Structure and expression of maize phytochrome family homeologs

Maize smart-canopy architecture enhances yield at high densities

Increasing planting density is a key strategy for enhancing maize yields1-3. An ideotype for dense planting requires a 'smart canopy' with leaf angles at different canopy layers differentially optimized to maximize light interception and photosynthesis4-6, among other features. Here we identified leaf angle architecture of smart canopy 1 (lac1), a natural mutant with upright upper leaves, less erect middle leaves and relatively flat lower leaves. lac1 has improved photosynthetic capacity and attenuated responses to shade under dense planting. lac1 encodes a brassinosteroid C-22 hydroxylase that predominantly regulates upper leaf angle. Phytochrome A photoreceptors accumulate in shade and interact with the transcription factor RAVL1 to promote its degradation via the 26S proteasome, thereby inhibiting activation of lac1 by RAVL1 and decreasing brassinosteroid levels. This ultimately decreases upper leaf angle in dense fields. Large-scale field trials demonstrate that lac1 boosts maize yields under high planting densities. To quickly introduce lac1 into breeding germplasm, we transformed a haploid inducer and recovered homozygous lac1 edits from 20 diverse inbred lines. The tested doubled haploids uniformly acquired smart-canopy-like plant architecture. We provide an important target and an accelerated strategy for developing high-density-tolerant cultivars, with lac1 serving as a genetic chassis for further engineering of a smart canopy in maize.

Light-Dependent Expression and Promoter Methylation of the Genes Encoding Succinate Dehydrogenase, Fumarase, and NAD-Malate Dehydrogenase in Maize (Zea mays L.) Leaves

The expression and methylation of promoters of the genes encoding succinate dehydrogenase, fumarase, and NAD-malate dehydrogenase in maize (Zea mays L.) leaves depending on the light regime were studied. The genes encoding the catalytic subunits of succinate dehydrogenase showed suppression of expression upon irradiation by red light, which was abolished by far-red light. This was accompanied by an increase in promoter methylation of the gene Sdh1-2 encoding the flavoprotein subunit A, while methylation was low for Sdh2-3 encoding the iron-sulfur subunit B under all conditions. The expression of Sdh3-1 and Sdh4 encoding the anchoring subunits C and D was not affected by red light. The expression of Fum1 encoding the mitochondrial form of fumarase was regulated by red and far-red light via methylation of its promoter. Only one gene encoding the mitochondrial NAD-malate dehydrogenase gene (mMdh1) was regulated by red and far-red light, while the second gene (mMdh2) did not respond to irradiation, and neither gene was controlled by promoter methylation. It is concluded that the dicarboxylic branch of the tricarboxylic acid cycle is regulated by light via the phytochrome mechanism, and promoter methylation is involved with the flavoprotein subunit of succinate dehydrogenase and the mitochondrial fumarase.

UB2/UB3/TSH4-anchored transcriptional networks regulate early maize inflorescence development in response to simulated shade

Increasing planting density has been adopted as an effective means to increase maize (Zea mays) yield. Competition for light from neighbors can trigger plant shade avoidance syndrome, which includes accelerated flowering. However, the regulatory networks of maize inflorescence development in response to high-density planting remain poorly understood. In this study, we showed that shade-mimicking treatments cause precocious development of the tassels and ears. Comparative transcriptome profiling analyses revealed the enrichment of phytohormone-related genes and transcriptional regulators among the genes co-regulated by developmental progression and simulated shade. Network analysis showed that three homologous Squamosa promoter binding protein (SBP)-like (SPL) transcription factors, Unbranched2 (UB2), Unbranched3 (UB3), and Tasselsheath4 (TSH4), individually exhibited connectivity to over 2,400 genes across the V3-to-V9 stages of tassel development. In addition, we showed that the ub2 ub3 double mutant and tsh4 single mutant were almost insensitive to simulated shade treatments. Moreover, we demonstrated that UB2/UB3/TSH4 could directly regulate the expression of Barren inflorescence2 (BIF2) and Zea mays teosinte branched1/cycloidea/proliferating cell factor30 (ZmTCP30). Furthermore, we functionally verified a role of ZmTCP30 in regulating tassel branching and ear development. Our results reveal a UB2/UB3/TSH4-anchored transcriptional regulatory network of maize inflorescence development and provide valuable targets for breeding shade-tolerant maize cultivars.

Population genomics of Zea species identifies selection signatures during maize domestication and adaptation

BACKGROUND

Maize (Zea mays L. ssp. mays) was domesticated from teosinte (Zea mays ssp. parviglumis) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide. Researchers have depicted the maize domestication and adaptation processes over the past two decades, but efforts have been limited either in sample size or genetic diversity. To better understand these processes, we conducted a genome-wide survey of 982 maize inbred lines and 190 teosinte accessions using over 40,000 single-nucleotide polymorphism markers.

RESULTS

Population structure, principal component analysis, and phylogenetic trees all confirmed the evolutionary relationship between maize and teosinte, and determined the evolutionary lineage of all species within teosinte. Shared haplotype analysis showed similar levels of ancestral alleles from Zea mays ssp. parviglumis and Zea mays ssp. mexicana in maize. Scans for selection signatures identified 394 domestication sweeps by comparing wild and cultivated maize and 360 adaptation sweeps by comparing tropical and temperate maize. Permutation tests revealed that the public association signals for flowering time were highly enriched in the domestication and adaptation sweeps. Genome-wide association study identified 125 loci significantly associated with flowering-time traits, ten of which identified candidate genes that have undergone selection during maize adaptation.

CONCLUSIONS

In this study, we characterized the history of maize domestication and adaptation at the population genomic level and identified hundreds of domestication and adaptation sweeps. This study extends the molecular mechanism of maize domestication and adaptation, and provides resources for basic research and genetic improvement in maize.

Genetic control of leaf angle in sorghum and its effect on light interception

Developing sorghum genotypes adapted to different light environments requires understanding of a plant's ability to capture light, determined through leaf angle specifically. This study dissected the genetic basis of leaf angle in 3 year field trials at two sites, using a sorghum diversity panel (729 accessions). A wide range of variation in leaf angle with medium heritability was observed. Leaf angle explained 36% variation in canopy light extinction coefficient, highlighting the extent to which variation in leaf angle influences light interception at the whole-canopy level. This study also found that the sorghum races of Guinea and Durra consistently having the largest and smallest leaf angle, respectively, highlighting the potential role of leaf angle in adaptation to distinct environments. The genome-wide association study detected 33 quantitative trait loci (QTLs) associated with leaf angle. Strong synteny was observed with previously detected leaf angle QTLs in maize (70%) and rice (40%) within 10 cM, among which the overlap was significantly enriched according to χ2 tests, suggesting a highly consistent genetic control in grasses. A priori leaf angle candidate genes identified in maize and rice were found to be enriched within a 1-cM window around the sorghum leaf angle QTLs. Additionally, protein domain analysis identified the WD40 protein domain as being enriched within a 1-cM window around the QTLs. These outcomes show that there is sufficient heritability and natural variation in the angle of upper leaves in sorghum which may be exploited to change light interception and optimize crop canopies for different contexts.

Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families

Many aspects of photoperception by plants and microorganisms are initiated by the phytochrome (Phy) family of photoreceptors that detect light through interconversion between red light- (Pr) and far-red light-absorbing (Pfr) states. Plants synthesize a small family of Phy isoforms (PhyA to PhyE) that collectively regulate photomorphogenesis and temperature perception through redundant and unique actions. While the selective roles of these isoforms have been partially attributed to their differing abundances, expression patterns, affinities for downstream partners, and turnover rates, we show here from analysis of recombinant Arabidopsis chromoproteins that the Phy isoforms also display distinct biophysical properties. Included are a hypsochromic shift in the Pr absorption for PhyC and varying rates of Pfr to Pr thermal reversion, part of which can be attributed to the core photosensory module in each. Most strikingly, PhyB combines strong temperature dependence of thermal reversion with an order-of-magnitude faster rate to likely serve as the main physiological thermosensor, whereby thermal reversion competes with photoconversion. In addition, comparisons of Pfr occupancies for PhyA and PhyB under a range of red- and white-light fluence rates imply that low-light environments are effectively sensed by PhyA, while high-light environments, such as full sun, are effectively sensed by PhyB. Parallel analyses of the Phy isoforms from potato and maize showed that the unique features within the Arabidopsis family are conserved, thus indicating that the distinct biophysical properties among plant Phy isoforms emerged early in Phy evolution, likely to enable full interrogation of their light and temperature environments.

CRISPR/Cas9-mediated knockout and overexpression studies reveal a role of maize phytochrome C in regulating flowering time and plant height

Maize is a major staple crop widely used for food, feedstocks and industrial products. Shade-avoidance syndrome (SAS), which is triggered when plants sense competition of light from neighbouring vegetation, is detrimental for maize yield production under high-density planting conditions. Previous studies have shown that the red and far-red photoreceptor phytochromes are responsible for perceiving the shading signals and triggering SAS in Arabidopsis; however, their roles in maize are less clear. In this study, we examined the expression patterns of ZmPHYC1 and ZmPHYC2 and found that ZmPHYC1, but not ZmPHYC2, is highly expressed in leaves and is regulated by the circadian clock. Both ZmPHYC1 and ZmPHYC2 proteins are localized to both the nucleus and cytoplasm under light conditions and both of them can interact with themselves or with ZmPHYBs. Heterologous expression of ZmPHYCs can complement the Arabidopsis phyC-2 mutant under constant red light conditions and confer an attenuated SAS in Arabidopsis in response to shading. Double knockout mutants of ZmPHYC1 and ZmPHYC2 created using the CRISPR/Cas9 technology display a moderate early-flowering phenotype under long-day conditions, whereas ZmPHYC2 overexpression plants exhibit a moderately reduced plant height and ear height. Together, these results provided new insight into the function of ZmPHYCs and guidance for breeding high-density tolerant maize cultivars.

Functional analysis of ZmCOP1 and ZmHY5 reveals conserved light signaling mechanism in maize and Arabidopsis

Plants have evolved light signaling mechanisms to optimally adapt developmental patterns to the ambient light environments. CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) and LONG HYPOCOTYL5 (HY5) are two critical components in the light signaling pathway in Arabidopsis thaliana. COP1 acts as an E3 ubiquitin ligase that targets positive regulators, such as HY5, leading to their degradation in darkness. However, functional analysis of the COP1-HY5 module in maize (Zea mays) has not been reported. Here, we investigated the expression patterns and roles of the COP1 and HY5 orthologs, ZmCOP1 and ZmHY5, in regulating photomorphogenesis. These two genes have high amino acid identities with their Arabidopsis homolog and were both regulated by light. Subcellular localization assay showed that ZmCOP1 was distributed in the cytosol and ZmHY5 localized in the nucleus. Exogenous expression of ZmCOP1 rescued the physiological defects of the cop1-4 mutant, and expression of ZmHY5 complemented the long hypocotyl phenotype of the hy5-215 mutant in Arabidopsis. Yeast two-hybrid and fluorescence resonance energy transfer assays showed that ZmCOP1 interacted with ZmHY5. Our study gains insight into the conserved function and regulatory mechanism of the COP1-HY5 signaling pathway in maize and Arabidopsis.

Transcriptomic network analyses shed light on the regulation of cuticle development in maize leaves

Plant cuticles provide barriers to water loss and arose as aquatic plants adapted to the dry terrestrial environment. The cuticle components, waxes and the fatty acid-based polymer cutin, are synthesized in the plant epidermis, exported across the cell wall, and deposited on the plant surface. This study suggests a role for PHYTOCHROME light receptors during cuticle development in leaves of maize and moss, diverse species that are separated by more than 400 million y of land plant evolution. We hypothesize that phytochrome-mediated light signaling contributed to the evolution of cuticles in land plants.

Plant cuticles are composed of wax and cutin and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip. Laser microdissection RNA Sequencing (LM-RNAseq) was performed along this proximodistal gradient, and complementary network analyses identified potential regulators of cuticle biosynthesis and deposition. A weighted gene coexpression network (WGCN) analysis suggested a previously undescribed function for PHYTOCHROME-mediated light signaling during the regulation of cuticular wax deposition. Genetic analyses reveal that phyB1 phyB2 double mutants of maize exhibit abnormal cuticle composition, supporting the predictions of our coexpression analysis. Reverse genetic analyses also show that phy mutants of the moss Physcomitrella patens exhibit abnormal cuticle composition, suggesting an ancestral role for PHYTOCHROME-mediated, light-stimulated regulation of cuticle development during plant evolution.

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.

Progress of Research on the Regulatory Pathway of the Plant Shade-Avoidance Syndrome

When subject to vegetational shading, shade-avoiding plants detect neighbors by perceiving reduced light quantity and altered light quality. The former includes decreases in the ratio of red to far-red wavelengths (low R:FR) and low blue light ratio (LBL) predominantly detected by phytochromes and cryptochromes, respectively. By integrating multiple signals, plants generate a suite of responses, such as elongation of a variety of organs, accelerated flowering, and reduced branching, which are collectively termed the shade-avoidance syndrome (SAS). To trigger the SAS, interactions between photoreceptors and phytochrome-interacting factors are the general switch for activation of downstream signaling pathways. A number of transcription factor families and phytohormones, especially auxin, gibberellins, ethylene, and brassinosteroids, are involved in the SAS processes. In this review, shade signals, the major photoreceptors involved, and the phenotypic characteristics of the shade-intolerant plant Arabidopsis thaliana are described in detail. In addition, integration of the signaling mechanisms that link photoreceptors with multiple hormone signaling pathways is presented and future research directions are discussed.

Characterization of Maize Phytochrome-Interacting Factors in Light Signaling and Photomorphogenesis

Increasing planting density has been an effective means of increasing maize (Zea mays ssp. mays) yield per unit of land area over the past few decades. However, high-density planting will cause a reduction in the ratio of red to far-red incident light, which could trigger the shade avoidance syndrome and reduce yield. The molecular mechanisms regulating the shade avoidance syndrome are well established in Arabidopsis (Arabidopsis thaliana) but poorly understood in maize. Here, we conducted an initial functional characterization of the maize Phytochrome-Interacting Factor (PIF) gene family in regulating light signaling and photomorphogenesis. The maize genome contains seven distinct PIF genes, which could be grouped into three subfamilies: ZmPIF3s, ZmPIF4s, and ZmPIF5s Similar to the Arabidopsis PIFs, all ZmPIF proteins are exclusively localized to the nucleus and most of them can form nuclear bodies upon light irradiation. We show that all of the ZmPIF proteins could interact with ZmphyB. Heterologous expression of each ZmPIF member could partially or fully rescue the phenotype of the Arabidopsis pifq mutant, and some of these proteins conferred enhanced shade avoidance syndrome in Arabidopsis. Interestingly, all ZmPIF proteins expressed in Arabidopsis are much more stable than their Arabidopsis counterparts upon exposure to red light. Moreover, the Zmpif3, Zmpif4, and Zmpif5 knockout mutants generated via CRISPR/Cas9 technology all showed severely suppressed mesocotyl elongation in dark-grown seedlings and were less responsive to simulated shade treatment. Taken together, our results reveal both conserved and distinct molecular properties of ZmPIFs in regulating light signaling and photomorphogenesis in maize.

Phytochrome B enhances plant growth, biomass and grain yield in field-grown maize

BACKGROUND AND AIMS

Phytochrome B (phyB) is a photosensory receptor important for the control of plant plasticity and resource partitioning. Whether phyB is required to optimize plant biomass accumulation in agricultural crops exposed to full sunlight is unknown. Here we investigated the impact of mutations in the genes that encode either phyB1 or phyB2 on plant growth and grain yield in field crops of Zea mays sown at contrasting population densities.

METHODS

Plants of maize inbred line France 2 wild type (WT) and the isogenic mutants lacking either phyB1 or phyB2 (phyB1 and phyB2) were cultivated in the field during two seasons. Plants were grown at two densities (9 and 30 plants m-2), irrigated and without restrictions of nutrients. Leaf and stem growth, leaf anatomy, light interception, above-ground biomass accumulation and grain yield were recorded.

KEY RESULTS

At high plant density, all the lines showed similar kinetics of biomass accumulation. However, compared with the WT, the phyB1 and phyB2 mutations impaired the ability to enhance plant growth in response to the additional resources available at low plant density. This effect was largely due to a reduced leaf area (fewer cells per leaf), which compromised light interception capacity. Grain yield was reduced in phyB1 plants.

CONCLUSIONS

Maize plants grown in the field at relatively low densities require phyB1 and phyB2 to sense the light environment and optimize the use of the available resources. In the absence of either of these two light receptors, leaf expansion is compromised, imposing a limitation to the interception of photosynthetic radiation and growth. These observations suggest that genetic variability at the locus encoding phyB could offer a breeding target to improve crop growth capacity in the field.

Dissection of Leaf Angle Variation in Maize through Genetic Mapping and Meta-Analysis

Maize ( L.) hybrids have transitioned to upright leaf angles (LAs) over the last 50 yr as maize yields and planting densities increased concurrently. Genetic mapping and a meta-analysis were conducted in the present study to dissect genetic factors controlling LA variation. We developed mapping populations using inbred lines B73 (Iowa Stiff Stalk Synthetic), PHW30 (Iodent, expired plant variety protection inbred), and Mo17 (Non-Stiff Stalk) that have distinct LA architectures and represent three important heterotic groups in the United States. These populations were genotyped using genotyping-by-sequencing (GBS), and phenotyped for LA in the F and F generation. Inclusive composite interval mapping across the two generations of the mapping populations revealed 12 quantitative trait loci (QTL), and a consistent QTL on chromosome 1 explained 10 to 17% of the phenotypic variance. To gain a comprehensive understanding of natural variations underlying LA variation, these detected QTL were compared with results from 19 previous studies. In total, 495 QTL were compiled and mapped into 143 genomic bins. A meta-analysis revealed that 58 genomic bins were associated with LA variation. Thirty-three candidate genes were identified in these genomic bins. Together, these results provide evidence of QTL controlling LA variation from inbred lines representing three important heterotic groups in the United States and a useful resource for future research into the molecular variants underlying specific regions of the genome associated with LA variation.

Multiple Pathways in the Control of the Shade Avoidance Response

To detect the presence of neighboring vegetation, shade-avoiding plants have evolved the ability to perceive and integrate multiple signals. Among them, changes in light quality and quantity are central to elicit and regulate the shade avoidance response. Here, we describe recent progresses in the comprehension of the signaling mechanisms underlying the shade avoidance response, focusing on Arabidopsis, because most of our knowledge derives from studies conducted on this model plant. Shade avoidance is an adaptive response that results in phenotypes with a high relative fitness in individual plants growing within dense vegetation. However, it affects the growth, development, and yield of crops, and the design of new strategies aimed at attenuating shade avoidance at defined developmental stages and/or in specific organs in high-density crop plantings is a major challenge for the future. For this reason, in this review, we also report on recent advances in the molecular description of the shade avoidance response in crops, such as maize and tomato, and discuss their similarities and differences with Arabidopsis.

Genome-Wide Identification of PIFs in Grapes (Vitis vinifera L.) and Their Transcriptional Analysis under Lighting/Shading Conditions

Phytochrome-interacting factors (PIFs), as the basic helix⁻loop⁻helix (bHLH) transcription factors, are the primary signaling partners for phytochromes (PHY) that play a key role in PHY-mediated light signal transduction. At present, there are few studies on PIFs in fruit trees. In order to clarify the status of PIFs in grapevines, we identified members of the grape PIFs family and conducted phylogenetic and expression analysis. We identified PIF1, PIF3, PIF4, and PIF7 in PIFs families of the grapevine (Vitis vinifera L.), which were distributed on four different chromosomes with similar gene structures. Except for the closer relationship with PIF1 of citrus, PIFs of grape were distant from the other fruit species such as apple, pear, peach, and strawberry. The VvPIFs (except VvPIF4) were located in the syntenic block with those from Arabidopsisthaliana, Solanum lycopersicum, or Citrus sinensis. In addition to PIF1, all PIFs in grapevines have conserved active PHYB binding (APB) sequences. VvPIF1 has a conserved PIF1-specific active PHYA binding (APA) sequence, while amino acid mutations occurred in the specific APA sequence in VvPIF3. Interestingly, two specific motifs were found in the PIF4 amino acid sequence. The photoreceptor-related elements in the VvPIFs promoter region were the most abundant. PIF1, LONG HYPOCOTYL 5 (HY5) and PIF3, PIF4, GIBBERELLIC ACID INSENSITIVE 1 (GAI1) may interact with each other and participate together in light signal transduction. The relative expression levels of the VvPIFs showed diverse patterns in the various organs at different developmental stages, of which PIF4 was most highly expressed. Prior to maturation, the expression of PIF4 and PIF7 in the skin of the different cultivars increased, while the expression of all PIFs in the flesh decreased. The transcription level of PIFs in grape leaves was sensitive to changes in lighting and shading. Shading treatment was beneficial for enhancing the transcription level of VvPIFs, but the effect on VvPIF3 and VvPIF4 was time-controlled. We concluded that PIFs in grapevines are both conservative and species-specific. The identification and analysis of grape PIFs could provide a theoretical foundation for the further construction of grape light regulation networks.

Genomics-Enabled Next-Generation Breeding Approaches for Developing System-Specific Drought Tolerant Hybrids in Maize

Breeding science has immensely contributed to the global food security. Several varieties and hybrids in different food crops including maize have been released through conventional breeding. The ever growing population, decreasing agricultural land, lowering water table, changing climate, and other variables pose tremendous challenge to the researchers to improve the production and productivity of food crops. Drought is one of the major problems to sustain and improve the productivity of food crops including maize in tropical and subtropical production systems. With advent of novel genomics and breeding tools, the way of doing breeding has been tremendously changed in the last two decades. Drought tolerance is a combination of several component traits with a quantitative mode of inheritance. Rapid DNA and RNA sequencing tools and high-throughput SNP genotyping techniques, trait mapping, functional characterization, genomic selection, rapid generation advancement, and other tools are now available to understand the genetics of drought tolerance and to accelerate the breeding cycle. Informatics play complementary role by managing the big-data generated from the large-scale genomics and breeding experiments. Genome editing is the latest technique to alter specific genes to improve the trait expression. Integration of novel genomics, next-generation breeding, and informatics tools will accelerate the stress breeding process and increase the genetic gain under different production systems.

Phytochromes and Phytochrome Interacting Factors

The basic helix-loop-helix domain-containing transcription factors that interact physically with the red and far-red light photoreceptors, phytochromes, are called PHYTOCHROME INTERACTING FACTORS (PIFs). In the last two decades, the phytochrome-PIF signaling module has been shown to be conserved from Physcomitrella patens to higher plants. Exciting recent studies highlight the discovery of at least four distinct kinases (PPKs, CK2, BIN2, and phytochrome itself) and four families of ubiquitin ligases (SCFEBF1/2, CUL3LRB, CUL3BOP, and CUL4COP1-SPA) that regulate PIF abundance both in dark and light conditions. This review discusses these recent discoveries with a focus on the central phytochrome signaling mechanisms that have a profound impact on plant growth and development in response to light.

NtPHYB1K326, a homologous gene of Arabidopsis PHYB, positively regulates the content of phenolic compounds in tobacco

Polyphenols are important secondary metabolites and bioactive compounds in plants. Light is a vital abiotic factor that greatly impacts the content of polyphenols in plants. In spite of their importance the mechanism of polyphenol regulation still remains unknown in tobacco. A phytochrome B homolog, NtPHYB1K326, was isolated from Nicotiana tabacum cv. K326 to investigate the role of light receptors in the regulation of polyphenol metabolism in tobacco leaves. Furthermore, role of NtPHYB1K326 in polyphenol metabolism was analyzed by over-expression and RNAi-silencing approaches. Consistent and complemented results indicated involvement of NtPHYB1K326 in the regulation of polyphenol metabolism in tobacco leaves. Moreover, high levels of NtPHYB1K326 transcripts favor the accumulation of chlorogenic acid and its isomers, the key polyphenol component in tobacco leaves. Transcriptome analysis was also carried out for exploring the regulation mechanism of NtPHYB1K326 in the polyphenol metabolism. Compared with WT, 1665 and 1421 differentially-expressed genes were found in NtPHYB1K326-GFP and NtPHYB1K326-RNAi transgenic lines, respectively. Among these, about 30 genes were related to phenylpropanoid pathway, which is predominantly involved in synthesis of polyphenols. Further evidences from quantitative RT-PCR confirmed that NtPHYB1K326 may control phenylpropanoid pathway through regulating the transcription of PAL4 (phenylalanine ammonialyase 4), 4CL1 (4-coumarate:coenzyme A ligase 1) and COMT (caffeic acid 3-O-methyltransferase) genes.

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.

Regulatory modules controlling early shade avoidance response in maize seedlings

BACKGROUND

Optimization of shade avoidance response (SAR) is crucial for enhancing crop yield in high-density planting conditions in modern agriculture, but a comprehensive study of the regulatory network of SAR is still lacking in monocot crops.

RESULTS

In this study, the genome-wide early responses in maize seedlings to the simulated shade (low red/far-red ratio) and also to far-red light treatment were transcriptionally profiled. The two processes were predominantly mediated by phytochrome B and phytochrome A, respectively. Clustering of differentially transcribed genes (DTGs) along with functional enrichment analysis identified important biological processes regulated in response to both treatments. Co-expression network analysis identified two transcription factor modules as potentially pivotal regulators of SAR and de-etiolation, respectively. A comprehensive cross-species comparison of orthologous DTG pairs between maize and Arabidopsis in SAR was also conducted, with emphasis on regulatory circuits controlling accelerated flowering and elongated growth, two physiological hallmarks of SAR. Moreover, it was found that the genome-wide distribution of DTGs in SAR and de-etiolation both biased toward the maize1 subgenome, and this was associated with differential retention of various cis-elements between the two subgenomes.

CONCLUSIONS

The results provide the first transcriptional picture for the early dynamics of maize phytochrome signaling. Candidate genes with regulatory functions involved in maize shade avoidance response have been identified, offering a starting point for further functional genomics investigation of maize adaptation to heavily shaded field conditions.

Regulatory modules controlling early shade avoidance response in maize seedlings

Background

Optimization of shade avoidance response (SAR) is crucial for enhancing crop yield in high-density planting conditions in modern agriculture, but a comprehensive study of the regulatory network of SAR is still lacking in monocot crops.

Results

In this study, the genome-wide early responses in maize seedlings to the simulated shade (low red/far-red ratio) and also to far-red light treatment were transcriptionally profiled. The two processes were predominantly mediated by phytochrome B and phytochrome A, respectively. Clustering of differentially transcribed genes (DTGs) along with functional enrichment analysis identified important biological processes regulated in response to both treatments. Co-expression network analysis identified two transcription factor modules as potentially pivotal regulators of SAR and de-etiolation, respectively. A comprehensive cross-species comparison of orthologous DTG pairs between maize and Arabidopsis in SAR was also conducted, with emphasis on regulatory circuits controlling accelerated flowering and elongated growth, two physiological hallmarks of SAR. Moreover, it was found that the genome-wide distribution of DTGs in SAR and de-etiolation both biased toward the maize1 subgenome, and this was associated with differential retention of various cis-elements between the two subgenomes.

Conclusions

The results provide the first transcriptional picture for the early dynamics of maize phytochrome signaling. Candidate genes with regulatory functions involved in maize shade avoidance response have been identified, offering a starting point for further functional genomics investigation of maize adaptation to heavily shaded field conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2593-6) contains supplementary material, which is available to authorized users.

Identification of Crowding Stress Tolerance Co-Expression Networks Involved in Sweet Corn Yield

Tolerance to crowding stress has played a crucial role in improving agronomic productivity in field corn; however, commercial sweet corn hybrids vary greatly in crowding stress tolerance. The objectives were to 1) explore transcriptional changes among sweet corn hybrids with differential yield under crowding stress, 2) identify relationships between phenotypic responses and gene expression patterns, and 3) identify groups of genes associated with yield and crowding stress tolerance. Under conditions of crowding stress, three high-yielding and three low-yielding sweet corn hybrids were grouped for transcriptional and phenotypic analyses. Transcriptional analyses identified from 372 to 859 common differentially expressed genes (DEGs) for each hybrid. Large gene expression pattern variation among hybrids and only 26 common DEGs across all hybrid comparisons were identified, suggesting each hybrid has a unique response to crowding stress. Over-represented biological functions of DEGs also differed among hybrids. Strong correlation was observed between: 1) modules with up-regulation in high-yielding hybrids and yield traits, and 2) modules with up-regulation in low-yielding hybrids and plant/ear traits. Modules linked with yield traits may be important crowding stress response mechanisms influencing crop yield. Functional analysis of the modules and common DEGs identified candidate crowding stress tolerant processes in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. Moreover, these biological functions were greatly inter-connected, indicating the importance of improving the mechanisms as a network.

Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

Cereal crop species including bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), and maize (Zea mays L.) provide the bulk of human nutrition and agricultural products for industrial use. These four cereals are central to meet future demands of food supply for an increasing world population under a changing climate. A prerequisite for cereal crop production is the transition from vegetative to reproductive and grain-filling phases starting with flower initiation, a key developmental switch tightly regulated in all flowering plants. Although studies in the dicotyledonous model plant Arabidopsis thaliana build the foundations of our current understanding of plant phenology genes and regulation, the availability of genome assemblies with high-confidence sequences for rice, maize, and more recently bread wheat and barley, now allow the identification of phenology-associated gene orthologs in monocots. Together with recent advances in next-generation sequencing technologies, QTL analysis, mutagenesis, complementation analysis, and RNA interference, many phenology genes have been functionally characterized in cereal crops and conserved as well as functionally divergent genes involved in flowering were found. Epigenetic and other molecular regulatory mechanisms that respond to environmental and endogenous triggers create an enormous plasticity in flowering behavior among cereal crops to ensure flowering is only induced under optimal conditions. In this review, we provide a summary of recent discoveries of flowering time regulators with an emphasis on four cereal crop species (bread wheat, barley, rice, and maize), in particular, crop-specific regulatory mechanisms and genes. In addition, pleiotropic effects on agronomically important traits such as grain yield, impact on adaptation to new growing environments and conditions, genetic sequence-based selection and targeted manipulation of phenology genes, as well as crop growth simulation models for predictive crop breeding, are discussed.

De novo assembly and characterization of the transcriptome of seagrass Zostera marina using Illumina paired-end sequencing

Background

The seagrass Zostera marina is a monocotyledonous angiosperm belonging to a polyphyletic group of plants that can live submerged in marine habitats. Zostera marina L. is one of the most common seagrasses and is considered a cornerstone of marine plant molecular ecology research and comparative studies. However, the mechanisms underlying its adaptation to the marine environment still remain poorly understood due to limited transcriptomic and genomic data.

Principal Findings

Here we explored the transcriptome of Z. marina leaves under different environmental conditions using Illumina paired-end sequencing. Approximately 55 million sequencing reads were obtained, representing 58,457 transcripts that correspond to 24,216 unigenes. A total of 14,389 (59.41%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. 45.18% and 46.91% of the unigenes had significant similarity with proteins in the Swiss-Prot database and Pfam database, respectively. Among these, 13,897 unigenes were assigned to 57 Gene Ontology (GO) terms and 4,745 unigenes were identified and mapped to 233 pathways via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). We compared the orthologous gene family of the Z. marina transcriptome to Oryza sativa and Pyropia yezoensis and 11,667 orthologous gene families are specific to Z. marina. Furthermore, we identified the photoreceptors sensing red/far-red light and blue light. Also, we identified a large number of genes that are involved in ion transporters and channels including Na⁺ efflux, K⁺ uptake, Cl⁻ channels, and H⁺ pumping.

Conclusions

Our study contains an extensive sequencing and gene-annotation analysis of Z. marina. This information represents a genetic resource for the discovery of genes related to light sensing and salt tolerance in this species. Our transcriptome can be further utilized in future studies on molecular adaptation to abiotic stress in Z. marina.

Suppression of β-catenin and cyclooxygenase-2 expression and cell proliferation in azoxymethane-induced colonic cancer in rats by rice bran phytic acid (PA)

BACKGROUND

Phytic acid (PA) is a polyphosphorylated carbohydrate that can be found in high amounts in most cereals, legumes, nut oil, seeds and soy beans. It has been suggested to play a significant role in inhibition of colorectal cancer. This study was conducted to investigate expression changes of β-catenin and cyclooxygenase-2 (COX-2) and cell proliferation in the adenoma-carcinoma sequence after treatment with rice bran PA by immunocytochemistry.

MATERIALS AND METHODS

Seventy-two male Sprague-Dawley rats were divided into 6 equal groups with 12 rats in each group. For cancer induction two intraperitoneal injections of azoxymethane (AOM) were given at 15 mg/kg bodyweight over a 2-weeks period. During the post initiation phase, two different concentrations of PA, 0.2% (w/v) and 0.5% (w/v) were administered in the diet.

RESULTS

Results of β-catenin, COX-2 expressions and cell proliferation of Ki-67 showed a significant contribution in colonic cancer progression. For β-catenin and COX-2 expression, there was a significant difference between groups at p<0.05. With Ki-67, there was a statistically significant lowering the proliferating index as compared to AOM alone (p<0.05). A significant positive correlation (p=0.01) was noted between COX-2 expression and proliferation. Total β-catenin also demonstrated a significant positive linear relationship with total COX-2 (p=0.044).

CONCLUSIONS

This study indicated potential value of PA extracted from rice bran in reducing colonic cancer risk in rats.

The phytochrome gene family in soybean and a dominant negative effect of a soybean PHYA transgene on endogenous Arabidopsis PHYA

KEY MESSAGE

The evolutionary origin of the phytochrome genes in soybean was analyzed. The expression profiles of PHYA paralogs were characterized. The heterologous expression of GmPHYA1 in Arabidopsis resulted in longer hypocotyls. The phytochromes (PHY) are a small family of red/far-red light photoreceptors which regulate a number of important developmental responses in plants. So far, the members of the PHY gene family in soybean (Glycine max) remain unclear and an understanding of each member's physiological functions is limited. Our present in silico analysis revealed that the soybean genome harbors four PHYA, two PHYB and two PHYE, totally four pairs of eight PHY loci. The phylogenetic analysis suggested that the four PHY paralogous pairs originated from the latest round of genome duplication (~13 million years ago) and the four copies of PHYA were remnants of the two rounds of genome duplication (~58 and ~13 million years ago). A possible evolutionary history of PHYA homologs in the three legume species (soybean, Medicago truncatula, and Lotus japonicus) was proposed and the fate of duplicate soybean PHYA genes following polyploidization was discussed. The expression profiles of a soybean PHYA paralogous pair (GmPHYA1 and GmPHYA2) showed that the transcript abundance was highest in the aerial organs of young plants. The physiological role of GmPHYA1 was explored by observing the de-etiolation phenotype of transgenic Arabidopsis plants constitutively expressing GmPHYA1. The GmPHYA1 protein interfered with the function of endogenous PHYA with respect to de-etiolation in a dominant negative manner when exogenously expressed in Arabidopsis. The elucidation of the PHY gene family members in soybean provide us with a general description and understanding of the photoreceptor gene family in this important crop plant.

Chlorophyll deficiency in the maize elongated mesocotyl2 mutant is caused by a defective heme oxygenase and delaying grana stacking

BACKGROUND

Etiolated seedlings initiate grana stacking and chlorophyll biosynthesis in parallel with the first exposure to light, during which phytochromes play an important role. Functional phytochromes are biosynthesized separately for two components. One phytochrome is biosynthesized for apoprotein and the other is biosynthesized for the chromophore that includes heme oxygenase (HO).

METHODOLOGY/PRINCIPAL FINDING

We isolated a ho1 homolog by map-based cloning of a maize elongated mesocotyl2 (elm2) mutant. cDNA sequencing of the ho1 homolog in elm2 revealed a 31 bp deletion. De-etiolation responses to red and far-red light were disrupted in elm2 seedlings, with a pronounced elongation of the mesocotyl. The endogenous HO activity in the elm2 mutant decreased remarkably. Transgenic complementation further confirmed the dysfunction in the maize ho1 gene. Moreover, non-appressed thylakoids were specifically stacked at the seedling stage in the elm2 mutant.

CONCLUSION

The 31 bp deletion in the ho1 gene resulted in a decrease in endogenous HO activity and disrupted the de-etiolation responses to red and far-red light. The specific stacking of non-appressed thylakoids suggested that the chlorophyll biosynthesis regulated by HO1 is achieved by coordinating the heme level with the regulation of grana stacking.

Comprehensive genotyping of the USA national maize inbred seed bank

BACKGROUND

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.

RESULTS

The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits.

CONCLUSIONS

The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.

Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes

Shade avoidance signaling involves perception of incident red/far-red (R/FR) light by phytochromes (PHYs) and modulation of downstream transcriptional networks. Although these responses are well studied in Arabidopsis, little is known about the role of PHYs and the transcriptional responses to shade in the woody perennial Populus. Tissue expression and subcellular localization of Populus PHYs was studied by quantitative real-time PCR (qRT-PCR) and protoplast transient assay. Transgenic lines with altered PHYB1 and/or PHYB2 expression were used in phenotypic assays and transcript profiling with qRT-PCR. RNA-Seq was used to identify transcriptional responses to enriched FR light. All three PHYs were differentially expressed among tissue types and PHYBs were targeted to the nucleus under white light. Populus PHYB1 rescued Arabidopsis phyB mutant phenotypes. Phenotypes of Populus transgenic lines and the expression of candidate shade response genes suggested that PHYB1 and PHYB2 have distinct yet overlapping functions. RNA-Seq analysis indicated that genes associated with cell wall modification and brassinosteroid signaling were induced under enriched FR light in Populus. This study is an initial attempt at deciphering the role of Populus PHYs by evaluating transcriptional reprogramming to enriched FR and demonstrates functional diversity and overlap of the Populus PHYB1 and PHYB2 in regulating shade responses.

A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling

The transition from the vegetative to reproductive development is a critical event in the plant life cycle. The accurate prediction of flowering time in elite germplasm is important for decisions in maize breeding programs and best agronomic practices. The understanding of the genetic control of flowering time in maize has significantly advanced in the past decade. Through comparative genomics, mutant analysis, genetic analysis and QTL cloning, and transgenic approaches, more than 30 flowering time candidate genes in maize have been revealed and the relationships among these genes have been partially uncovered. Based on the knowledge of the flowering time candidate genes, a conceptual gene regulatory network model for the genetic control of flowering time in maize is proposed. To demonstrate the potential of the proposed gene regulatory network model, a first attempt was made to develop a dynamic gene network model to predict flowering time of maize genotypes varying for specific genes. The dynamic gene network model is composed of four genes and was built on the basis of gene expression dynamics of the two late flowering id1 and dlf1 mutants, the early flowering landrace Gaspe Flint and the temperate inbred B73. The model was evaluated against the phenotypic data of the id1 dlf1 double mutant and the ZMM4 overexpressed transgenic lines. The model provides a working example that leverages knowledge from model organisms for the utilization of maize genomic information to predict a whole plant trait phenotype, flowering time, of maize genotypes.

Ectopic expression reveals a conserved PHYB homolog in soybean

Phytochromes sense red/far-red light and trigger a cascade of physiological responses in plant. Here, a phytochrome B homolog, GmPHYB1, was amplified from the soybean genome, and its expression profiles were obtained for various parts of the plant and at various developmental stages. The gene was ectopically expressed in Arabidopsis thaliana, driven by CaMV 35S promoter, to study the physiological functions of the gene product. The overexpressors of GmPHYB1 behaved similarly to those of AtPHYB, but with some subtle differences with respect to the acceleration of flowering under short day conditions and the growth of the hypocotyl under certain light fluence rate. The results suggested that this soybean PHYB homolog was well conserved both at the level of sequence and physiological function.

Robust expression and association of ZmCCA1 with circadian rhythms in maize

In plants, the circadian clock is an endogenous mechanism that controls a wide range of biological processes. To date, as one of the key world crops, little is known about the molecular mechanism and components of the circadian clock in maize (Zea mays). In this study, we characterized the CIRCADIAN CLOCK ASSOCIATED1 gene of maize (ZmCCA1), an ortholog of CCA1 in Arabidopsis thaliana (AtCCA1). Quantitative real-time PCR analysis revealed that ZmCCA1 was expressed in leaves and stem apex meristems in a rhythmic pattern under long day and short day conditions, and its peak gene expression appeared during the morning. ZmCCA1 transcripts accumulated in all tissues evaluated, with higher levels in tassels and ears. Additionally, the expression of another photoperiod gene ZmTOC1 peaked 12 h after dawn on long days and at 10 h after dawn on short days. Subcellular localization analysis revealed that the ZmCCA1 protein is directed to the cell nucleus. Overexpression of ZmCCA1 in Arabidopsis reduced the expression levels of downstream genes, including GIGANTEA (AtGI), CONSTANS (AtCO), and FLOWERING LOCUST (AtFT), and resulted in longer hypocotyls and delayed flowering. Taken together, our data suggest that ZmCCA1 may be a core component of the circadian clock in maize.

Physiological and genetic characterization of end-of-day far-red light response in maize seedlings

Developmental responses associated with end-of-day far-red light (EOD-FR) signaling were investigated in maize (Zea mays subspecies mays) seedlings. A survey of genetically diverse inbreds of temperate and tropical/semitropical origins, together with teosinte (Zea mays subspecies parviglumis) and a modern hybrid, revealed distinct elongation responses. A mesocotyl elongation response to the EOD-FR treatment was largely absent in the tropical/semitropical lines, but both hybrid and temperate inbred responses were of the same magnitude as in teosinte, suggesting that EOD-FR-mediated mesocotyl responses were not lost during the domestication or breeding process. The genetic architecture underlying seedling responses to EOD-FR was investigated using the intermated B73 x Mo17 mapping population. Among the different quantitative trait loci identified, two were consistently detected for elongation and responsiveness under EOD-FR, but none were associated with known light signaling loci. The central role of phytochromes in mediating EOD-FR responses was shown using a phytochromeB1 phytochromeB2 (phyB1 phyB2) mutant series. Unlike the coleoptile and first leaf sheath, EOD-FR-mediated elongation of the mesocotyl appears predominantly controlled by gibberellin. EOD-FR also reduced abscisic acid (ABA) levels in the mesocotyl for both the wild type and phyB1 phyB2 double mutants, suggesting a FR-mediated but PHYB-independent control of ABA accumulation. EOD-FR elongation responses were attenuated in both the wild type and phyB1 phyB2 double mutants when a chilling stress was applied during the dark period, concomitant with an increase in ABA levels. We present a model for the EOD-FR response that integrates light and hormonal control of seedling elongation.

Hybridization and polyploidy of an aquatic plant, Ruppia (Ruppiaceae), inferred from plastid and nuclear DNA phylogenies

PREMISE OF THE STUDY

The monogeneric family Ruppiaceae is found primarily in brackish water and is widely distributed on all continents, many islands, and from subartic to tropical zones. Ruppia taxonomy has been confusing because of its simplified morphology yet high phenotypic plasticity and the existence of polyploidy and putative hybrids. This study addresses the current classification of species in the genus, the origin of putative hybrids and polyploids, and the distribution of Ruppia species. •

METHODS

Separate molecular phylogenetic analyses using plastid DNA and nuclear-encoded PHYB data sets were performed after chromosome observations. •

KEY RESULTS

The resultant trees were largely congruent between genomes, but were incongruent in two respects: the first incongruence may be caused by long outgroup branches and their effect on ingroup rooting, and the second is caused by the existence of heterogeneous PHYB sequences for several accessions that may reflect several independent hybridization events. Several morphological species recognized in previous taxonomic revisions appear paraphyletic in plastid DNA and PHYB trees. •

CONCLUSIONS

Given the molecular phylogenies, and considering chromosome number and morphology, three species and one species complex comprising six lineages were discerned. A putative allotriploid, an allotetraploid, and a lineage of hybrid origin were identified within the species complex, and a hybrid was found outside the species complex, and their respective putative parental taxa were inferred. With respect to biogeography, a remarkably discontinuous distribution was identified in two cases, for which bird-mediated seed dispersal may be a reasonable explanation.

Red light and calmodulin regulate the expression of the psbA binding protein genes in Chlamydomonas reinhardtii

In the unicellular green alga Chlamydomonas reinhardtii, translation of the chloroplast-encoded psbA mRNA is regulated by the light-dependent binding of a nuclear-encoded protein complex (RB38, RB47, RB55 and RB60) to the 5'-untranslated region of the RNA. Despite the absence of any report identifying a red light photoreceptor within this alga, we show that the expression of the rb38, rb47 and rb60 genes, as well as the nuclear-encoded psbO gene that directs the synthesis of OEE1 (oxygen evolving enhancer 1), is differentially regulated by red light. Further elucidation of the signal transduction pathway shows that calmodulin is an important messenger in the signaling cascade that leads to the expression of rb38, rb60 and psbO, and that a chloroplast signal affects rb47 at the translational level. While there may be several factors involved in the cascade of events from the perception of red light to the expression of the rb and psbO genes, our data suggest the involvement of a red light photoreceptor. Future studies will elucidate this receptor and the additional components of this red light signaling expression pathway in C. reinhardtii.

Genetic control of photoperiod sensitivity in maize revealed by joint multiple population analysis

Variation in maize for response to photoperiod is related to geographical adaptation in the species. Maize possesses homologs of many genes identified as regulators of flowering time in other species, but their relation to the natural variation for photoperiod response in maize is unknown. Candidate gene sequences were mapped in four populations created by crossing two temperate inbred lines to two photoperiod-sensitive tropical inbreds. Whole-genome scans were conducted by high-density genotyping of the populations, which were phenotyped over 3 years in both short- and long-day environments. Joint multiple population analysis identified genomic regions controlling photoperiod responses in flowering time, plant height, and total leaf number. Four key genome regions controlling photoperiod response across populations were identified, referred to as ZmPR1-4. Functional allelic differences within these regions among phenotypically similar founders suggest distinct evolutionary trajectories for photoperiod adaptation in maize. These regions encompass candidate genes CCA/LHY, CONZ1, CRY2, ELF4, GHD7, VGT1, HY1/SE5, TOC1/PRR7/PPD-1, PIF3, ZCN8, and ZCN19.

Composition and phylogenetic analysis of wheat cryptochrome gene family

Cryptochrome (CRY) gene family encodes photoreceptors mediating developmental responses to blue light throughout the life of plants. We report here the characterization of CRY gene family in hexaploid wheat. Degenerate PCR amplification of the regions encoding the conserved flavin-binding domain of CRY proteins yielded seven bands, resulting from amplification of CRY1a, CRY1b and CRY2 homologous genes. Assignment of individual amplicons to subgenomes was accomplished by comparing their sequence compositions with those from the ancestor species of wheat. ESTs coding for CRY-DASH like proteins were identified in wheat EST database in GenBank. Southern blot showed that TaCRY1a, TaCRY1b and TaCRY2 are single copy genes. We mapped TaCRY1a and TaCRY2 to chromosomes of homoeologous group 6, TaCRY1b to group 2, and TaCRY-DASH to group 7. Phylogenetic analysis showed that CRY subfamily diversification occurred before the divergence of monocots and dicots. The regulatory and functional changes of CRY members within subfamily are discussed.

The ornamental variety, Japanese striped corn, contains high anthocyanin levels and PAL specific activity: establishing the potential for development of an oral therapeutic

Phenylalanine ammonia-lyase [PAL, EC 4.3.1.24 (formerly EC 4.3.1.5)], functions in the plant phenylpropanoid biosynthetic pathway to deaminate the amino acid L-phenylalanine forming trans-cinnamic acid and ammonia. The human inherited metabolic disorder phenylketonuria (PKU) is characterized by an inability of individuals to metabolize phenylalanine. Toward the development of a plant-PAL based therapeutic for the treatment of this disorder, a comparative analysis of PAL activities within various members of the Poaceae was undertaken. This led to the identification of a Zea mays cultivar, Japanese Striped corn with very high levels of PAL specific activity in seedling tissues. The root tissues of this corn variety contain greater levels of PAL gene transcripts and PAL activities, compared to those of the shoot tissues, and are intensely colored due to the accumulation of anthocyanin pigments. PAL activities in the root tissues of young seedlings of another corn variety that lacked root anthocyanins (Indian Blue corn) were generally 30-50% lower than those of Japanese Striped corn seedlings at equivalent growth stages. In general, various stress or hormonal treatments led to minimal changes in PAL specific activity of maize tissues, as compared to controls. The PAL enzymes of Japanese Striped corn root tissues are robust; roots retained 90% of their PAL activity after freeze-drying and >50% activity after freeze-drying and a subsequent 15-week storage at 4 degrees C. This work serves as a prelude to the formulation of a dietary supplement for treatment of PKU based on preserved edible cereal root tissues with high levels of intrinsic PAL activity.

Genetic analysis of photoperiod sensitivity in a tropical by temperate maize recombinant inbred population using molecular markers

Photoperiod sensitivity is an important consideration in maize cultivation. Flowering time is affected by photoperiod and sensitivity to it limits the potential for successful exchange of germplasm across different latitudes. For resolving the genetic basis of photoperiod sensitivity in maize, a set of 207 recombinant inbred lines derived from a temperate and tropical inbred line cross was evaluated for 2 years in a long-day and short-day environment. Genetic linkage maps were constructed using 237 SSR markers with a total length 1,974.3 cM, and an average space between two makers of 8.33 cM. Twenty-nine QTL were detected for the five measured photoperiod sensitivity traits using composite interval mapping and multiple interval mapping. QTL for flowering time, plant height and leaf number, under long-day conditions, were found clustered on chromosome 10, while QTL for short-day conditions resided on chromosome 3. The QTL in the bin 10.04 region of chromosome 10 were detected associated with photoperiod sensitivity and related traits during long days. These results indicated that this region might contain an important photoperiod sensitivity element.

Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant

During maize (Zea mays) C(4) differentiation, mesophyll (M) and bundle sheath (BS) cells accumulate distinct sets of photosynthetic enzymes, with very low photosystem II (PSII) content in BS chloroplasts. Consequently, there is little linear electron transport in the BS and ATP is generated by cyclic electron flow. In contrast, M thylakoids are very similar to those of C(3) plants and produce the ATP and NADPH that drive metabolic activities. Regulation of this differentiation process is poorly understood, but involves expression and coordination of nuclear and plastid genomes. Here, we identify a recessive allele of the maize high chlorophyll fluorescence (Hcf136) homolog that in Arabidopsis (Arabidopsis thaliana) functions as a PSII stability or assembly factor located in the thylakoid lumen. Proteome analysis of the thylakoids and electron microscopy reveal that Zmhcf136 lacks PSII complexes and grana thylakoids in M chloroplasts, consistent with the previously defined Arabidopsis function. Interestingly, hcf136 is also defective in processing the full-length psbB-psbT-psbH-petB-petD polycistron specifically in M chloroplasts. To determine whether the loss of PSII in M cells affects C(4) differentiation, we performed cell-type-specific transcript analysis of hcf136 and wild-type seedlings. The results indicate that M and BS cells respond uniquely to the loss of PSII, with little overlap in gene expression changes between data sets. These results are discussed in the context of signals that may drive differential gene expression in C(4) photosynthesis.

Shade avoidance

The threat to plant survival presented by light limitation has driven the evolution of highly plastic adaptive strategies to either tolerate or avoid shading by neighbouring vegetation. When subject to vegetational shading, plants are exposed to a variety of informational signals, which include altered light quality and a reduction in light quantity. The former includes a decrease in the ratio of red to far-red wavelengths (low R : FR) and is detected by the phytochrome family of plant photoreceptors. Monitoring of R : FR ratio can provide an early and unambiguous warning of the presence of competing vegetation, thereby evoking escape responses before plants are actually shaded. The molecular mechanisms underlying physiological responses to alterations in light quality have now started to emerge, with major roles suggested for the PIF (PHYTOCHROME INTERACTING FACTOR) and DELLA families of transcriptional regulators. Such studies suggest a complex interplay between endogenous and exogenous signals, mediated by multiple photoreceptors. The phenotypic similarities between physiological responses habitually referred to as 'the shade avoidance syndrome' and other abiotic stress responses suggest plants may integrate common signalling mechanisms to respond to multiple perturbations in their natural environment.

Subfunctionalization of PhyB1 and PhyB2 in the control of seedling and mature plant traits in maize

Phytochromes are the primary red/far-red photoreceptors of higher plants, mediating numerous developmental processes throughout the life cycle, from germination to flowering. In seed plants, phytochromes are encoded by a small gene family with each member performing both distinct and redundant roles in mediating physiological responses to light cues. Studies in both eudicot and monocot species have defined a central role for phytochrome B in mediating responses to light in the control of several agronomically important traits, including plant height, transitions to flowering and axillary branch meristem development. Here we characterize Mutator-induced alleles of PhyB1 and a naturally occurring deletion allele of PhyB2 in Zea mays (maize). Using single and double mutants, we show that the highly similar PhyB1 and PhyB2 genes encode proteins with both overlapping and non-redundant functions that control seedling and mature plant traits. PHYB1 and PHYB2 regulate elongation of sheath and stem tissues of mature plants and contribute to the light-mediated regulation of PhyA and Cab gene transcripts. However, PHYB1 and not PHYB2 contributes significantly to the inhibition of mesocotyl elongation under red light, whereas PHYB2 and to a lesser extent PHYB1 mediate the photoperiod-dependent floral transition. This sub functionalization of PHYB activities in maize has probably occurred since the tetraploidization of maize, and may contribute to flowering time variation in modern-day varieties.

Phytochrome-mediated development in land plants: red light sensing evolves to meet the challenges of changing light environments

Phytochromes are photoreceptors that provide plants with circadian, seasonal, and positional information critical for the control of germination, seedling development, shade avoidance, reproduction, dormancy, and sleep movements. Phytochromes are unique among photoreceptors in their capacity to interconvert between a red-absorbing form (absorption maximum of approximately 660 nm) and a far-red absorbing form (absorption maximum of approximately 730 nm), which occur in a dynamic equilibrium within plant cells, corresponding to the proportions of red and far-red energy in ambient light. Because pigments in stems and leaves absorb wavelengths below about 700 nm, this provides plants with an elegant system for detecting their position relative to other plants, with which the plants compete for light. Certain aspects of phytochrome-mediated development outside of flowering plants are strikingly similar to those that have been characterized in Arabidopsis thaliana and other angiosperms. However, early diverging land plants have fewer distinct phytochrome gene lineages, suggesting that both diversification and subfunctionalization have been important in the evolution of the phytochrome gene family. There is evidence that subfunctionalization proceeded by the partitioning among paralogues of photosensory specificity, physiological response modes, and light-regulated gene expression and protein stability. Parallel events of duplication and functional divergence may have coincided with the evolution of canopy shade and the increasing complexity of the light environment. Within angiosperms, patterns of functional divergence are clade-specific and the roles of phytochromes in A. thaliana change across environments, attesting to the evolutionary flexibility and contemporaneous plasticity of phytochrome signalling in the control of development.

A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture

Although quantitative trait locus (QTL) mapping has been successful in describing the genetic architecture of complex traits, the molecular basis of quantitative variation is less well understood, especially in plants such as maize that have large genome sizes. Regulatory changes at the teosinte branched1 (tb1) gene have been proposed to underlie QTLs of large effect for morphological differences that distinguish maize (Zea mays ssp. mays) from its wild ancestors, the teosintes (Z. mays ssp. parviglumis and mexicana). We used a fine mapping approach to show that intergenic sequences approximately 58-69 kb 5' to the tb1 cDNA confer pleiotropic effects on Z. mays morphology. Moreover, using an allele-specific expression assay, we found that sequences >41 kb upstream of tb1 act in cis to alter tb1 transcription. Our findings show that the large stretches of noncoding DNA that comprise the majority of many plant genomes can be a source of variation affecting gene expression and quantitative phenotypes.

Ac-immobilized, a stable source of Activator transposase that mediates sporophytic and gametophytic excision of Dissociation elements in maize

We have identified and characterized a novel Activator (Ac) element that is incapable of excision yet contributes to the canonical negative dosage effect of Ac. Cloning and sequence analysis of this immobilized Ac (Ac-im) revealed that it is identical to Ac with the exception of a 10-bp deletion of sequences at the left end of the element. In screens of approximately 6800 seeds, no germinal transpositions of Ac-im were detected. Importantly, Ac-im catalyzes germinal excisions of a Ds element resident at the r1 locus resulting in the recovery of independent transposed Ds insertions in approximately 4.5% of progeny kernels. Many of these transposition events occur during gametophytic development. Furthermore, we demonstrate that Ac-im transactivates multiple Ds insertions in somatic tissues including those in reporter alleles at bronze1, anthocyaninless1, and anthocyaninless2. We propose a model for the generation of Ac-im as an aberrant transposition event that failed to generate an 8-bp target site duplication and resulted in the deletion of Ac end sequences. We also discuss the utility of Ac-im in two-component Ac/Ds gene-tagging programs in maize.

Cereal phytochromes: targets of selection, targets for manipulation?

Plants respond to shading through an adaptive syndrome termed shade avoidance. In high-density crop plantings, shade avoidance generally increases extension growth at the expense of yield and can be at odds with the agronomic performance of the crop as a whole. Studies in Arabidopsis are beginning to reveal the essential role phytochromes play in regulating this process and to identify genes underlying the response. In this article, we focus on how phytochrome signaling networks have been targeted in cereal breeding programs in the past and discuss the potential to alter these pathways through breeding and transgenic manipulation to develop crops that perform better under typical high density conditions.

Distribution of Activator (Ac) throughout the maize genome for use in regional mutagenesis

A collection of Activator (Ac)-containing, near-isogenic W22 inbred lines has been generated for use in regional mutagenesis experiments. Each line is homozygous for a single, precisely positioned Ac element and the Ds reporter, r1-sc:m3. Through classical and molecular genetic techniques, 158 transposed Ac elements (tr-Acs) were distributed throughout the maize genome and 41 were precisely placed on the linkage map utilizing multiple recombinant inbred populations. Several PCR techniques were utilized to amplify DNA fragments flanking tr-Ac insertions up to 8 kb in length. Sequencing and database searches of flanking DNA revealed that the majority of insertions are in hypomethylated, low- or single-copy sequences, indicating an insertion site preference for genic sequences in the genome. However, a number of Ac transposition events were to highly repetitive sequences in the genome. We present evidence that suggests Ac expression is regulated by genomic context resulting in subtle variations in Ac-mediated excision patterns. These tr-Ac lines can be utilized to isolate genes with unknown function, to conduct fine-scale genetic mapping experiments, and to generate novel allelic diversity in applied breeding programs.

The Elm1 (ZmHy2) gene of maize encodes a phytochromobilin synthase

The light insensitive maize (Zea mays) mutant elongated mesocotyl1 (elm1) has previously been shown to be deficient in the synthesis of the phytochrome chromophore 3E-phytochromobilin (PPhiB). To identify the Elm1 gene, a maize homolog of the Arabidopsis PPhiB synthase gene AtHY2 was isolated and designated ZmHy2. ZmHy2 encodes a 297-amino acid protein of 34 kD that is 50% identical to AtHY2. ZmHY2 was predicted to be plastid localized and was targeted to chloroplasts following transient expression in tobacco (Nicotiana plumbaginifolia) leaves. Molecular mapping indicated that ZmHy2 is a single copy gene in maize that is genetically linked to the Elm1 locus. Sequence analysis revealed that the ZmHy2 gene of elm1 mutants contains a single G to A transition at the 3' splice junction of intron III resulting in missplicing and premature translational termination. However, flexibility in the splicing machinery allowed a small pool of in-frame ZmHy2 transcripts to accumulate in elm1 plants. In addition, multiple ZmHy2 transcript forms accumulated in both wild-type and elm1 mutant plants. ZmHy2 splice variants were expressed in Escherichia coli and products examined for activity using a coupled apophytochrome assembly assay. Only full-length ZmHY2 (as defined by homology to AtHY2) was found to exhibit PPhiB synthase activity. Thus, the elm1 mutant of maize is deficient in phytochrome response due to a lesion in a gene encoding phytochromobilin synthase that severely compromises the PPhiB pool.