) and optimum temperature), basic vegetative phase, photoperiod sensitivity and cold acclimation, and to conduct a genome-wide association study for these traits using 16 232 anonymous single-nucleotide polymorphism (SNP) markers. The RIDEV model after genotypic parameter optimization explained 96% of variation in time to flowering for Senegal alone and 91% for Senegal and Madagascar combined. The latter was improved to 94% by including an acclimation parameter reducing Tbase when the crop experienced low temperatures during early vegetative development. Eighteen significant (P<1.0 × 10-5) quantitative trait loci (QTLs) were identified, namely ten for RIDEV parameters and eight for climatic index variables (difference in time to flowering between key environments). Co-localization of QTLs for different traits were rare. RIDEV parameters gave QTLs that were mostly more significant and distinct from QTLs for index variables. Candidate genes were investigated within the estimated 50% linkage disequilibrium regions of 39 kB. In addition to several known flowering network genes, they included genes related to thermal stress adaptation and epigenetic control mechanisms. The peak SNP for a QTL for the crop parameter Tbase (P=2.0 × 10-7) was located within HD3a, a florigen that was recently identified as implicated in flowering under cool conditions.

Rice Flowering Locus T 1 plays an important role in heading date influencing yield traits in rice

Important role of flowering genes in enhancing grain productivity in rice has become well recognized for a number of key genes regulating the florigen production, but little has been known for the two florigen genes themselves. In this study, pleiotropism of Rice Flowering Locus T 1 (RFT1), one of the two florigen genes in rice, was firstly evaluated using near isogenic lines (NILs) carrying RFT1 alleles from the indica rice cultivars Zhenshan 97 (ZS97) and Milyang 46, respectively, and then determined by transformation of the RFT1^ZS97 allele into a japonica rice variety, Zhonghua 11. The RFT1^ZS97 allele was shown to delay heading and increase plant height, grain weight, grain number and grain yield, indicating that RFT1 plays an important role in the growth and development of rice. This study has also validated the potential of using a new type of genetic resource, sequential residual heterozygotes (SeqRHs), for QTL fine-mapping. A step-by-step approach was employed for SeqRHs identification, NIL development and QTL fine-mapping. The heterozygous segments and candidate QTL regions were gradually narrowed down. Eventually, the QTL region was delimited to a 1.7 kb region containing a single gene.

Genome-wide identification of Major Intrinsic Proteins in Glycine soja and characterization of GmTIP2;1 function under salt and water stress

In different plant species, aquaporins (AQPs) facilitate water movement by regulating root hydraulic conductivity under diverse stress conditions such as salt and water stresses. To improve survival and yield of crop plants, a detailed understanding of stress responses is imperative and required. We used Glycine soja genome as a tool to study AQPs, considering it shows abundant genetic diversity and higher salt environment tolerance features and identified 62 Gs AQP genes. Additionally, this study identifies major aquaporins responsive to salt and drought stresses in soybean and elucidates their mode of action through yeast two-hybrid assay and BiFC. Under stress condition, the expression analysis of AQPs in roots and leaves of two contrasting ecotypes of soybean revealed diverse expression patterns suggesting complex regulation at transcriptional level. Based on expression analysis, we identify GmTIP2;1 as a potential candidate involved in salinity and drought responses. The overexpression of GmTIP2;1 in Saccharomyces cerevisiae as well as in-planta enhanced salt and drought tolerance. We identified that GmTIP2;1 forms homodimers as well as interacts with GmTIP1;7 and GmTIP1;8. This study augments our knowledge of stress responsive pathways and also establishes GmTIP2;1 as a new stress responsive gene in imparting salt stress tolerance in soybean.

Establishment of a vernalization requirement in Brachypodium distachyon requires REPRESSOR OF VERNALIZATION1

A requirement for vernalization, the process by which prolonged cold exposure provides competence to flower, is an important adaptation to temperate climates that ensures flowering does not occur before the onset of winter. In temperate grasses, vernalization results in the up-regulation of VERNALIZATION1 (VRN1) to establish competence to flower; however, little is known about the mechanism underlying repression of VRN1 in the fall season, which is necessary to establish a vernalization requirement. Here, we report that a plant-specific gene containing a bromo-adjacent homology and transcriptional elongation factor S-II domain, which we named REPRESSOR OF VERNALIZATION1 (RVR1), represses VRN1 before vernalization in Brachypodium distachyon That RVR1 is upstream of VRN1 is supported by the observations that VRN1 is precociously elevated in an rvr1 mutant, resulting in rapid flowering without cold exposure, and the rapid-flowering rvr1 phenotype is dependent on VRN1 The precocious VRN1 expression in rvr1 is associated with reduced levels of the repressive chromatin modification H3K27me3 at VRN1, which is similar to the reduced VRN1 H3K27me3 in vernalized plants. Furthermore, the transcriptome of vernalized wild-type plants overlaps with that of nonvernalized rvr1 plants, indicating loss of rvr1 is similar to the vernalized state at a molecular level. However, loss of rvr1 results in more differentially expressed genes than does vernalization, indicating that RVR1 may be involved in processes other than vernalization despite a lack of any obvious pleiotropy in the rvr1 mutant. This study provides an example of a role for this class of plant-specific genes.

OsFTIP1-Mediated Regulation of Florigen Transport in Rice Is Negatively Regulated by the Ubiquitin-Like Domain Kinase OsUbDKγ4

Flowering time is a critical agronomic trait that determines successful seed production and adaptation of crop plants. Photoperiodic control of this process in flowering plants is mediated by the long-distance mobile signal called florigen partly encoded by FLOWERING LOCUS T (FT) in Arabidopsis thaliana and its orthologs in other plant species. Despite the progress in understanding FT transport in the dicot model Arabidopsis, the mechanisms of florigen transport in monocots, which provide most of the biomass in agriculture, are unknown. Here, we show that rice FT-INTERACTING PROTEIN1 (OsFTIP1), a member of the family of multiple C2 domain and transmembrane region proteins (MCTPs) and the closest ortholog of Arabidopsis FTIP1, is required for export of RICE FLOWERING LOCUS T 1 (RFT1) from companion cells to sieve elements. This affects RFT1 movement to the shoot apical meristem and its regulation of rice flowering time under long days. We further reveal that a ubiquitin-like domain kinase γ4, OsUbDKγ4, interacts with OsFTIP1 and modulates its degradation in leaves through the 26S proteasome, which in turn affects RFT1 transport to the shoot apical meristem. Thus, dynamic modulation of OsFTIP1 abundance in leaves by a negative regulator OsUbDKγ4 is integral to the role of OsFTIP1 in mediating RFT1 transport in rice and provides key evidence for a conserved role of FTIP1-like MCTPs in mediating florigen transport in flowering plants.

Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice

The transition from vegetative to reproductive growth is a critical process in the life cycle of higher plants. Previously, we cloned Rice Indeterminate 1 (RID1), which acts as the master switch for the transition from the vegetative to reproductive phase in rice. Although the photoperiod pathway of RID1 inducing expression of the florigen genes Hd3a and RFT1 via Ehd1 has been established, the alternative pathways for the essential flowering transition need to be further examined. Here, we identified a Suppressor of rid1 (SID1), which rescues the never-flowering phenotype of rid1. SID1 encodes an INDETERMINATE DOMAIN (IDD) transcription factor. Mutation in SID1 showed the delayed flowering phenotype. Gain-of-function of SID1, OsIDD1, or OsIDD6 could restore the rid1 to flowering. Further analyses showed SID1 and RID1 directly target the promoter regions of Hd3a and RFT1, two florigen genes in rice. Taken together, our results reveal an autonomous flowering pathway might be mediated by RID1, thereby controlling the phase transition from vegetative to reproductive development in rice.

Transition from vegetative to reproductive phase is a critical developmental switch in the life cycle of higher plants. In rice, our previous work suggested Rice Indeterminate 1 (RID1) acts as the master switch for the transition to flowering. Mutation in RID1 results in a never-flowering phenotype. In order to uncover the molecular network regulated by RID1, a Suppressor of rid1 (SID1) was identified in this study. Both SID1 and RID1 encode a plant-specific INDETERMINATE DOMAIN (IDD) transcription factor. Overexpression of SID1, OsIDD1, or OsIDD6 could rescue the never-flowering phenotype of rid1. Molecular data indicate both SID1 and RID1 physically bind the promoters of the florigen genes Hd3a and RFT1 in rice. Thus, we propose that the transition to flowering could be regulated by RID1 through the autonomous pathway, in addition to the photoperiod pathway.

Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes

Rice flowering is controlled by changes in the photoperiod that promote the transition to the reproductive phase as days become shorter. Natural genetic variation for flowering time has been largely documented and has been instrumental to define the genetics of the photoperiodic pathway, as well as providing valuable material for artificial selection of varieties better adapted to local environments. We mined genetic variation in a collection of rice varieties highly adapted to European regions and isolated distinct variants of the long day repressor HEADING DATE 1 (Hd1) that perturb its expression or protein function. Specific variants allowed us to define novel features of the photoperiodic flowering pathway. We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a). Artificial selection has locally favored an Hd1 variant unable to assemble in such heterotrimeric complex. The causal polymorphism was defined as a single conserved lysine in the CCT domain of the Hd1 protein. Our results indicate how genetic variation can be stratified and explored at multiple levels, and how its description can contribute to the molecular understanding of basic developmental processes.

Many plant species flower in response to changes in day length and can be categorized depending on their requirements for long or short days. Rice has tropical origins and normally flowers in response to shortening days. However, artificial selection operated by ancient farmers or modern breeders adapted rice cultivation to several environments, including those typical of temperate regions characterized by long days during the cropping season. Modifications of the genetic network controlling flowering that are causal to such expansion have been the subject of extensive studies, but the full complement of genes that regulate it and the molecular bases of their activity remains unknown. We took advantage of germplasm cultivated in Europe—and highly adapted to flower under long days–to isolate widespread variants of the HEADING DATE 1 (Hd1) gene that limits flowering in temperate areas, and showed that such variants are non-functional and unable to prevent long day flowering. We identified the DNA changes causing the gene to be non-functional and used such mutant alleles as tools to demonstrate that Hd1 can bind a specific DNA sequence in the promoter of a florigenic rice gene. Mining genetic diversity becomes thus instrumental to define the molecular properties of regulatory pathways.

Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data

Flowering time is a major determinant of biomass yield in switchgrass (Panicum virgatum), a perennial bioenergy crop, because later flowering allows for an extended period of vegetative growth and increased biomass production. A better understanding of the genetic regulation of flowering time in switchgrass will aid the development of switchgrass varieties with increased biomass yields, particularly at northern latitudes, where late-flowering but southern-adapted varieties have high winter mortality. We use genotypes derived from recently published exome-capture sequencing, which mitigates challenges related to the large, highly repetitive and polyploid switchgrass genome, to perform genome-wide association studies (GWAS) using flowering time data from a switchgrass association panel in an effort to characterize the genetic architecture and genes underlying flowering time regulation in switchgrass. We identify associations with flowering time at multiple loci, including in a homolog of FLOWERING LOCUS T and in a locus containing TIMELESS, a homolog of a key circadian regulator in animals. Our results suggest that flowering time variation in switchgrass is due to variation at many positions across the genome. The relationship of flowering time and geographic origin indicates likely roles for genes in the photoperiod and autonomous pathways in generating switchgrass flowering time variation.

Circadian Clock and Photoperiodic Flowering in Arabidopsis: CONSTANS Is a Hub for Signal Integration

The circadian clock and light signaling regulate CONSTANS function through intricate mechanisms that reside in phloem companion cells of leaves for controlling photoperiodic flowering in Arabidopsis.

The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals

Flowering is the result of the coordination between genetic information and environmental cues. Gene regulatory networks have evolved in plants in order to measure diurnal and seasonal variation of day length (or photoperiod), thus aligning the reproductive phase with the most favorable season of the year. The capacity of plants to discriminate distinct photoperiods classifies them into long and short day species, depending on the conditions that induce flowering. Plants of tropical origin and adapted to short day lengths include rice, maize, and sorghum, whereas wheat and barley were originally domesticated in the Fertile Crescent and are considered long day species. In these and other crops, day length measurement mechanisms have been artificially modified during domestication and breeding to adapt plants to novel areas, to the extent that a wide diversity of responses exists within any given species. Notwithstanding the ample natural and artificial variation of day length responses, some of the basic molecular elements governing photoperiodic flowering are widely conserved. However, as our understanding of the underlying mechanisms improves, it becomes evident that specific regulators exist in many lineages that are not shared by others, while apparently conserved components can be recruited to novel functions during evolution.

Genetic control of flowering time in rice: integration of Mendelian genetics and genomics

Integration of previous Mendelian genetic analyses and recent molecular genomics approaches, such as linkage mapping and QTL cloning, dramatically strengthened our current understanding of genetic control of rice flowering time. Flowering time is one of the most important agronomic traits for seed production in rice (Oryza sativa L.). It is controlled mainly by genes associated with photoperiod sensitivity, particularly in short-day plants such as rice. Since the early twentieth century, rice breeders and researchers have been interested in elucidating the genetic basis of flowering time because its modification is important for regional adaptation and yield optimization. Although flowering time is a complex trait controlled by many quantitative trait loci (QTLs), classical genetic studies have shown that many associated genes are inherited in accordance with Mendelian laws. Decoding the rice genome sequence opened a new era in understanding the genetic control of flowering time on the basis of genome-wide mapping and gene cloning. Heading date 1 (Hd1) was the first flowering time QTL to be isolated using natural variation in rice. Recent accumulation of information on rice genome has facilitated the cloning of other QTLs, including those with minor effects on flowering time. This information has allowed us to rediscover some of the flowering genes that were identified by classical Mendelian genetics. The genes characterized so far, including Hd1, have been assigned to specific photoperiod pathways. In this review, we provide an overview of the studies that led to an in-depth understanding of the genetic control of flowering time in rice, and of the current state of improving and fine-tuning this trait for rice breeding.

Effects of Hd2 in the presence of the photoperiod-insensitive functional allele of Hd1 in rice

The role of photoperiod sensitivity (PS) of flowering genes have become well recognized in rice, whereas little attention has been drawn to the non-PS component of these genes, especially to their influence on gene-by-gene interactions. Rice populations in which the photoperiod-sensitive allele at Hd1 has become insensitive to photoperiod but continued to affect heading date (HD) were used in this study to fine-map a quantitative trait locus (QTL) for HD and analyze its genetic relationship to Hd1. The QTL was delimitated to a 96.3-kb region on the distal end of the long arm of chromosome 7. Sequence comparison revealed that this QTL is identical to Hd2. In the near-isogenic line (NIL) populations analyzed, Hd1 and Hd2 were shown to be photoperiod insensitive and have pleiotropic effects for HD, plant height and yield traits. The two genes were found to largely act additively in regulating HD and yield traits. The results indicate that non-PS components of flowering genes involved in photoperiod response play an important role in controlling flowering time and grain yield in rice, which should allow breeders to better manipulate pleiotropic genes for balancing adaptability and high-yielding accumulation.

Summary: We show that photoperiod-insensitive components of alleles of Hd1 and Hd2 play an important role in balancing ecological adaptability and high-yield accumulation in rice.

CONSTANS-Like 9 (OsCOL9) Interacts with Receptor for Activated C-Kinase 1(OsRACK1) to Regulate Blast Resistance through Salicylic Acid and Ethylene Signaling Pathways

In a previous transcriptome analysis of early response genes in rice during Magnaporthe oryzae infection, we identified a CONSTANS-like (COL) gene OsCOL9. In the present study, we investigated the functional roles of OsCOL9 in blast resistance. OsCOL9 belonged to group II of the COL protein family, and it contained a BB-box and a C-terminal CCT (CONSTANS, COL and TOC1) domain. OsCOL9 was found in the nucleus of rice cells, and it exerted transcriptional activation activities through its middle region (MR). Magnaporthe oryzae infection induced OsCOL9 expression, and transgenic OsCOL9 knock-out rice plants showed increased pathogen susceptibility. OsCOL9 was a critical regulator of pathogen-related genes, especially PR1b, which were also activated by exogenous salicylic acid (SA) and 1-aminocyclopropane-1-carboxylicacid (ACC), the precursor of ethylene (ET). Further analysis indicated that OsCOL9 over-expression increased the expressions of phytohormone biosynthetic genes, NPR1, WRKY45, OsACO1 and OsACS1, which were related to SA and ET biosynthesis. Interestingly, we found that OsCOL9 physically interacted with the scaffold protein OsRACK1 through its CCT domain, and the OsRACK1 expression was induced in response to exogenous SA and ACC as well as M. oryzae infection. Taken together, these results indicated that the COL protein OsCOL9 interacted with OsRACK1, and it enhanced the rice blast resistance through SA and ET signaling pathways.

Seed maturation: Simplification of control networks in plants

Networks controlling developmental or metabolic processes in plants are often complex as a consequence of the duplication and specialisation of the regulatory genes as well as the numerous levels of transcriptional and post-transcriptional controls added during evolution. Networks serve to accommodate multicellular complexity and increase robustness to environmental changes. Mathematical simplification by regrouping genes or pathways in a limited number of hubs has facilitated the construction of models for complex traits. In a complementary approach, a biological simplification can be achieved by using genetic modification to understand the core and singular ancestral function of the network, which is likely to be more prevalent within the plant kingdom rather than specific to a species. With this viewpoint, we review examples of simplification successfully undertaken in yeast and other organisms. A strategy of progressive complementation of single, double and triple mutants of seed maturation confirmed the fundamental role of the AFL sub-family of B3 transcription factors as master regulators of seed maturation, illustrating that biological simplification of complex networks could be more widely applied in plants. Defining minimal control networks will facilitate evolutionary comparisons of regulatory processes and the identification of an essential gene set for synthetic biology.

Y flowering? Regulation and activity of CONSTANS and CCT-domain proteins in Arabidopsis and crop species

Changes in day length regulate the proper timing of flowering in several plant species. The genetic architecture of this process is based on CCT-domain proteins, many of which interact with NF-Y subunits to regulate transcription of target genes. In the model plant Arabidopsis thaliana, the CONSTANS CCT-domain protein is a central photoperiodic sensor. We will discuss how the diurnal rhythms of its transcription and protein accumulation are generated, and how the protein engages into multiple complexes to control production of a systemic flowering signal. Regulatory parallels will be drawn between Arabidopsis and major crops that indicate conservation of some CCT/NF-Y modules during plant evolution. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.

A Catalog of Regulatory Sequences for Trait Gene for the Genome Editing of Wheat

Wheat has been cultivated for 10000 years and ever since the origin of hexaploid wheat it has been exempt from natural selection. Instead, it was under the constant selective pressure of human agriculture from harvest to sowing during every year, producing a vast array of varieties. Wheat has been adopted globally, accumulating variation for genes involved in yield traits, environmental adaptation and resistance. However, one small but important part of the wheat genome has hardly changed: the regulatory regions of both the x- and y-type high molecular weight glutenin subunit (HMW-GS) genes, which are alone responsible for approximately 12% of the grain protein content. The phylogeny of the HMW-GS regulatory regions of the Triticeae demonstrates that a genetic bottleneck may have led to its decreased diversity during domestication and the subsequent cultivation. It has also highlighted the fact that the wild relatives of wheat may offer an unexploited genetic resource for the regulatory region of these genes. Significant research efforts have been made in the public sector and by international agencies, using wild crosses to exploit the available genetic variation, and as a result synthetic hexaploids are now being utilized by a number of breeding companies. However, a newly emerging tool of genome editing provides significantly improved efficiency in exploiting the natural variation in HMW-GS genes and incorporating this into elite cultivars and breeding lines. Recent advancement in the understanding of the regulation of these genes underlines the needs for an overview of the regulatory elements for genome editing purposes.

Identification of LATE BLOOMER2 as a CYCLING DOF FACTOR Homolog Reveals Conserved and Divergent Features of the Flowering Response to Photoperiod in Pea

The molecular pathways responsible for the flowering response to photoperiod have been extensively studied in Arabidopsis thaliana and cereals but remain poorly understood in other major plant groups. Here, we describe a dominant mutant at the LATE BLOOMER2 (LATE2) locus in pea (Pisum sativum) that is late-flowering with a reduced response to photoperiod. LATE2 acts downstream of light signaling and the circadian clock to control expression of the main photoperiod-regulated FT gene, FTb2, implying that it plays a primary role in photoperiod measurement. Mapping identified the CYCLING DOF FACTOR gene CDFc1 as a strong candidate for LATE2, and the late2-1D mutant was found to carry a missense mutation in CDFc1 that impairs its capacity to bind to the blue-light photoreceptor FKF1 in yeast two-hybrid assays and delays flowering in Arabidopsis when overexpressed. Arabidopsis CDF genes are important negative regulators of CONSTANS (CO) transcription, but we found no effect of LATE2 on the transcription of pea CO-LIKE genes, nor on genes in any other families previously implicated in the activation of FT in Arabidopsis. Our results reveal an important component of the pea photoperiod response pathway and support the view that regulation of FTb2 expression by photoperiod occurs via a CO-independent mechanism.

CONSTANS-like 9 (COL9) delays the flowering time in Oryza sativa by repressing the Ehd1 pathway

Flowering or heading is one of most important agronomic traits in rice. It has been characterized that CONSTANS (CO) and CONSTANS-like (COL) proteins are critical flowering regulators in response to photoperiodic stress in plants. We have previously identified that the COL family member OsCOL9 can positively enhance the rice blast resistance. In the present study, we aimed to explore the functional role of OsCOL9 in modulating the photoperiodic flowering. Our data showed that overexpression of OsCOL9 delayed the flowering time under both short-day (SD) and long-day (LD) conditions, leading to suppressed expressions of EHd1, RFT and Hd3a at the mRNA Level. OsCOL9 expression exhibited two types of circadian patterns under different daylight conditions, and it could delay the heading date by suppressing the Ehd1 photoperiodic flowering pathway. In contrast, the expressions of previously reported flowering regulators were not significantly changed in OsCOL9 transgenic plants, indicating that OsCOL9 functioned independently of other flowering pathways. In addition, OsCOL9 served as a potential yield gene, and its deficiency reduced the grain number of main panicle in plants. Furthermore, yeast two-hybrid assay indicated that OsCOL9 physically interacted with Receptor for Activated C-kinase 1 (OsRACK1). Rhythmic pattern analysis suggested that OsRACK1 responded to the change of daylight, which was regulated by the circadian clock. Taken together, our results revealed that OsCOL9 could delay the flowering time in rice by repressing the Ehd1 pathway.

Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice

Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between long and short day model species.

Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

Background

Many genes involved in responses to photoperiod and vernalization have been characterized or predicted in Arabidopsis (Arabidopsis thaliana), Brachypodium (Brachypodium distachyon), wheat (Triticum aestivum) and barley (Hordeum vulgare). However, little is known about the transcription regulation of these genes, especially in the large, complex genomes of wheat and barley.

Results

We identified 68, 60, 195 and 61 genes that are known or postulated to control pathways of photoperiod (PH), vernalization (VE) and pathway integration (PI) in Arabidopsis, Brachypodium, wheat and barley for predicting transcription factor binding sites (TFBSs) in the promoters of these genes using the FIMO motif search tool of the MEME Suite. The initial predicted TFBSs were filtered to confirm the final numbers of predicted TFBSs to be 1066, 1379, 1528, and 789 in Arabidopsis, Brachypodium, wheat and barley, respectively. These TFBSs were mapped onto the PH, VE and PI pathways to infer about the regulation of gene expression in Arabidopsis and cereal species. The GC contents in promoters, untranslated regions (UTRs), coding sequences and introns were higher in the three cereal species than those in Arabidopsis. The predicted TFBSs were most abundant for two transcription factor (TF) families: MADS-box and CSD (cold shock domain). The analysis of publicly available gene expression data showed that genes with similar numbers of MADS-box and CSD TFBSs exhibited similar expression patterns across several different tissues and developmental stages. The intra-specific Tajima D-statistics of TFBS motif diversity showed different binding specificity among different TF families. The inter-specific Tajima D-statistics suggested faster TFBS divergence in TFBSs than in coding sequences and introns. Mapping TFBSs onto the PH, VE and PI pathways showed the predominance of MADS-box and CSD TFBSs in most genes of the four species, and the difference in the pathway regulations between Arabidopsis and the three cereal species.

Conclusion

Our approach to associating the key flowering genes with their potential TFs through prediction of putative TFBSs provides a framework to explore regulatory mechanisms of photoperiod and vernalization responses in flowering plants. The predicted TFBSs in the promoters of the flowering genes provide a basis for molecular characterization of transcription regulation in the large, complex genomes of important crop species, wheat and barley.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2916-7) contains supplementary material, which is available to authorized users.

Cool night-time temperatures induce the expression of CONSTANS and FLOWERING LOCUS T to regulate flowering in Arabidopsis

Day length and ambient temperature are major stimuli controlling flowering time. To understand flowering mechanisms in more natural conditions, we explored the effect of daily light and temperature changes on Arabidopsis thaliana. Seedlings were exposed to different day/night temperature and day-length treatments to assess expression changes in flowering genes. Cooler temperature treatments increased CONSTANS (CO) transcript levels at night. Night-time CO induction was diminished in flowering bhlh (fbh)-quadruple mutants. FLOWERING LOCUS T (FT) transcript levels were reduced at dusk, but increased at the end of cooler nights. The dusk suppression, which was alleviated in short vegetative phase (svp) mutants, occurred particularly in younger seedlings, whereas the increase during the night continued over 2 wk. Cooler temperature treatments altered the levels of FLOWERING LOCUS M-β (FLM-β) and FLM-δ splice variants. FT levels correlated strongly with flowering time across treatments. Day/night temperature changes modulate photoperiodic flowering by changing FT accumulation patterns. Cooler night-time temperatures enhance FLOWERING BHLH (FBH)-dependent induction of CO and consequently increase CO protein. When plants are young, cooler temperatures suppress FT at dusk through SHORT VEGETATIVE PHASE (SVP) function, perhaps to suppress precocious flowering. Our results suggest day length and diurnal temperature changes combine to modulate FT and flowering time.

Dissection of the qTGW1.1 region into two tightly-linked minor QTLs having stable effects for grain weight in rice

BACKGROUND

Most agronomical traits of crop species are complex traits controlled by multiple genes and affected by environmental factors. While considerable efforts have been made to fine-map and clone major quantitative trait loci (QTLs) for yield-related traits in rice, it is not until recently that the attention has been paid to minor QTLs. Following previous dissection of QTLs for grain weight and grain size in a 12-Mb interval on the long arm of chromosome 1 in rice, this study targeted at one putative QTL region for a more precise mapping and for analyzing the genotype-by-environment interaction of minor QTLs.

RESULTS

Four BC2F10 plants of the indica rice cross ZS97///ZS97//ZS97/MY46 were selected. They carried overlapped heterozygous segments that jointly covered the entire putative region for qTGW1.1 detected previously. Four sets of near isogenic lines (NILs) were developed from selfing progenies of the four plants. Each NIL set consisted of 32 ZS97 homozygous lines and 32 MY46 homozygous lines that differed in the corresponding heterozygous region. They were grown in two locations having distinct ecological conditions and measured for 1000-grain weight, grain length and grain width. Two QTLs were separated in an 835.2-kb interval flanked by DNA markers Wn28447 and RM11569. They both showed consistent effects across the two environments. The qTGW1.1a located within the 120.4-kb interval Wn28447 - RM11543 significantly affect all the three traits with the enhancing allele derived from ZS97, showing a stronger influence on grain weight than on grain length and width. The qTGW1.1b located in the 521.8-kb interval RM11554 - RM11569 significantly affect grain weight and length with the enhancing allele derived from MY46, having a stronger influence on grain length than on grain weight. Consistent performance of the two QTLs was confirmed in a validation experiment using five NIL-F2 populations segregated for either qTGW1.1a or qTGW1.1b.

CONCLUSION

Separation of closely-linked QTLs having small effects is achievable in the absence of major-QTL segregation. Minor QTLs for complex traits could act consistently in diverse environments, offering the potential of pyramiding beneficial alleles of multiple minor QTLs through marker-assisted selection.

De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering

Background

The appropriate timing of bolting and flowering is pivotal for reproductive success in Brassicaceae crops including radish (Raphanus sativus L.). Although several flowering regulatory pathways had been described in some plant species, no study on genetic networks of bolting and flowering regulation was performed in radish. In this study, to generate dataset of radish unigene sequences for large-scale gene discovery and functional pathway identification, a cDNA library from mixed radish leaves at different developmental stages was subjected to high-throughput RNA sequencing (RNA-seq).

Results

A total of 54.64 million clean reads and 111,167 contigs representing 53,642 unigenes were obtained from the radish leaf transcriptome. Among these, 50,385 unigenes were successfully annotated by BLAST searching against the public protein databases. Functional classification and annotation indicated that 42,903 and 15,382 unique sequences were assigned to 55 GO terms and 25 COG categories, respectively. KEGG pathway analysis revealed that 25,973 unigenes were classified into 128 functional pathways, among which 24 candidate genes related to plant circadian rhythm were identified. Moreover, 142 potential bolting and flowering-related genes involved in various flowering pathways were identified. In addition, seven critical bolting and flowering-related genes were isolated and profiled by T-A cloning and RT-qPCR analysis. Finally, a schematic network model of bolting and flowering regulation and pathways was put forward in radish.

Conclusions

This study is the first report on systematic identification of bolting and flowering-related genes based on transcriptome sequencing and assembly in radish. These results could provide a foundation for further investigating bolting and flowering regulatory networks in radish, and facilitate dissecting molecular genetic mechanisms underlying bolting and flowering in Brassicaceae vegetable crops.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2633-2) contains supplementary material, which is available to authorized users.

Hd1,a CONSTANS ortholog in rice, functions as an Ehd1 repressor through interaction with monocot-specific CCT-domain protein Ghd7

Flowering time is an important agronomic trait that affects crop yields. In cereals, several CCT-domain proteins unique to monocots, such as Grain number, plant height, and heading date 7 (Ghd7) gene, have been identified as key floral repressors, although the corresponding molecular mechanisms have been unknown until now. In rice, a short-day plant, Heading date 1 (Hd1) gene, a rice ortholog of Arabidopsis floral activator CONSTANS (CO), represses flowering under non-inductive long-day (LD) conditions and induces it under inductive short-day (SD) conditions. Here, we report biological interactions between Ghd7 and Hd1, which together repress Early heading date 1 (Ehd1), a key floral inducer under non-inductive LD conditions. In addition to this genetic interaction between them, Co-IP experiments further demonstrated that a Ghd7-Hd1 protein formed a complex in vivo and ChIP and luciferase reporter analyses suggested that this complex specifically binds to a cis-regulatory region in Ehd1 and represses its expression. These findings imply that Hd1, an evolutionally conserved transcriptional activator, can function as a strong transcriptional repressor within a monocot-specific flowering-time pathway through with Ghd7.

Rapid, Long-Distance Electrical and Calcium Signaling in Plants

Plants integrate activities throughout their bodies using long-range signaling systems in which stimuli sensed by just a few cells are translated into mobile signals that can influence the activities in distant tissues. Such signaling can travel at speeds well in excess of millimeters per second and can trigger responses as diverse as changes in transcription and translation levels, posttranslational regulation, alterations in metabolite levels, and even wholesale reprogramming of development. In addition to the use of mobile small molecules and hormones, electrical signals have long been known to propagate throughout the plant. This electrical signaling network has now been linked to waves of Ca(2+) and reactive oxygen species that traverse the plant and trigger systemic responses. Analysis of cell type specificity in signal propagation has revealed the movement of systemic signals through specific cell types, suggesting that a rapid signaling network may be hardwired into the architecture of the plant.

The genetic architecture of leaf number and its genetic relationship to flowering time in maize

The number of leaves and their distributions on plants are critical factors determining plant architecture in maize (Zea mays), and leaf number is frequently used as a measure of flowering time, a trait that is key to local environmental adaptation. Here, using a large set of 866 maize-teosinte BC2 S3 recombinant inbred lines genotyped by using 19,838 single nucleotide polymorphism markers, we conducted a comprehensive genetic dissection to assess the genetic architecture of leaf number and its genetic relationship to flowering time. We demonstrated that the two components of total leaf number, the number of leaves above (LA) and below (LB) the primary ear, were under relatively independent genetic control and might be subject to differential directional selection during maize domestication and improvement. Furthermore, we revealed that flowering time and leaf number are commonly regulated at a moderate level. The pleiotropy of the genes ZCN8, dlf1 and ZmCCT on leaf number and flowering time were validated by near-isogenic line analysis. Through fine mapping, qLA1-1, a major-effect locus that specifically affects LA, was delimited to a region with severe recombination suppression derived from teosinte. This study provides important insights into the genetic basis of traits affecting plant architecture and adaptation. The genetic independence of LA from LB enables the optimization of leaf number for ideal plant architecture breeding in maize.

Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis

The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.

Multiple paths to similar germination behavior in Arabidopsis thaliana

Germination timing influences plant fitness, and its sensitivity to temperature may cause it to change as climate shifts. These changes are likely to be complex because temperatures that occur during seed maturation and temperatures that occur post-dispersal interact to define germination timing. We used the model organism Arabidopsis thaliana to determine how flowering time (which defines seed-maturation temperature) and post-dispersal temperature influence germination and the expression of genetic variation for germination. Germination responses to temperature (germination envelopes) changed as seeds aged, or after-ripened, and these germination trajectories depended on seed-maturation temperature and genotype. Different combinations of genotype, seed-maturation temperature, and after-ripening produced similar germination envelopes. Likewise, different genotypes and seed-maturation temperatures combined to produce similar germination trajectories. Differences between genotypes were most likely to be observed at high and low germination temperatures. The germination behavior of some genotypes responds weakly to maternal temperature but others are highly plastic. We hypothesize that weak dormancy induction could synchronize germination of seeds dispersed at different times. By contrast, we hypothesize that strongly responsive genotypes may spread offspring germination over several possible germination windows. Considering germination responses to temperature is important for predicting phenology expression and evolution in future climates.

Systematic Investigation of FLOWERING LOCUS T-Like Poaceae Gene Families Identifies the Short-Day Expressed Flowering Pathway Gene, TaFT3 in Wheat (Triticum aestivum L.)

To date, a small number of major flowering time loci have been identified in the related Triticeae crops, bread wheat (Triticum aestivum), durum wheat (T. durum), and barley (Hordeum vulgare). Natural genetic variants at these loci result in major phenotypic changes which have adapted crops to the novel environments encountered during the spread of agriculture. The polyploid nature of bread and durum wheat means that major flowering time loci in which recessive alleles confer adaptive advantage in related diploid species have not been readily identified. One such example is the PPD-H2 flowering time locus encoded by FLOWERING LOCUS T 3 (HvFT3) in the diploid crop barley, for which recessive mutant alleles confer delayed flowering under short day (SD) photoperiods. In autumn-sown barley, such alleles aid the repression of flowering over the winter, which help prevent the development of cold-sensitive floral organs until the onset of inductive long day (LD) photoperiods the following spring. While the identification of orthologous loci in wheat could provide breeders with alternative mechanisms to fine tune flowering time, systematic identification of wheat orthologs of HvFT3 has not been reported. Here, we characterize the FT gene families in six Poaceae species, identifying novel members in all taxa investigated, as well as FT3 homoeologs from the A, B and D genomes of hexaploid (TaFT3) and tetraploid wheat. Sequence analysis shows TaFT3 homoeologs display high similarity to the HvFT3 coding region (95-96%) and predicted protein (96-97%), with conservation of intron/exon structure across the five cereal species investigated. Genetic mapping and comparative analyses in hexaploid and tetraploid wheat find TaFT3 homoeologs map to the long arms of the group 1 chromosomes, collinear to HvFT3 in barley and FT3 orthologs in rice, foxtail millet and brachypodium. Genome-specific expression analyses show FT3 homoeologs in tetraploid and hexaploid wheat are upregulated under SD photoperiods, but not under LDs, analogous to the expression of HvFT3. Collectively, these results indicate that functional wheat orthologs of HvFT3 have been identified. The molecular resources generated here provide the foundation for engineering a novel major flowering time locus in wheat using forward or reverse genetics approaches.

Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice

Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical day length to get flowering. Sensitivity to photoperiod has been suggested as a major selection target in cultivated or weedy rice. The modern rice varieties in Taiwan may be cultivated twice a year. These varieties contain loss-of-function of two important flowering-time related genes, Heading date 1 (Hd1) and Early heading date 1 (Ehd1), and are mainly from a mega variety, Taichung 65. However, the parental lines of this variety were sensitive to photoperiod, thus, how Taichung 65 loss its sensitivity is a mystery. In this study, we used accession-specific single nucleotide polymorphism analysis to reveal the gene flow that occurred between different rice accessions decades ago and demonstrate that two landraces introgressed during the breeding process, which led to the loss of photoperiod sensitivity. Both Hd1 and Ehd1 may be important during artificial selection for flowering time, especially in a subtropical region such as Taiwan. This is a good example of introgression playing important roles during rice domestication.

Rice FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1) promotes flowering independent of photoperiod

In the facultative long-day (LD) plant Arabidopsis thaliana, FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) is activated by blue light and promotes flowering through the transcriptional and post-translational regulation of CONSTANS under inductive LD conditions. By contrast, the facultative short day (SD) plant rice (Oryza sativa) flowers early under inductive SD and late under non-inductive LD conditions; the regulatory function of OsFKF1 remains elusive. Here we show that osfkf1 mutants flower late under SD, LD and natural LD conditions. Transcriptional analysis revealed that OsFKF1 up-regulates the expression of the floral activator Ehd2 and down-regulates the expression of the floral repressor Ghd7; these regulators up- and down-regulate Ehd1 expression, respectively. Moreover, OsFKF1 can up-regulate Ehd1 expression under blue light treatment, without affecting the expression of Ehd2 and Ghd7. In contrast to the LD-specific floral activator Arabidopsis FKF1, OsFKF1 likely acts as an autonomous floral activator because it promotes flowering independent of photoperiod, probably via its distinct roles in controlling the expression of rice-specific genes including Ehd2, Ghd7 and Ehd1. Like Arabidopsis FKF1, which interacts with GI and CDF1, OsFKF1 also interacts with OsGI and OsCDF1 (also termed OsDOF12). Thus, we have identified similar and distinct roles of FKF1 in Arabidopsis and rice.

Genetic interactions between diverged alleles of Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/ RICE FLOWERING LOCUS T1 (RFT1) control differential heading and contribute to regional adaptation in rice (Oryza sativa)

Initiation of flowering, also called heading, in rice (Oryza sativa) is determined by the florigens encoded by Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1). Early heading date 1 (Ehd1) regulates Hd3a and RFT1. However, different rice varieties have diverged alleles of Ehd1 and Hd3a/RFT1 and their genetic interactions remain largely unclear. Here we generated three segregating populations for different combinations of diverged Ehd1 and Hd3a/RFT1 alleles, and analyzed their genetic interactions between these alleles. We demonstrated that, in an ehd1 mutant background, Hd3a was silenced, but RFT1 was expressed (although at lower levels than in plants with a functional Ehd1) under short-day (SD) and long-day (LD) conditions. We identified a nonfunctional RFT1 allele (rft1); the lines carrying homozygous ehd1 and Hd3a/rft1 failed to induce the floral transition under SD and LD conditions. Like Hd3a, RFT1 also interacted with 14-3-3 proteins, the florigen receptors, but a nonfunctional RFT1 with a crucial E105K mutation failed to interact with 14-3-3 proteins. Furthermore, analyses of sequence variation and geographic distribution suggested that functional RFT1 alleles were selected during rice adaptation to high-latitude regions. Our results demonstrate the important roles of RFT1 in rice flowering and regional adaptation.

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.