Isolation and characterization of rice phytochrome A mutants

Far-red light enrichment affects gene expression and architecture as well as growth and photosynthesis in rice

Plants use light as a resource and signal. Photons within the 400-700 nm waveband are considered photosynthetically active. Far-red photons (FR, 700-800 nm) are used by plants to detect nearby vegetation and elicit the shade avoidance syndrome. In addition, FR photons have also been shown to contribute to photosynthesis, but knowledge about these dual effects remains scarce. Here, we study shoot-architectural and photosynthetic responses to supplemental FR light during the photoperiod in several rice varieties. We observed that FR enrichment only mildly affected the rice transcriptome and shoot architecture as compared to established model species, whereas leaf formation, tillering and biomass accumulation were clearly promoted. Consistent with this growth promotion, we found that CO2-fixation in supplemental FR was strongly enhanced, especially in plants acclimated to FR-enriched conditions as compared to control conditions. This growth promotion dominates the effects of FR photons on shoot development and architecture. When substituting FR enrichment with an end-of-day FR pulse, this prevented photosynthesis-promoting effects and elicited shade avoidance responses. We conclude that FR photons can have a dual role, where effects depend on the environmental context: in addition to being an environmental signal, they are also a potent source of harvestable energy.

Molecular and biochemical characterization of rice developed through conventional integration of nDart1-0 transposon gene

Mutations, the genetic variations in genomic sequences, play an important role in molecular biology and biotechnology. During DNA replication or meiosis, one of the mutations is transposons or jumping genes. An indigenous transposon nDart1-0 was successfully introduced into local indica cultivar Basmati-370 from transposon-tagged line viz., GR-7895 (japonica genotype) through conventional breeding technique, successive backcrossing. Plants from segregating populationsshowed variegated phenotypes were tagged as BM-37 mutants. Blast analysis of the sequence data revealed that the GTP-binding protein, located on the BAC clone OJ1781_H11 of chromosome 5, contained an insertion of DNA transposon nDart1-0. The nDart1-0 has "A" at position 254 bp, whereas nDart1 homologs have "G", which efficiently distinguishes nDart1-0 from its homologs. The histological analysis revealed that the chloroplast of mesophyll cells in BM-37 was disrupted with reduction in size of starch granules and higher number of osmophillic plastoglobuli, which resulted in decreased chlorophyll contents and carotenoids, gas exchange parameters (Pn, g, E, Ci), and reduced expression level of genes associated with chlorophyll biosynthesis, photosynthesis and chloroplast development. Along with the rise of GTP protein, the salicylic acid (SA) and gibberellic acid (GA) and antioxidant contents(SOD) and MDA levels significantly enhanced, while, the cytokinins (CK), ascorbate peroxidase (APX), catalase (CAT), total flavanoid contents (TFC) and total phenolic contents (TPC) significantly reduced in BM-37 mutant plants as compared with WT plants. These results support the notion that GTP-binding proteins influence the process underlying chloroplast formation. Therefore, it is anticipated that to combat biotic or abiotic stress conditions, the nDart1-0 tagged mutant (BM-37) of Basmati-370 would be beneficial.

SCARECROW-like GRAS protein PES positively regulates petunia floral scent production

Emission of scent volatiles by flowers is important for successful pollination and consequently, reproduction. Petunia (Petunia hybrida) floral scent is formed mainly by volatile products of the phenylpropanoid pathway. We identified and characterized a regulator of petunia scent production: the GRAS protein PHENYLPROPANOID EMISSION-REGULATING SCARECROW-LIKE (PES). Its expression increased in petals during bud development and was highest in open flowers. Overexpression of PES increased the production of floral volatiles, while its suppression resulted in scent reduction. We showed that PES upregulates the expression of genes encoding enzymes of the phenylpropanoid and shikimate pathways in petals, and of the core regulator of volatile biosynthesis ODORANT1 by activating its promoter. PES is an ortholog of Arabidopsis (Arabidopsis thaliana) PHYTOCHROME A SIGNAL TRANSDUCTION 1, involved in physiological responses to far-red (FR) light. Analyses of the effect of nonphotosynthetic irradiation (low-intensity FR light) on petunia floral volatiles revealed FR light as a scent-activating factor. While PHYTOCHROME A regulated scent-related gene expression and floral scent production under FR light, the influence of PES on volatile production was not limited by FR light conditions.

Evolution of flowering time genes in rice: From the paleolithic to the anthropocene

The evolutionary paths of humans and plants have crossed more than once throughout millennia. While agriculture contributed to the evolution of societies in prehistory, human selection of desirable traits contributed to the evolution of crops during centuries of cultivation. Among cereal crops, rice is currently grown around the globe and represents staple food for almost half of the world population. Over time, rice cultivation has expanded from subtropical to temperate regions thanks to artificial selection of mutants with impaired response to photoperiod. Additional regulatory mechanisms control flowering in response to diverse environmental cues, anticipating or delaying the floral transition to produce seeds in more favourable conditions. Nevertheless, the changing climate is threatening grain production because modern cultivars are sensitive to external fluctuations that go beyond their physiological range. One possibility to guarantee food production could be the exploitation of novel varieties obtained by crossing highly productive Asian rice with stress tolerant African rice. This review explores the genetic basis of the key traits that marked the long journey of rice cultivation from the end of the paleolithic to the anthropocene, with a focus on heading date. By 2050, will rice plants of the future flower in the outer space?

A base substitution in OsphyC disturbs its Interaction with OsphyB and affects flowering time and chlorophyll synthesis in rice

BACKGROUND

Phytochromes are important photoreceptors in plants, and play essential roles in photomorphogenesis. The functions of PhyA and PhyB in plants have been fully analyzed, while those of PhyC in plant are not well understood.

RESULTS

A rice mutant, late heading date 3 (lhd3), was characterized, and the gene LHD3 was identified with a map-based cloning strategy. LHD3 encodes phytochrome C in rice. Animo acid substitution in OsphyC disrupted its interaction with OsphyB or itself, restraining functional forms of homodimer or heterodimer formation. Compared with wild-type plants, the lhd3 mutant exhibited delayed flowering under both LD (long-day) and SD (short-day) conditions, and delayed flowering time was positively associated with the day length via the Ehd1 pathway. In addition, lhd3 showed a pale-green-leaf phenotype and a slower chlorophyll synthesis rate during the greening process. The transcription patterns of many key genes involved in photoperiod-mediated flowering and chlorophyll synthesis were altered in lhd3.

CONCLUSION

The dimerization of OsPhyC is important for its functions in the regulation of chlorophyll synthesis and heading. Our findings will facilitate efforts to further elucidate the function and mechanism of OsphyC and during light signal transduction in rice.

Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops

In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.

Genome-Wide Identification and Expression of FAR1 Gene Family Provide Insight Into Pod Development in Peanut (Arachis hypogaea)

The far-red-impaired response 1 (FAR1) transcription family were initially identified as important factors for phytochrome A (phyA)-mediated far-red light signaling in Arabidopsis; they play crucial roles in controlling the growth and development of plants. The reported reference genome sequences of Arachis, including A. duranensis, A. ipaensis, A. monticola, and A. hypogaea, and its related species Glycine max provide an opportunity to systematically perform a genome-wide identification of FAR1 homologous genes and investigate expression patterns of these members in peanut species. Here, a total of 650 FAR1 genes were identified from four Aarchis and its closely related species G. max. Of the studied species, A. hypogaea contained the most (246) AhFAR1 genes, which can be classified into three subgroups based on phylogenic relationships. The synonymous (Ks) and non-synonymous (Ka) substitution rates, phylogenetic relationship and synteny analysis of the FAR1 family provided deep insight into polyploidization, evolution and domestication of peanut AhFAR1 genes. The transcriptome data showed that the AhFAR1 genes exhibited distinct tissue- and stage-specific expression patterns in peanut. Three candidate genes including Ahy_A10g049543, Ahy_A06g026579, and Ahy_A10g048401, specifically expressed in peg and pod, might participate in pod development in the peanut. The quantitative real-time PCR (qRT-PCR) analyses confirmed that the three selected genes were highly and specifically expressed in the peg and pod. This study systematically analyzed gene structure, evolutionary characteristics and expression patterns of FAR1 gene family, which will provide a foundation for the study of genetic and biological function in the future.

Fine mapping of a heading date QTL, Se16(t), under extremely long day conditions in rice

Heading date (flowering time) is a key trait that determines the yield and the adaptability of rice varieties. In the past 20 years, a number of genetic studies have been carried out to elucidate the genetic control of rice heading date, and many important genes have been cloned. These genes were identified under natural day (ND) conditions; however, little is known about the heading behavior under extreme day-length conditions. In this study, we identified a japonica variety, Sasanishiki, that showed sensitivity to extremely long days (ELD). Its heading date was significantly delayed for about 20 days under artificial ELD conditions that were achieved by setting a light emitting diode (LED) lamp beside a paddy field. We found that the late heading phenotype of Sasanishiki was induced when the day length was more than 14.75 h, and the LED light intensity was above 2 µmol m-2 s-1. Genetic analysis revealed that the photoperiod sensitivity of Sasanishiki was controlled by a dominant locus, temporarily named Se16(t). It was fine mapped to a 30.4-kb interval on chromosome 3, containing five predicted genes, including PHYC, a phytochrome encoding gene of rice. Our findings provide new information on the heading date under ELD conditions in rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01263-8.

Modulation of Phototropin Signalosome with Artificial Illumination Holds Great Potential in the Development of Climate-Smart Crops

Changes in environmental conditions like temperature and light critically influence crop production. To deal with these changes, plants possess various photoreceptors such as Phototropin (PHOT), Phytochrome (PHY), Cryptochrome (CRY), and UVR8 that work synergistically as sensor and stress sensing receptors to different external cues. PHOTs are capable of regulating several functions like growth and development, chloroplast relocation, thermomorphogenesis, metabolite accumulation, stomatal opening, and phototropism in plants. PHOT plays a pivotal role in overcoming the damage caused by excess light and other environmental stresses (heat, cold, and salinity) and biotic stress. The crosstalk between photoreceptors and phytohormones contributes to plant growth, seed germination, photo-protection, flowering, phototropism, and stomatal opening. Molecular genetic studies using gene targeting and synthetic biology approaches have revealed the potential role of different photoreceptor genes in the manipulation of various beneficial agronomic traits. Overexpression of PHOT2 in Fragaria ananassa leads to the increase in anthocyanin content in its leaves and fruits. Artificial illumination with blue light alone and in combination with red light influence the growth, yield, and secondary metabolite production in many plants, while in algal species, it affects growth, chlorophyll content, lipid production and also increases its bioremediation efficiency. Artificial illumination alters the morphological, developmental, and physiological characteristics of agronomic crops and algal species. This review focuses on PHOT modulated signalosome and artificial illumination-based photo-biotechnological approaches for the development of climate-smart crops.

Rice Non-Specific Phospholipase C6 Is Involved in Mesocotyl Elongation

Mesocotyl elongation of rice is crucial for seedlings pushing out of deep soil. The underlying mechanisms of phospholipid signaling in mesocotyl growth of rice are elusive. Here we report that the rice non-specific phospholipase C6 (OsNPC6) is involved in mesocotyl elongation. Our results indicated that all five OsNPCs (OsNPC1, OsNPC2, OsNPC3, OsNPC4 and OsNPC6) hydrolyzed the substrate phosphatidylcholine to phosphocholine (PCho), and all of them showed plasma membrane localization. Overexpression (OE) of OsNPC6 produced plants with shorter mesocotyls compared to those of Nipponbare and npc6 mutants. Although the mesocotyl growth of npc6 mutants was not much affected without gibberellic acid (GA)3, it was obviously elongated by treatment with GA. Upon GA3 treatment, SLENDER RICE1 (SLR1), the DELLA protein of GA signaling, was drastically increased in OE plants; by contrast, the level of SLR1 was found decreased in npc6 mutants. The GA-enhanced mesocotyl elongation and the GA-impaired SLR1 level in npc6 mutants were attenuated by the supplementation of PCho. Further analysis indicated that the GA-induced expression of phospho-base N-methyltransferase 1 in npc6 mutants was significantly weakened by the addition of PCho. In summary, our results suggest that OsNPC6 is involved in mesocotyl development via modulation of PCho in rice.

The transcription factor gene RDD4 contributes to the control of nutrient ion accumulation in rice

In this study, we investigated the expression and functions of the transcription factor gene RDD4 (rice Dof daily fluctuations 4), which has sequence similarity to RDD1 that controls nutrient ion accumulation in rice. RDD4 protein was highly accumulated in leaf sheaths and localized to vascular bundles. RDD4-overexpressing plants (RDD4-OX) improved the accumulation of various nutrient ions, irrespective of nutrient concentration in a hydroponic solution. K⁺ and Cl^- deficiencies induced the accumulation of other cations and anions, respectively. Interestingly, in RDD4-OX plants K⁺ and Cl^- deficiencies increased PO₄ ^3- and Mg²⁺ contents, respectively, despite opposite electric charges. Furthermore, PO₄ ^3- deficiency induced NO₃ ^- and Mg²⁺ accumulation in RDD4-OX plants. These data show that RDD4 is associated with the control of nutrient ion contents within plants. Also, photosynthetic CO₂ assimilation in RDD4-OX plants was higher than in wild-type (WT) plants, although the sizes of shoots and panicles decreased in RDD4-OX plants. Subsequent microarray analysis indicated that OsFWL7, similar to maize CNR1 that negatively regulates plant size, showed the most significant difference in its expression levels between WT and RDD4-OX plants. Based on these results, it is hypothesized that a prominent increase in the OsFWL7 expression reduces plant size in RDD4-OX plants.

Era-like GTP protein gene expression in rice

The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.

Molecular basis of heading date control in rice

Flowering time is of great significance for crop reproduction, yield, and regional adaptability, which is intricately regulated by various environmental cues and endogenous signals. Genetic approaches in Arabidopsis have revealed the elaborate underlying mechanisms of sensing the dynamic change of photoperiod via a coincidence between light signaling and circadian clock, the cellular time keeping system, to precisely control photoperiodic flowering time, and many other signaling pathways including internal hormones and external temperature cues. Extensive studies in rice (Oryza sativa.), one of the short-day plants (SDP), have uncovered the multiple major genetic components in regulating heading date, and revealed the underlying mechanisms for regulating heading date. Here we summarize the current progresses on the molecular basis for rice heading date control, especially focusing on the integration mechanism between photoperiod and circadian clock, and epigenetic regulation and heading procedures in response to abiotic stresses.

Karrikin Signaling Acts Parallel to and Additively with Strigolactone Signaling to Regulate Rice Mesocotyl Elongation in Darkness

Seedling emergence in monocots depends mainly on mesocotyl elongation, requiring coordination between developmental signals and environmental stimuli. Strigolactones (SLs) and karrikins are butenolide compounds that regulate various developmental processes; both are able to negatively regulate rice (Oryza sativa) mesocotyl elongation in the dark. Here, we report that a karrikin signaling complex, DWARF14-LIKE (D14L)-DWARF3 (D3)-O. sativa SUPPRESSOR OF MAX2 1 (OsSMAX1) mediates the regulation of rice mesocotyl elongation in the dark. We demonstrate that D14L recognizes the karrikin signal and recruits the SCFD3 ubiquitin ligase for the ubiquitination and degradation of OsSMAX1, mirroring the SL-induced and D14- and D3-dependent ubiquitination and degradation of D53. Overexpression of OsSMAX1 promoted mesocotyl elongation in the dark, whereas knockout of OsSMAX1 suppressed the elongated-mesocotyl phenotypes of d14l and d3 OsSMAX1 localizes to the nucleus and interacts with TOPLESS-RELATED PROTEINs, regulating downstream gene expression. Moreover, we showed that the GR24 enantiomers GR245DS and GR24 ent-5DS specifically inhibit mesocotyl elongation and regulate downstream gene expression in a D14- and D14L-dependent manner, respectively. Our work revealed that karrikin and SL signaling play parallel and additive roles in modulating downstream gene expression and negatively regulating mesocotyl elongation in the dark.

Light modulates the gravitropic responses through organ-specific PIFs and HY5 regulation of LAZY4 expression in Arabidopsis

Light and gravity are two key environmental factors that control plant growth and architecture. However, the molecular basis of the coordination of light and gravity signaling in plants remains obscure. Here, we report that two classes of transcription factors, PHYTOCHROME INTERACTING FACTORS (PIFs) and ELONGATED HYPOCOTYL5 (HY5), can directly bind and activate the expression of LAZY4, a positive regulator of gravitropism in both shoots and roots in Arabidopsis In hypocotyls, light promotes degradation of PIFs to reduce LAZY4 expression, which inhibits the negative gravitropism of hypocotyls. LAZY4 overexpression can partially rescue the negative gravitropic phenotype of pifq in the dark without affecting amyloplast development. Our identification of the PIFs-LAZY4 regulatory module suggests the presence of another role for PIF proteins in gravitropism, in addition to a previous report demonstrating that PIFs positively regulate amyloplast development to promote negative gravitropism in hypocotyls. In roots, light promotes accumulation of HY5 proteins to activate expression of LAZY4, which promotes positive gravitropism in roots. Together, our data indicate that light exerts opposite regulation of LAZY4 expression in shoots and roots by mediating the protein levels of PIFs and HY5, respectively, to inhibit the negative gravitropism of shoots and promote positive gravitropism of roots in Arabidopsis.

Red and blue light differentially impact retrograde signalling and photoprotection in rice

Chloroplast-to-nucleus retrograde signalling (RS) is known to impact plant growth and development. In Arabidopsis, we and others have shown that RS affects seedling establishment by inhibiting deetiolation. In the presence of lincomycin, a chloroplast protein synthesis inhibitor that triggers RS, Arabidopsis light-grown seedlings display partial skotomorphogenesis with undeveloped plastids and closed cotyledons. By contrast, RS in monocotyledonous has been much less studied. Here, we show that emerging rice seedlings exposed to lincomycin do not accumulate chlorophyll but otherwise remain remarkably unaffected. However, by using high red (R) and blue (B) monochromatic lights in combination with lincomycin, we have uncovered a RS inhibition of length and a reduction in the B light-induced declination of the second leaf. Furthermore, we present data showing that seedlings grown in high B and R light display different non-photochemical quenching capacity. Our findings support the view that excess B and R light impact seedling photomorphogenesis differently to photoprotect and optimize the response to high-light stress. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B

The constitutively active missense allele of Arabidopsis phytochrome B, AtPHYBY276H or AtYHB, encodes a polypeptide that adopts a light-insensitive, physiologically active conformation capable of sustaining photomorphogenesis in darkness. Here, we show that the orthologous OsYHB allele of rice phytochrome B (OsPHYBY283H ) also encodes a dominant "constitutively active" photoreceptor through comparative phenotypic analyses of AtYHB and OsYHB transgenic lines of four eudicot species, Arabidopsis thaliana, Nicotiana tabacum (tobacco), Nicotiana sylvestris and Solanum lycopersicum cv. MicroTom (tomato), and of two monocot species, Oryza sativa ssp. japonica and Brachypodium distachyon. Reciprocal transformation experiments show that the gain-of-function constitutive photomorphogenic (cop) phenotypes by YHB expression are stronger in host plants within the same class than across classes. Our studies also reveal additional YHB-dependent traits in adult plants, which include extreme shade tolerance, both early and late flowering behaviors, delayed leaf senescence, reduced tillering, and even viviparous seed germination. However, the strength of these gain-of-function phenotypes depends on the specific combination of YHB allele and species/cultivar transformed. Flowering and tillering of OsYHB- and OsPHYB-expressing lines of rice Nipponbare and Kitaake cultivars were compared, also revealing differences in YHB/PHYB allele versus genotype interaction on the phenotypic behavior of the two rice cultivars. In view of recent evidence that the regulatory activity of AtYHB is not only light insensitive but also temperature insensitive, selective YHB expression is expected to yield improved agronomic performance of both dicot and monocot crop plant species not possible with wild-type PHYB alleles.

The Rice Actin-Binding Protein RMD Regulates Light-Dependent Shoot Gravitropism

Light and gravity are two key determinants in orientating plant stems for proper growth and development. The organization and dynamics of the actin cytoskeleton are essential for cell biology and critically regulated by actin-binding proteins. However, the role of actin cytoskeleton in shoot negative gravitropism remains controversial. In this work, we report that the actin-binding protein Rice Morphology Determinant (RMD) promotes reorganization of the actin cytoskeleton in rice (Oryza sativa) shoots. The changes in actin organization are associated with the ability of the rice shoots to respond to negative gravitropism. Here, light-grown rmd mutant shoots exhibited agravitropic phenotypes. By contrast, etiolated rmd shoots displayed normal negative shoot gravitropism. Furthermore, we show that RMD maintains an actin configuration that promotes statolith mobility in gravisensing endodermal cells, and for proper auxin distribution in light-grown, but not dark-grown, shoots. RMD gene expression is diurnally controlled and directly repressed by the phytochrome-interacting factor-like protein OsPIL16. Consequently, overexpression of OsPIL16 led to gravisensing and actin patterning defects that phenocopied the rmd mutant. Our findings outline a mechanism that links light signaling and gravity perception for straight shoot growth in rice.

Characterization of phytochrome C functions in the control of de-etiolation and agronomic traits in rice

Although phytochrome A (phyA) and phyB have been functionally characterized, functions of phyC in rice growth and development have remained elusive because of the functional dependency of phyC on the phyB protein. In this study, we introduced PHYB(C364A), in which the chromophore attachment site cysteine 364 was converted to alanine, into the phyAphyB double mutant (aabb) and the phyAphyBphyC triple mutant (aabbcc) to produce PHYB(C364A)/aabb lines and PHYB(C364A)/aabbcc lines, respectively. PHYB(C364A)/aabbcc lines were insensitive to red light (R) and far-red light (FR), suggesting that PHYB(C364A) protein was biologically inactive. Functions of phyC were characterized using the PHYB(C364A)/aabb lines, without the functional interference of phyA or phyB. Phytochrome C responded to R and FR to trigger de-etiolation in the very-low-fluence response and low-fluence response in the PHYB(C364A)/aabb lines. Compared with the aabb mutant, seedlings of PHYB(C364A)/aabb lines showed higher chlorophyll content and reduced leaf angle. The PHYB(C364A)/aabb lines also showed a delayed heading date under long-day conditions. Phytochrome C-regulated agronomic traits were measured at the mature stage. The PHYB(C364A)/aabb lines showed significantly increased plant height, panicle length, grain number per main panicle, seed-setting rate, grain size, and grain weight, compared with those of the aabb mutant. Taken together, the present findings confirm that phyC perceives R and FR, and plays an important role in photomorphogenesis and yield determination in rice.

Phytochrome A signal transduction 1 and CONSTANS-LIKE 13 coordinately orchestrate shoot branching and flowering in leafy Brassica juncea

Branching is a major determinant of crop yield, and enables vigorous shoot growth and the production of a dense canopy. Phytochrome A signal transduction 1 (PAT1) positively regulates phytochrome A signal transduction in response to light, but its effects on branching remain unknown. In this study, we mapped PAT1, and revealed a previously unknown role related to branching and flowering in leafy Brassica juncea. Earlier and increased branching was observed when PAT1 expression was down-regulated, implying that PAT1 negatively regulates shoot branching. Additionally, down-regulated PAT1 expression reversed the inhibited branching induced by far-red light, suggesting PAT1 is involved in the shade avoidance response. PAT1 negatively regulated branching only after bud initiation. The observed interaction between PAT1 and BRC1 implied that PAT1 influences bud outgrowth in a BRC1-dependent manner. Biochemical and genetic evidence indicate that PAT1 directly interacts with CONSTANS-LIKE 13 (COL13), which negatively regulates flowering, with the resulting PAT1-COL13 complex mediating shoot branching and flowering. Our findings reveal a new crosstalk modality between phytochrome signalling and flowering pathways during the regulation of shoot branching and flowering. The data presented herein may be useful for future studies involving the editing of the GRAS family transcription factor PAT1 gene to enhance crop productivity and enable earlier harvesting.

Cas9/sgRNA-based genome editing and other reverse genetic approaches for functional genomic studies in rice

One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. The advent of rice genome research and the annotation of high-quality genome sequencing along with the developments in databases and computer searches have enabled the functional characterization of unknown genes in rice. Further, with the improvements in the efficiency of regeneration and transformation protocols, it has now become feasible to produce sizable mutant populations in indica rice varieties also. In this review, various mutagenesis methods, the current status of the mutant resources, limitations and strengths of insertional mutagenesis approaches and also results obtained with suitable screens for stress tolerance in rice are discussed. In addition, targeted genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or Cas9/single-guide RNA system and its potential applications in generating transgene-free rice plants through genome engineering as an efficient alternative to classical transgenic technology are also discussed.

Molecular mechanisms and ecological function of far-red light signalling

Land plants possess the ability to sense and respond to far-red light (700-760 nm), which serves as an important environmental cue. Due to the nature of far-red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far-red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far-red light through phyA and the physiological responses to this light quality. Light-activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1^COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red-light responses, phyA is transported from the cytoplasm to the nucleus in far-red light by the shuttle proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far-red light; current hypotheses are discussed.

Development of transgenic crops based on photo-biotechnology

The phenotypes associated with plant photomorphogenesis such as the suppressed shade avoidance response and de-etiolation offer the potential for significant enhancement of crop yields. Of many light signal transducers and transcription factors involved in the photomorphogenic responses of plants, this review focuses on the transgenic overexpression of the photoreceptor genes at the uppermost stream of the signalling events, particularly phytochromes, crytochromes and phototropins as the transgenes for the genetic engineering of crops with improved harvest yields. In promoting the harvest yields of crops, the photoreceptors mediate the light regulation of photosynthetically important genes, and the improved yields often come with the tolerance to abiotic stresses such as drought, salinity and heavy metal ions. As a genetic engineering approach, the term photo-biotechnology has been coined to convey the idea that the greater the photosynthetic efficiency that crop plants can be engineered to possess, the stronger the resistance to biotic and abiotic stresses. Development of GM crops based on photoreceptor transgenes (mainly phytochromes, crytochromes and phototropins) is reviewed with the proposal of photo-biotechnology that the photoreceptors mediate the light regulation of photosynthetically important genes, and the improved yields often come with the added benefits of crops' tolerance to environmental stresses.

The Rice Phytochrome Genes, PHYA and PHYB, Have Synergistic Effects on Anther Development and Pollen Viability

Phytochromes are the main plant photoreceptors regulating multiple developmental processes. However, the regulatory network of phytochrome-mediated plant reproduction has remained largely unexplored. There are three phytochromes in rice, phyA, phyB and phyC. No changes in fertility are observed in the single mutants, whereas the seed-setting rate of the phyA phyB double mutant is significantly reduced. Histological and cytological analyses showed that the reduced fertility of the phyA phyB mutant was due to defects in both anther and pollen development. The four anther lobes in the phyA phyB mutant were developed at different stages with fewer pollen grains, most of which were aborted. At the mature stage, more than one lobe in the double mutant was just consisted of several cell layers. To identify genes involved in phytochrome-mediated anther development, anther transcriptomes of phyA, phyB and phyA phyB mutants were compared to that of wild-type rice respectively. Analysis of 2,241 double-mutant-specific differentially expressed transcripts revealed that the metabolic profiles, especially carbohydrate metabolism, were altered greatly, and heat-shock responses were activated in the double mutant. This study firstly provides valuable insight into the complex regulatory networks underlying phytochrome-mediated anther and pollen development in plants, and offers novel clues for hybrid rice breeding.

Ethylene-Inhibited Jasmonic Acid Biosynthesis Promotes Mesocotyl/Coleoptile Elongation of Etiolated Rice Seedlings

Elongation of the mesocotyl and coleoptile facilitates the emergence of rice (Oryza sativa) seedlings from soil and is affected by various genetic and environment factors. The regulatory mechanism underlying this process remains largely unclear. Here, we examined the regulation of mesocotyl and coleoptile growth by characterizing a gaoyao1 (gy1) mutant that exhibits a longer mesocotyl and longer coleoptile than its original variety of rice. GY1 was identified through map-based cloning and encodes a PLA1-type phospholipase that localizes in chloroplasts. GY1 functions at the initial step of jasmonic acid (JA) biosynthesis to repress mesocotyl and coleoptile elongation in etiolated rice seedlings. Ethylene inhibits the expression of GY1 and other genes in the JA biosynthesis pathway to reduce JA levels and enhance mesocotyl and coleoptile growth by promoting cell elongation. Genetically, GY1 acts downstream of the OsEIN2-mediated ethylene signaling pathway to regulate mesocotyl/coleoptile growth. Through analysis of the resequencing data from 3000 rice accessions, we identified a single natural variation of the GY1 gene, GY1376T , which contributes to mesocotyl elongation in rice varieties. Our study reveals novel insights into the regulatory mechanism of mesocotyl/coleoptile elongation and should have practical applications in rice breeding programs.

Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling

Two maize phytochrome-interacting factor (PIF) basic helix-loop-helix (bHLH) family members, ZmPIF3.1 and ZmPIF3.2, were identified, cloned and expressed in vitro to investigate light-signaling interactions. A phylogenetic analysis of sequences of the maize bHLH transcription factor gene family revealed the extent of the PIF family, and a total of seven predicted PIF-encoding genes were identified from genes encoding bHLH family VIIa/b proteins in the maize genome. To investigate the role of maize PIFs in phytochrome signaling, full-length cDNAs for phytochromes PhyA2, PhyB1, PhyB2 and PhyC1 from maize were cloned and expressed in vitro as chromophorylated holophytochromes. We showed that ZmPIF3.1 and ZmPIF3.2 interact specifically with the Pfr form of maize holophytochrome B1 (ZmphyB1), showing no detectable affinity for the Pr form. Maize holophytochrome B2 (ZmphyB2) showed no detectable binding affinity for PIFs in either Pr or Pfr forms, but phyB Pfr from Arabidopsis interacted with ZmPIF3.1 similarly to ZmphyB1 Pfr. We conclude that subfunctionalization at the protein-protein interaction level has altered the role of phyB2 relative to that of phyB1 in maize. Since the phyB2 mutant shows photomorphogenic defects, we conclude that maize phyB2 is an active photoreceptor, without the binding of PIF3 seen in other phyB family proteins.

Phytochrome B Negatively Affects Cold Tolerance by Regulating OsDREB1 Gene Expression through Phytochrome Interacting Factor-Like Protein OsPIL16 in Rice

Cross talk between light signaling and cold signaling has been elucidated in the model plant Arabidopsis and tomato, but little is known about their relationship in rice. Here, we report that phytochrome B (phyB) mutants exhibit improved cold tolerance compared with wild type (WT) rice (Oryza sativa L. cv. Nipponbare). The phyB mutants had a lower electrolyte leakage index and malondialdehyde concentration than the WT, suggesting that they had greater cell membrane integrity and less lipid peroxidation. Real-time PCR analysis revealed that the expression levels of dehydration-responsive element binding protein 1 (OsDREB1) family genes, which functions in the cold stress response in rice, were increased in the phyB mutant under normal and cold stress conditions. PIFs are central players in phytochrome-mediated light signaling networks. To explore the relationship between rice PIFs and OsDREB1 gene expression, we produced overexpression lines of rice PIF genes. OsDREB1 family genes were up-regulated in OsPIL16-overexpression lines, which had improved cold tolerance relative to the WT. Chromatin immunoprecipitation (ChIP)-qPCR assay revealed that OsPIL16 can bind to the N-box region of OsDREB1B promoter. Expression pattern analyses revealed that OsPIL16 transcripts were induced by cold stress and was significantly higher in the phyB mutant than in the WT. Moreover, yeast two-hybrid assay showed that OsPIL16 can bind to rice PHYB. Based on these results, we propose that phyB deficiency positively regulates OsDREB1 expression through OsPIL16 to enhance cell membrane integrity and to reduce the malondialdehyde concentration, resulting in the improved cold tolerance of the phyB mutants.

Light-modulated seminal wavy roots in rice mediated by nitric oxide-dependent signaling

Rice (Oryza sativa L.) seminal roots from germinated seeds help establish seedlings, but the seminal root growth and morphology are sensitive to environmental factors. Our previous research showed that several indica-type rice varieties such as Taichung native 1 (TCN1) showed light-induced wavy roots. Also, auxin and oxylipins are two signaling factors regulating the wavy root photomorphology. To investigate the signaling pathway, here, we found that nitric oxide (NO) was a second messenger triggering the signal transduction of light stimuli to induce the wavy morphology of seminal roots in rice. Moreover, interactions between oxylipins and phytohormones such as ethylene and auxin participating in the NO-dependent regulatory pathway of light-induced wavy roots were examined. The order of action of signaling components in the pathway was NO, oxylipins, ethylene, and auxin.

Phytochrome B Mediates the Regulation of Chlorophyll Biosynthesis through Transcriptional Regulation of ChlH and GUN4 in Rice Seedlings

Accurate regulation of chlorophyll synthesis is crucial for chloroplast formation during the greening process in angiosperms. In this study, we examined the role of phytochrome B (phyB) in the regulation of chlorophyll synthesis in rice seedlings (Oryza sativa L.) through the characterization of a pale-green phenotype observed in the phyB mutant grown under continuous red light (Rc) irradiation. Our results show that the Rc-induced chlorophyll accumulation can be divided into two components—a phyB-dependent and a phyB-independent component, and that the pale-green phenotype is caused by the absence of the phyB-dependent component. To elucidate the role of the missing component we established an Rc-induced greening experiment, the results of which revealed that several genes encoding proteins on the chlorophyll branch were repressed in the phyB mutant. Notable among them were ChlH and GUN4 genes, which encode subunit H and an activating factor of magnesium chelatase (Mg-chelatase), respectively, that were largely repressed in the mutant. Moreover, the kinetic profiles of chlorophyll precursors suggested that Mg-chelatase activity simultaneously decreased with the reduction in the transcript levels of ChlH and GUN4. These results suggest that phyB mediates the regulation of chlorophyll synthesis through transcriptional regulation of these two genes, whose products exert their action at the branching point of the chlorophyll biosynthesis pathway. Reduction of 5-aminolevulinic acid (5-ALA) synthesis could be detected in the mutant, but the kinetic profiles of chlorophyll precursors indicated that it was an event posterior to the reduction of the Mg-chelatase activity. It means that the repression of 5-ALA synthesis should not be a triggering event for the appearance of the pale-green phenotype. Instead, the repression of 5-ALA synthesis might be important for the subsequent stabilization of the pale-green phenotype for preventing excessive accumulation of hazardous chlorophyll precursors, which is an inevitable consequence of the reduction of Mg-chelatase activity.

How and why do root apices sense light under the soil surface?

Light can penetrate several centimeters below the soil surface. Growth, development and behavior of plant roots are markedly affected by light despite their underground lifestyle. Early studies provided contrasting information on the spatial and temporal distribution of light-sensing cells in the apical region of root apex and discussed the physiological roles of plant hormones in root responses to light. Recent biological and microscopic advances have improved our understanding of the processes involved in the sensing and transduction of light signals, resulting in subsequent physiological and behavioral responses in growing root apices. Here, we review current knowledge of cellular distributions of photoreceptors and their signal transduction pathways in diverse root tissues and root apex zones. We are discussing also the roles of auxin transporters in roots exposed to light, as well as interactions of light signal perceptions with sensing of other environmental factors relevant to plant roots.

Photo-biotechnology as a tool to improve agronomic traits in crops

Phytochromes are photosensory phosphoproteins with crucial roles in plant developmental responses to light. Functional studies of individual phytochromes have revealed their distinct roles in the plant's life cycle. Given the importance of phytochromes in key plant developmental processes, genetically manipulating phytochrome expression offers a promising approach to crop improvement. Photo-biotechnology refers to the transgenic expression of phytochrome transgenes or variants of such transgenes. Several studies have indicated that crop cultivars can be improved by modulating the expression of phytochrome genes. The improved traits include enhanced yield, improved grass quality, shade-tolerance, and stress resistance. In this review, we discuss the transgenic expression of phytochrome A and its hyperactive mutant (Ser599Ala-PhyA) in selected crops, such as Zoysia japonica (Japanese lawn grass), Agrostis stolonifera (creeping bentgrass), Oryza sativa (rice), Solanum tuberosum (potato), and Ipomea batatas (sweet potato). The transgenic expression of PhyA and its mutant in various plant species imparts biotechnologically useful traits. Here, we highlight recent advances in the field of photo-biotechnology and review the results of studies in which phytochromes or variants of phytochromes were transgenically expressed in various plant species. We conclude that photo-biotechnology offers an excellent platform for developing crops with improved properties.

Enhancing the productivity of grasses under high-density planting by engineering light responses: from model systems to feedstocks

The successful commercialization of bioenergy grasses as lignocellulosic feedstocks requires that they be produced, processed, and transported efficiently. Intensive breeding for higher yields in food crops has resulted in varieties that perform optimally under high-density planting but often with high input costs. This is particularly true of maize, where most yield gains in the past have come through increased planting densities and an abundance of fertilizer. For lignocellulosic feedstocks, biomass rather than grain yield and digestibility of cell walls are two of the major targets for improvement. Breeding for high-density performance of lignocellulosic crops has been much less intense and thus provides an opportunity for improving the feedstock potential of these grasses. In this review, we discuss the role of vegetative shade on growth and development and suggest targets for manipulating this response to increase harvestable biomass under high-density planting. To engineer grass architecture and modify biomass properties at increasing planting densities, we argue that new model systems are needed and recommend Setaria viridis, a panicoid grass, closely related to major fuel and bioenergy grasses as a model genetic system.

The phytochrome B/phytochrome C heterodimer is necessary for phytochrome C-mediated responses in rice seedlings

Background

PhyC levels have been observed to be markedly lower in phyB mutants than in Arabidopsis or rice wild type etiolated seedlings, but the mechanism of this phenomenon has not been fully elucidated.

Results

In the present study, we investigated the mechanism by which phyB affects the protein concentration and photo-sensing abilities of phyC and demonstrated that rice phyC exists predominantly as phyB/phyC heterodimers in etiolated seedlings. PHYC-GFP protein was detected when expressed in phyA phyC mutants, but not in phyA phyB mutants, suggesting that phyC requires phyB for its photo-sensing abilities. Interestingly, when a mutant PHYB gene that has no chromophore binding site, PHYB(C364A), was introduced into phyB mutants, the phyC level was restored. Moreover, when PHYB(C364A) was introduced into phyA phyB mutants, the seedlings exhibited de-etiolation under both far-red light (FR) and red light (R) conditions, while the phyA phyB mutants were blind to both FR and R. These results are the first direct evidence that phyC is responsible for regulating seedling de-etiolation under both FR and R. These findings also suggest that phyB is indispensable for the expression and function of phyC, which depends on the formation of phyB/phyC heterodimers.

Significance

The present report clearly demonstrates the similarities and differences in the properties of phyC between Arabidopsis and rice and will advance our understanding of phytochrome functions in monocots and dicots.

Light Signaling in Bud Outgrowth and Branching in Plants

Branching determines the final shape of plants, which influences adaptation, survival and the visual quality of many species. It is an intricate process that includes bud outgrowth and shoot extension, and these in turn respond to environmental cues and light conditions. Light is a powerful environmental factor that impacts multiple processes throughout plant life. The molecular basis of the perception and transduction of the light signal within buds is poorly understood and undoubtedly requires to be further unravelled. This review is based on current knowledge on bud outgrowth-related mechanisms and light-mediated regulation of many physiological processes. It provides an extensive, though not exhaustive, overview of the findings related to this field. In parallel, it points to issues to be addressed in the near future.

Overexpression of an S-like ribonuclease gene, OsRNS4, confers enhanced tolerance to high salinity and hyposensitivity to phytochrome-mediated light signals in rice

S-like ribonucleases (S-like RNases) are homologous to S-ribonucleases (S-RNases), but are not involved in self-incompatibility. In dicotyledonous plants, S-like RNases play an important role in phosphate recycling during senescence and are induced by inorganic phosphate-starvation and in response to defense and mechanical wounding. However, little information about the functions of the S-like RNase in monocots has been reported. Here, we investigated the expression patterns and roles of an S-like RNase gene, OsRNS4, in abscisic acid (ABA)-mediated responses and phytochrome-mediated light responses as well as salinity tolerance in rice. The OsRNS4 gene was expressed at relatively high levels in leaves although its transcripts were detected in various organs. OsRNS4 expression was regulated by salt, PEG and ABA. The seedlings overexpressing OsRNS4 had longer coleoptiles and first leaves than wild-type seedlings under red light (R) and far-red light (FR), suggesting negative regulation of OsRNS4 in photomorphogenesis in rice seedlings. Moreover, ABA-induced growth inhibition of rice seedlings was significantly increased in the OsRNS4-overexpression (OsRNS4-OX) lines compared with that in WT, suggesting that OsRNS4 probably acts as a positive regulator in ABA responses in rice seedlings. In addition, our results demonstrate that OsRNS4-OX lines have enhanced tolerance to high salinity compared to WT. Our findings supply new evidence on the functions of monocot S-like RNase in regulating photosensitivity and abiotic stress responses.

Involvement of phytochrome A in suppression of photomorphogenesis in rice seedling grown in red light

Plants have evolved a remarkable capacity to track and respond to fluctuations of light quality and intensity that influence photomorphogenesis facilitated through several photoreceptors, which include a small family of phytochromes. Rice seedlings grown on germination paper in red light for 48 h having their shoot bottom exposed had suppressed photomorphogenesis and were deficient in chlorophyll. Seedlings grown under identical light regime having their shoot bottom covered were green and accumulated chlorophyll. Further, etiolated seedlings with their shoot bottom exposed, when grown in 4 min red/far-red cycles for 48 h, accumulated chlorophyll demonstrating the reversal of suppression of photomorphogenesis by far-red light. It implicates the involvement of phytochrome. Immunoblot analysis showed the persistence of photolabile phytochrome A protein for 48 h in seedlings grown in red light with their shoot bottom exposed, suggesting its involvement in suppression of photomorphogenesis. This was further corroborated in phyA seedlings that turned green when grown in red light having their shoot bottom exposed. Calmodulin (CaM) antagonist N-(6-aminohexyl)-5-chloro-1-napthalene sulphonamide or trifluoperazine substantially restored photomorphogenesis both in the wild type (WT) and phyA demonstrating the involvement of CaM-dependent kinases in the down-regulation of the greening process. Results demonstrate that red light-induced suppression of photomorphogenesis, perceived in the shoot bottom, is a red high irradiance response of PhyA.

Differences and similarities in the photoregulation of gibberellin metabolism between rice and dicots

In rice seedlings, elongation of leaf sheaths is suppressed by light stimuli. The response is mediated by two classes of photoreceptors, phytochromes and cryptochromes. However, it remains unclear how these photoreceptors interact in the process. Our recent study using phytochrome mutants and novel cryptochrome RNAi lines revealed that cryptochromes and phytochromes function cooperatively, but independently to reduce active GA contents in seedlings in visible light. Blue light captured by cryptochrome 1 (cry1a and cry1b) induces robust expression of GA 2-oxidase genes (OsGA2ox4-7). In parallel, phytochrome B with auxiliary action of phytochrome A mediates repression of GA 20-oxidase genes (OsGA20ox2 and OsGA20ox4). The independent effects cumulatively reduce active GA contents, leading to a suppression of leaf sheath elongation. These regulatory mechanisms are distinct from phytochrome B function in dicots. We discuss reasons why the distinct system appeared in rice, and advantages of the rice system in early photomorphogenesis.

Cryptochrome and phytochrome cooperatively but independently reduce active gibberellin content in rice seedlings under light irradiation

In contrast to a wealth of knowledge about the photoregulation of gibberellin metabolism in dicots, that in monocots remains largely unclear. In this study, we found that a blue light signal triggers reduction of active gibberellin content in rice seedlings with simultaneous repression of two gibberellin 20-oxidase genes (OsGA20ox2 and OsGA20ox4) and acute induction of four gibberellin 2-oxidase genes (OsGA2ox4-OsGA2ox7). For further examination of the regulation of these genes, we established a series of cryptochrome-deficient lines through reverse genetic screening from a Tos17 mutant population and construction of knockdown lines based on an RNA interference technique. By using these lines and phytochrome mutants, we elucidated that cryptochrome 1 (cry1), consisting of two species in rice plants (cry1a and cry1b), is indispensable for robust induction of the GA2ox genes. On the other hand, repression of the GA20ox genes is mediated by phytochromes. In addition, we found that the phytochromes also mediate the repression of a gibberellin 3-oxidase gene (OsGA3ox2) in the light. These results imply that, in rice seedlings, phytochromes mediate the repression of gibberellin biosynthesis capacity, while cry1 mediates the induction of gibberellin inactivation capacity. The cry1 action was demonstrated to be dominant in the reduction of active gibberellin content, but, in rice seedlings, the cumulative effects of these independent actions reduced active gibberellin content in the light. This pathway design in which different types of photoreceptors independently but cooperatively regulate active gibberellin content is unique from the viewpoint of dicot research. This redundancy should provide robustness to the response in rice plants.

Overexpression of a phytochrome-regulated tandem zinc finger protein gene, OsTZF1, confers hypersensitivity to ABA and hyposensitivity to red light and far-red light in rice seedlings

Tandem zinc finger proteins (TZFs) in plants are involved in gene regulation, developmental responses, and hormone-mediated environmental responses in Arabidopsis. However, little information about the functions of the TZF family in monocots has been reported. Here, we investigated a cytoplasmic TZF protein, OsTZF1, which is involved in photomorphogenesis and ABA responses in rice seedlings. The OsTZF1 gene was expressed at relatively high levels in leaves and shoots, although its transcripts were detected in various organs. Red light (R)- and far-red light (FR)-mediated repression of OsTZF1 gene expression was attributed to phytochrome B (phyB) and phytochrome C (phyC), respectively. In addition, OsTZF1 expression was regulated by salt, PEG, and ABA. Overexpression of OsTZF1 caused a long leaf sheath relative to wild type (WT) under R and FR, suggesting that OsTZF1 probably acts as a negative regulator of photomorphogenesis in rice seedlings. Moreover, ABA-induced growth inhibition of rice seedlings was marked in the OsTZF1-overexpression lines compared with WT, suggesting the positive regulation of OsTZF1 to ABA responses. Genome-wide expression analysis further revealed that OsTZF1 also functions in other hormone or stress responses. Our findings supply new evidence on the functions of monocot TZF proteins in phytochrome-mediated light and hormone responses.

KEY MESSAGE

OsTZF1 encodes a cytoplasm-localized tandem zinc finger protein and is regulated by both ABA and phytochrome-mediated light signaling. OsTZF1 functions in phytochrome-mediated light and ABA responses in rice.

Light-dependent regulation of the jasmonate pathway

Jasmonates (JAs) are plant hormones which are crucial for the response of plants to several biotic and abiotic stresses. Beside this important function, they are involved in several developmental processes throughout plant life. In this short review, we would like to summarize the recent findings about the function of JAs in photomorphogenesis with a main focus on the model plant rice. Early plant development is determined to a large extent by light. Depending on whether seedlings are raised in darkness or in light, they show a completely different appearance which led to the terms skoto- and photomorphogenesis, respectively. The different appearance depending on the light conditions has been used to screen for mutants in photoperception and signalling. By this approach, mutants for several photoreceptors and in the downstream signalling pathways could be isolated. In rice, we and others isolated mutants with a very intriguing phenotype. The mutated genes have been cloned by map-based cloning, and all of them encode for JA biosynthesis genes. The most bioactive form of JAs identified so far is the amino acid conjugate jasmonoyl-isoleucin (JA-Ile). In order to conjugate JA to Ile, an enzyme of the GH3 family, JASMONATE RESISTANT 1, is required. We characterized mutants of OsJAR1 on a physiological and biochemical level and found evidence for redundantly active enzymes in rice.

The 14-3-3 proteins of Arabidopsis regulate root growth and chloroplast development as components of the photosensory system

The 14-3-3 proteins specifically bind a number of client proteins to influence important pathways, including flowering timing via the photosensory system. For instance, 14-3-3 proteins influence the photosensory system through interactions with Constans (CO) protein. 14-3-3 associations with the photosensory system were further studied in this investigation using 14-3-3 T-DNA insertion mutants to study root and chloroplast development. The 14-3-3 μ T-DNA insertion mutant, 14-3-3μ-1, had shorter roots than the wild type and the difference in root length could be influenced by light intensity. The 14-3-3 ν T-DNA insertion mutants also had shorter roots, but only when grown under narrow-bandwidth red light. Five-day-old 14-3-3 T-DNA insertion and co mutants all had increased root greening compared with the wild type, which was influenced by light wavelength and intensity. However, beyond 10 d of growth, 14-3-3μ-1 roots did not increase in greening as much as wild-type roots. This study reveals new developmental roles of 14-3-3 proteins in roots and chloroplasts, probably via association with the photosensory system.

RPL1, a gene involved in epigenetic processes regulates phenotypic plasticity in rice

Organisms can adjust their phenotype in response to changing environmental conditions. This phenomenon is termed phenotypic plasticity. Despite its ubiquitous occurrence, there has been very little study on the molecular mechanism of phenotypic plasticity. In this study, we isolated a rice (Oryza sativa L.) mutant, rice plasticity 1 (rpl1), that displayed increased environment-dependent phenotypic variations. RPL1 was expressed in all tissues examined. The protein was localized in the nucleus and its distribution in the nucleus overlapped with heterochromatin. The rpl1 mutation led to an increase in DNA methylation on repetitive sequences and a decrease in overall histone acetylation. In addition, the mutation affected responses of the rice plant to phytohormones such as brassinosteroid, gibberellin, and cytokinin. Analysis of the putative rice brassinosteroid receptor OsBRI1, a key hormone signaling gene, indicated that RPL1 may be involved in the regulation of epigenomic modification of the gene. These data suggest that RPL1 regulated phenotypic plasticity likely through its involvement in epigenetic processes affecting responses of the plant to phytohormones.

Phytochromes A and C cooperatively regulate early and transient gene expression after red-light irradiation in rice seedlings

Phytochromes are red/far-red photoreceptors encoded by a small gene family in higher plants. Differences in phenotype among mutants suggest distinct functions among phytochrome subfamilies. We attempted to find distinct functions among phytochromes by oligo-microarray analysis of single, double, and triple mutants in rice. In most cases, gene expression was redundantly regulated by phytochromes A and B after irradiation by a red light pulse in etiolated rice shoots. However, we found that several genes were specifically regulated by phytochromes A and C. Most of them were expressed immediately after the red light pulse in a transient manner. They are stress-related genes that may be involved in resistance to light stress when etiolated seedlings are exposed to light. These genes were not expressed in green leaves after the red light pulse, suggesting that they have a function specific to etiolated seedlings.

Phytochrome B control of total leaf area and stomatal density affects drought tolerance in rice

We report that phytochrome B (phyB) mutants exhibit improved drought tolerance compared to wild type (WT) rice (Oryza sativa L. cv. Nipponbare). To understand the underlying mechanism by which phyB regulates drought tolerance, we analyzed root growth and water loss from the leaves of phyB mutants. The root system showed no significant difference between the phyB mutants and WT, suggesting that improved drought tolerance has little relation to root growth. However, phyB mutants exhibited reduced total leaf area per plant, which was probably due to a reduction in the total number of cells per leaf caused by enhanced expression of Orysa;KRP1 and Orysa;KRP4 (encoding inhibitors of cyclin-dependent kinase complex activity) in the phyB mutants. In addition, the developed leaves of phyB mutants displayed larger epidermal cells than WT leaves, resulting in reduced stomatal density. phyB deficiency promoted the expression of both putative ERECTA family genes and EXPANSIN family genes involved in cell expansion in leaves, thus causing greater epidermal cell expansion in the phyB mutants. Reduced stomatal density resulted in reduced transpiration per unit leaf area in the phyB mutants. Considering all these findings, we propose that phyB deficiency causes both reduced total leaf area and reduced transpiration per unit leaf area, which explains the reduced water loss and improved drought tolerance of phyB mutants.

Genetic and molecular bases of photoperiod responses of flowering in soybean

Flowering is one of the most important processes involved in crop adaptation and productivity. A number of major genes and quantitative trait loci (QTLs) for flowering have been reported in soybean (Glycine max). These genes and QTLs interact with one another and with the environment to greatly influence not only flowering and maturity but also plant morphology, final yield, and stress tolerance. The information available on the soybean genome sequence and on the molecular bases of flowering in Arabidopsis will undoubtedly facilitate the molecular dissection of flowering in soybean. Here, we review the present status of our understanding of the genetic and molecular mechanisms of flowering in soybean. We also discuss our identification of orthologs of Arabidopsis flowering genes from among the 46,367 genes annotated in the publicly available soybean genome database Phytozome Glyma 1.0. We emphasize the usefulness of a combined approach including QTL analysis, fine mapping, and use of candidate gene information from model plant species in genetic and molecular studies of soybean flowering.