A conserved superlocus regulates above- and belowground root initiation.

Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato (Solanum lycopersicum) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS (SBRL). Evolutionary analysis reveals that SBRL's function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.

ZmCCT regulates photoperiod-dependent flowering and response to stresses in maize.

BACKGROUND: Appropriate flowering time is very important to the success of modern agriculture. Maize (Zea mays L.) is a major cereal crop, originated in tropical areas, with photoperiod sensitivity. Which is an important obstacle to the utilization of tropical/subtropical germplasm resources in temperate regions. However, the study on the regulation mechanism of photoperiod sensitivity of maize is still in the early stage. Although it has been previously reported that ZmCCT is involved in the photoperiod response and delays maize flowering time under long-day conditions, the underlying mechanism remains unclear. RESULTS: Here, we showed that ZmCCT overexpression delays flowering time and confers maize drought tolerance under LD conditions. Implementing the Gal4-LexA/UAS system identified that ZmCCT has a transcriptional inhibitory activity, while the yeast system showed that ZmCCT has a transcriptional activation activity. DAP-Seq analysis and EMSA indicated that ZmCCT mainly binds to promoters containing the novel motifs CAAAAATC and AAATGGTC. DAP-Seq and RNA-Seq analysis showed that ZmCCT could directly repress the expression of ZmPRR5 and ZmCOL9, and promote the expression of ZmRVE6 to delay flowering under long-day conditions. Moreover, we also demonstrated that ZmCCT directly binds to the promoters of ZmHY5, ZmMPK3, ZmVOZ1 and ZmARR16 and promotes the expression of ZmHY5 and ZmMPK3, but represses ZmVOZ1 and ZmARR16 to enhance stress resistance. Additionally, ZmCCT regulates a set of genes associated with plant development. CONCLUSIONS: ZmCCT has dual functions in regulating maize flowering time and stress response under LD conditions. ZmCCT negatively regulates flowering time and enhances maize drought tolerance under LD conditions. ZmCCT represses most flowering time genes to delay flowering while promotes most stress response genes to enhance stress tolerance. Our data contribute to a comprehensive understanding of the regulatory mechanism of ZmCCT in controlling maize flowering time and stress response.

The impact of stress combination on reproductive processes in crops.

Historically, extended droughts combined with heat waves caused severe reductions in crop yields estimated at billions of dollars annually. Because global warming and climate change are driving an increase in the frequency and intensity of combined water-deficit and heat stress episodes, understanding how these episodes impact yield is critical for our efforts to develop climate change-resilient crops. Recent studies demonstrated that a combination of water-deficit and heat stress exacerbates the impacts of water-deficit or heat stress on reproductive processes of different cereals and legumes, directly impacting grain production. These studies identified several different mechanisms potentially underlying the effects of stress combination on anthers, pollen, and stigma development and function, as well as fertilization. Here we review some of these findings focusing on unbalanced reactive oxygen accumulation, altered sugar concentrations, and conflicting functions of different hormones, as contributing to the reduction in yield during a combination of water-deficit and heat stress. Future studies focused on the effects of water-deficit and heat stress combination on reproduction of different crops are likely to unravel additional mechanisms, as well as reveal novel ways to develop stress combination-resilient crops. These could mitigate some of the potentially devastating impacts of this stress combination on agriculture.

Zn tolerance in the evergreen shrub, Aucuba japonica, naturally growing at a mine site: Cell wall immobilization, aucubin production, and Zn adsorption on fungal mycelia.

Aucuba japonica Thunb. is an evergreen understory shrub that grows naturally at a mine site. The mine soil contains high concentrations of heavy metals, and A. japonica appears to maintain detoxification mechanisms against heavy metals in the study site's understory. This study aimed to investigate the heavy metal tolerance mechanisms in A. japonica, considering the possible roles of arbuscular mycorrhizal and root-endophytic fungi. We conducted fieldwork in summer (canopy-foliation season) and winter (canopy-defoliation season) to measure the heavy metal concentrations in leaves, branches, and roots and analyze possible detoxicants in the roots. The infection rates of arbuscular mycorrhizal and root-endophytic fungi were evaluated via microscopic observation, and heavy metal (Zn) localization in A. japonica roots was observed using confocal laser scanning microscopy. Field analysis showed that A. japonica accumulated excessive Zn and produced aucubin and citric acid in the roots in both summer and winter. Zn localization observations clarified that Zn was distributed in thickened epidermal and cortical cell walls, suggesting that the cell walls functioned as Zn deposition sites, reducing Zn toxicity. It was further clarified that Zn was contained within cortical cells, indicating that Zn might be detoxified by aucubin and citric acid. Arbuscular mycorrhizal and root-endophytic fungi within cortical cells adsorbed Zn on fungal cell walls, indicating that these fungi would reduce Zn content within root cells and might alleviate Zn toxicity. Our results indicated that A. japonica would maintain Zn tolerance in both summer and winter via Zn immobilization in the cell walls and production of aucubin and citric acid, and that arbuscular mycorrhizal and root-endophytic fungi might play important roles in the Zn tolerance of A. japonica.

Reproductive innovations and pulsed rise in plant complexity.

Morphological complexity is a notable feature of multicellular life, although whether it evolves gradually or in early bursts is unclear. Vascular plant reproductive structures, such as flowers, are familiar examples of complex morphology. In this study, we use a simple approach based on the number of part types to analyze changes in complexity over time. We find that reproductive complexity increased in two pulses separated by ~250 million years of stasis, including an initial rise in the Devonian with the radiation of vascular plants and a pronounced increase in the Late Cretaceous that reflects flowering plant diversification. These pulses are associated with innovations that increased functional diversity, suggesting that shifts in complexity are linked to changes in function regardless of whether they occur early or late in the history of vascular plants.

Seagrass habitat suitability model for Redang Marine Park using multibeam echosounder data: Testing different spatial resolutions and analysis window sizes.

Integrating Multibeam Echosounder (MBES) data (bathymetry and backscatter) and underwater video technology allows scientists to study marine habitats. However, use of such data in modeling suitable seagrass habitats in Malaysian coastal waters is still limited. This study tested multiple spatial resolutions (1 and 50 m) and analysis window sizes (3 × 3, 9 × 9, and 21 × 21 cells) probably suitable for seagrass-habitat relationships in Redang Marine Park, Terengganu, Malaysia. A maximum entropy algorithm was applied, using 12 bathymetric and backscatter predictors to develop a total of 6 seagrass habitat suitability models. The results indicated that both fine and coarse spatial resolution datasets could produce models with high accuracy (>90%). However, the models derived from the coarser resolution dataset displayed inconsistent habitat suitability maps for different analysis window sizes. In contrast, habitat models derived from the fine resolution dataset exhibited similar habitat distribution patterns for three different analysis window sizes. Bathymetry was found to be the most influential predictor in all the models. The backscatter predictors, such as angular range analysis inversion parameters (characterization and grain size), gray-level co-occurrence texture predictors, and backscatter intensity levels, were more important for coarse resolution models. Areas of highest habitat suitability for seagrass were predicted to be in shallower (<20 m) waters and scattered between fringing reefs (east to south). Some fragmented, highly suitable habitats were also identified in the shallower (<20 m) areas in the northwest of the prediction models and scattered between fringing reefs. This study highlighted the importance of investigating the suitable spatial resolution and analysis window size of predictors from MBES for modeling suitable seagrass habitats. The findings provide important insight on the use of remote acoustic sonar data to study and map seagrass distribution in Malaysia coastal water.

Geographic distribution of the E1 family of genes and their effects on reproductive timing in soybean.

BACKGROUND: Soybean is an economically important crop which flowers predominantly in response to photoperiod. Several major loci controlling the quantitative trait for reproductive timing have been identified, of which allelic combinations at three of these loci, E1, E2, and E3, are the dominant factors driving time to flower and reproductive period. However, functional genomics studies have identified additional loci which affect reproductive timing, many of which are less understood. A better characterization of these genes will enable fine-tuning of adaptation to various production environments. Two such genes, E1La and E1Lb, have been implicated in flowering by previous studies, but their effects have yet to be assessed under natural photoperiod regimes. RESULTS: Natural and induced variants of E1La and E1Lb were identified and introgressed into lines harboring either E1 or its early flowering variant, e1-as. Lines were evaluated for days to flower and maturity in a Maturity Group (MG) III production environment. These results revealed that variation in E1La and E1Lb promoted earlier flowering and maturity, with stronger effects in e1-as background than in an E1 background. The geographic distribution of E1La alleles among wild and cultivated soybean revealed that natural variation in E1La likely contributed to northern expansion of wild soybean, while breeding programs in North America exploited e1-as to develop cultivars adapted to northern latitudes. CONCLUSION: This research identified novel alleles of the E1 paralogues, E1La and E1Lb, which promote flowering and maturity under natural photoperiods. These loci represent sources of genetic variation which have been under-utilized in North American breeding programs to control reproductive timing, and which can be valuable additions to a breeder's molecular toolbox.

Transcriptomic study of the night break in Chenopodium rubrum reveals possible upstream regulators of the floral activator CrFTL1.

The transition from vegetative to reproductive phases is the most fundamental and tightly controlled switch in the life of flowering plants. The short-day plant Chenopodium rubrum is a fast cycling annual plant lacking a juvenile phase. It can be induced to flowering at the seedling stage by exposure to a single period of darkness. This floral induction may then be cancelled by a short pulse of red light at midnight called night break (NB), which also inhibits the floral activator FLOWERING LOCUS T LIKE 1 (CrFTL1). We performed a comparative transcriptomic study between C. rubrum seedlings treated by NB and ones growing through uninterrupted night, and found about six hundred differentially expressed genes, including the B-BOX DOMAIN (BBX) genes. We focused on the CrBBX19 and BOLTING TIME CONTROL 1 (BTC1) genes, homologous to the upstream regulators of the BvFT2, a floral inducer in sugar beet. The transcription patterns of the two genes were compatible with their putative role as a sensor of the dark period length optimal for flowering (CrBBX19), and a signal of lights-on (CrBTC1), but the participation of other genes cannot be excluded. The expression profiles of CrBBX19 and the homolog of the core endogenous clock gene LATE ELONGATED HYPOCOTYL (LHY) were highly similar, which suggested their co-regulation.

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants.

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

Consequences of LED Lights on Root Morphological Traits and Compounds Accumulation in Sarcandra glabra Seedlings.

This study evaluated the effects of different light spectra (white light; WL, blue light; BL and red light; RL) on the root morphological traits and metabolites accumulation and biosynthesis in Sarcandra glabra. We performed transcriptomic and metabolomic profiling by RNA-seq and ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS), respectively. When morphological features were compared to WL, BL substantially increased under-ground fresh weight, root length, root surface area, and root volume, while RL inhibited these indices. A total of 433 metabolites were identified, of which 40, 18, and 68 compounds differentially accumulated in roots under WL (WG) vs. roots under BL (BG), WG vs. roots under RL (RG), and RG vs. BG, respectively. In addition, the contents of sinapyl alcohol, sinapic acid, fraxetin, and 6-methylcoumarin decreased significantly in BG and RG. In contrast, chlorogenic acid, rosmarinyl glucoside, quercitrin and quercetin were increased considerably in BG. Furthermore, the contents of eight terpenoids compounds significantly reduced in BG. Following transcriptomic profiling, several key genes related to biosynthesis of phenylpropanoid-derived and terpenoids metabolites were differentially expressed, such as caffeic acid 3-O-methyltransferase) (COMT), hydroxycinnamoyl-CoA shikimate hydroxycinnamoyl transferase (HCT), O-methyltransferase (OMT), and 1-deoxy-D-xylulose-5-phosphate synthetase (DXS). In summary, our findings showed that BL was suitable for growth and accumulation of bioactive metabolites in root tissue of S. glabra. Exposure to a higher ratio of BL might have the potential to improve the production and quality of S. glabra seedlings, but this needs to be confirmed further.

Local scale interventions dominate over catchment scale controls to accelerate the recovery of a degraded stream.

A premise of stream restoration theory and practice is that it is often futile to attempt to restore a stream at the reach scale (101-103 metres) until catchment scale problems have been addressed. This study considers reach scale restoration actions undertaken in Bryan Creek, a sand bed river in south east Australia impacted by a sediment pulse, after catchment sediment sources have been addressed. Local scale interventions, which were in-stream sand extraction, fencing to exclude stock and riparian revegetation, were evaluated by quantifying cross-section and thalweg variability, mapping in-stream and riparian vegetation and by classifying the morphology that emerged following each intervention. Following intervention channel reaches moved to one of three distinct states: simple clay bed, eroding reaches dominated by Juncus acutus, and reaches with deep pools and Phragmites australis. Boundaries between the intervention reaches were sharp, suggesting local scale interventions dominate over catchment scale processes. The magnitude and spread of variability metrics were similar between all reaches and differences in variability bore no relation to intervention type, despite the stark difference in post-intervention morphology. These findings suggest that cross-section and thalweg variability metrics are an inadequate proxy for the effectiveness of local scale interventions in accelerating the recovery of sand bed reaches from a bedload pulse. The most important implications for river managers is that local scale interventions can lead to substantial and rapid improvements in condition, and the change in condition of these reaches is almost independent of other reaches. In this case, the key to the pattern of reach scale geomorphic recovery is excluding stock from waterways so that a specific macrophyte can establish, trap sediment and develop pools.

Inter-species functional compatibility of the Theobroma cacao and Arabidopsis FT orthologs: 90 million years of functional conservation of meristem identity genes.

BACKGROUND: In angiosperms the transition to flowering is controlled by a complex set of interacting networks integrating a range of developmental, physiological, and environmental factors optimizing transition time for maximal reproductive efficiency. The molecular mechanisms comprising these networks have been partially characterized and include both transcriptional and post-transcriptional regulatory pathways. Florigen, encoded by FLOWERING LOCUS T (FT) orthologs, is a conserved central integrator of several flowering time regulatory pathways. To characterize the molecular mechanisms involved in controlling cacao flowering time, we have characterized a cacao candidate florigen gene, TcFLOWERING LOCUS T (TcFT). Understanding how this conserved flowering time regulator affects cacao plant's transition to flowering could lead to strategies to accelerate cacao breeding. RESULTS: BLAST searches of cacao genome reference assemblies identified seven candidate members of the CENTRORADIALIS/TERMINAL FLOWER1/SELF PRUNING gene family including a single florigen candidate. cDNA encoding the predicted cacao florigen was cloned and functionally tested by transgenic genetic complementation in the Arabidopsis ft-10 mutant. Transgenic expression of the candidate TcFT cDNA in late flowering Arabidopsis ft-10 partially rescues the mutant to wild-type flowering time. Gene expression studies reveal that TcFT is spatially and temporally expressed in a manner similar to that found in Arabidopsis, specifically, TcFT mRNA is shown to be both developmentally and diurnally regulated in leaves and is most abundant in floral tissues. Finally, to test interspecies compatibility of florigens, we transformed cacao tissues with AtFT resulting in the remarkable formation of flowers in tissue culture. The morphology of these in vitro flowers is normal, and they produce pollen that germinates in vitro with high rates. CONCLUSION: We have identified the cacao CETS gene family, central to developmental regulation in angiosperms. The role of the cacao's single FT-like gene (TcFT) as a general regulator of determinate growth in cacao was demonstrated by functional complementation of Arabidopsis ft-10 late-flowering mutant and through gene expression analysis. In addition, overexpression of AtFT in cacao resulted in precocious flowering in cacao tissue culture demonstrating the highly conserved function of FT and the mechanisms controlling flowering in cacao.

Plastid Genomes of Flowering Plants: Essential Principles.

The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.

Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants.

In monocots other than maize (Zea mays) and rice (Oryza sativa), the repertoire and diversity of microRNAs (miRNAs) and the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly characterized. To remedy this, we sequenced small RNAs (sRNA) from vegetative and dissected inflorescence tissue in 28 phylogenetically diverse monocots and from several early-diverging angiosperm lineages, as well as publicly available data from 10 additional monocot species. We annotated miRNAs, small interfering RNAs (siRNAs) and phasiRNAs across the monocot phylogeny, identifying miRNAs apparently lost or gained in the grasses relative to other monocot families, as well as a number of transfer RNA fragments misannotated as miRNAs. Using our miRNA database cleaned of these misannotations, we identified conservation at the 8th, 9th, 19th, and 3'-end positions that we hypothesize are signatures of selection for processing, targeting, or Argonaute sorting. We show that 21-nucleotide (nt) reproductive phasiRNAs are far more numerous in grass genomes than other monocots. Based on sequenced monocot genomes and transcriptomes, DICER-LIKE5, important to 24-nt phasiRNA biogenesis, likely originated via gene duplication before the diversification of the grasses. This curated database of phylogenetically diverse monocot miRNAs, siRNAs, and phasiRNAs represents a large collection of data that should facilitate continued exploration of sRNA diversification in flowering plants.

YABBY Genes in the Development and Evolution of Land Plants.

Mounting evidence from genomic and transcriptomic studies suggests that most genetic networks regulating the morphogenesis of land plant sporophytes were co-opted and modified from those already present in streptophyte algae and gametophytes of bryophytes sensu lato. However, thus far, no candidate genes have been identified that could be responsible for "planation", a conversion from a three-dimensional to a two-dimensional growth pattern. According to the telome theory, "planation" was required for the genesis of the leaf blade in the course of leaf evolution. The key transcription factors responsible for leaf blade development in angiosperms are YABBY proteins, which until recently were thought to be unique for seed plants. Yet, identification of a YABBY homologue in a green alga and the recent findings of YABBY homologues in lycophytes and hornworts suggest that YABBY proteins were already present in the last common ancestor of land plants. Thus, these transcriptional factors could have been involved in "planation", which fosters our understanding of the origin of leaves. Here, we summarise the current data on functions of YABBY proteins in the vegetative and reproductive development of diverse angiosperms and gymnosperms as well as in the development of lycophytes. Furthermore, we discuss a putative role of YABBY proteins in the genesis of multicellular shoot apical meristems and in the evolution of leaves in early divergent terrestrial plants.

Epigenetic regulation and intercellular communication during male gametophyte development.

The male gametophyte of angiosperms has long been recognized as an ideal system for the study of the molecular mechanisms regulating cell fate determination. Recent findings on histone variants in two cell lineages, vegetative-cell-derived small interfering RNA and transposable element expression provide new power for relevant investigations.

A Role for Auxin in Triggering Lamina Outgrowth of Unifacial Leaves.

A common morphological feature of typical angiosperms is the patterning of lateral organs along primary axes of asymmetry-a proximodistal, a mediolateral, and an adaxial-abaxial axis. Angiosperm leaves usually have distinct adaxial-abaxial identity, which is required for the development of a flat shape. By contrast, many unifacial leaves, consisting of only the abaxial side, show a flattened morphology. This implicates a unique mechanism that allows leaf flattening independent of adaxial-abaxial identity. In this study, we report a role for auxin in outgrowth of unifacial leaves. In two closely related unifacial-leaved species of Juncaceae, Juncus prismatocarpus with flattened leaves, and Juncus wallichianus with transversally radialized leaves, the auxin-responsive gene GLYCOSIDE HYDROLASE3 displayed spatially different expression patterns within leaf primordia. Treatment of J. prismatocarpus seedlings with exogenous auxin or auxin transport inhibitors, which disturb endogenous auxin distribution, eliminated leaf flatness, resulting in a transversally radialized morphology. These treatments did not affect the radialized morphology of leaves of J. wallichianus. Moreover, elimination of leaf flatness by these treatments accompanied dysregulated expression of genetic factors needed to specify the leaf central-marginal polarity in J. prismatocarpus. The findings imply that lamina outgrowth of unifacial leaves relies on proper placement of auxin, which might induce initial leaf flattening and subsequently act to specify leaf polarity, promoting further flattening growth of leaves.

Genetic regulation of flowering time and inflorescence architecture by MtFDa and MtFTa1 in Medicago truncatula.

Regulation of floral transition and inflorescence development is crucial for plant reproductive success. FLOWERING LOCUS T (FT) is one of the central players in the flowering genetic regulatory network, whereas FLOWERING LOCUS D (FD), an interactor of FT and TERMINAL FLOWER 1 (TFL1), plays significant roles in both floral transition and inflorescence development. Here we show the genetic regulatory networks of floral transition and inflorescence development in Medicago truncatula by characterizing MtFTa1 and MtFDa and their genetic interactions with key inflorescence meristem (IM) regulators. Both MtFTa1 and MtFDa promote flowering; the double mutant mtfda mtfta1 does not proceed to floral transition. RNAseq analysis reveals that a broad range of genes involved in flowering regulation and flower development are up- or downregulated by MtFTa1 and/or MtFDa mutations. Furthermore, mutation of MtFDa also affects the inflorescence architecture. Genetic analyses of MtFDa, MtFTa1, MtTFL1, and MtFULc show that MtFDa is epistatic to MtFULc and MtTFL1 in controlling IM identity. Our results demonstrate that MtFTa1 and MtFDa are major flowering regulators in M. truncatula, and MtFDa is essential both in floral transition and secondary inflorescence development. The study will advance our understanding of the genetic regulation of flowering time and inflorescence development in legumes.

Nuclear DNA replicates during zygote development in Arabidopsis and Torenia fournieri.

The progression of the cell cycle is continuous in most cells, but gametes (sperm and egg cells) exhibit an arrest of the cell cycle to await fertilization to form a zygote, which then continues through the subsequent phases to complete cell division. The phase in which gametes of flowering plants arrest has been a matter of debate, since different phases have been reported for the gametes of different species. In this study, we reassessed the phase of cell-cycle arrest in the gametes of two species, Arabidopsis (Arabidopsis thaliana) and Torenia fournieri. We first showed that 4', 6-diamidino-2-phenylindole staining was not feasible to detect changes in gametic nuclear DNA in T. fournieri. Next, using 5-ethynyl-2'-deoxyuridine (EdU) staining that detects DNA replication by labeling the EdU absorbed by deoxyribonucleic acid, we found that the replication of nuclear DNA did not occur during gamete development but during zygote development, revealing that the gametes of these species have a haploid nuclear DNA content before fertilization. We thus propose that gametes in the G1 phase participate in the fertilization event in Arabidopsis and T. fournieri.