Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination

Physiology and transcriptome of Eucommia ulmoides seeds at different germination stages

E. ulmoides (Eucommia ulmoides) has significant industrial and medicinal value and high market demand. E. ulmoides grows seedlings through sowing. According to previous studies, plant hormones have been shown to regulate seed germination. To understand the relationship between hormones and E. ulmoides seed germination, we focused on examining the changes in various indicators during the germination stage of E. ulmoides seeds. We measured the levels of physiological and hormone indicators in E. ulmoides seeds at different germination stages and found that the levels of abscisic acid (ABA), gibberellin (GA), and indole acetic acid (IAA) significantly varied as the seeds germinated. Furthermore, we confirmed that ABA, GA, and IAA are essential hormones in the germination of E. ulmoides seeds using Gene Ontology and Kyoto Encyclopedia of Genes and Genomics enrichment analyses of the transcriptome. The discovery of hormone-related synthesis pathways in the control group of Eucommia seeds at different germination stages further confirmed this conclusion. This study provides a basis for further research into the regulatory mechanisms of E. ulmoides seeds at different germination stages and the relationship between other seed germination and plant hormones.

Dynamic transcriptome landscape of developing maize ear

Seed number and harvesting ability in maize (Zea mays L.) are primarily determined by the architecture of female inflorescence, namely the ear. Therefore, ear morphogenesis contributes to grain yield and as such is one of the key target traits during maize breeding. However, the molecular networks of this highly dynamic and complex grain-bearing inflorescence remain largely unclear. As a first step toward characterizing these networks, we performed a high-spatio-temporal-resolution investigation of transcriptomes using 130 ear samples collected from developing ears with length from 0.1 mm to 19.0 cm. Comparisons of these mRNA populations indicated that these spatio-temporal transcriptomes were clearly separated into four distinct stages stages I, II, III, and IV. A total of 23 793 genes including 1513 transcription factors (TFs) were identified in the investigated developing ears. During the stage I of ear morphogenesis, 425 genes were predicted to be involved in a co-expression network established by eight hub TFs. Moreover, 9714 ear-specific genes were identified in the seven kinds of meristems. Additionally, 527 genes including 59 TFs were identified as especially expressed in ear and displayed high temporal specificity. These results provide a high-resolution atlas of gene activity during ear development and help to unravel the regulatory modules associated with the differentiation of the ear in maize.

ZmEREB92 plays a negative role in seed germination by regulating ethylene signaling and starch mobilization in maize

Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.

Analyzing Changes in Maize Leaves Orientation due to GxExM Using an Automatic Method from RGB Images

The sowing pattern has an important impact on light interception efficiency in maize by determining the spatial distribution of leaves within the canopy. Leaves orientation is an important architectural trait determining maize canopies light interception. Previous studies have indicated how maize genotypes may adapt leaves orientation to avoid mutual shading with neighboring plants as a plastic response to intraspecific competition. The goal of the present study is 2-fold: firstly, to propose and validate an automatic algorithm (Automatic Leaf Azimuth Estimation from Midrib detection [ALAEM]) based on leaves midrib detection in vertical red green blue (RGB) images to describe leaves orientation at the canopy level; and secondly, to describe genotypic and environmental differences in leaves orientation in a panel of 5 maize hybrids sowing at 2 densities (6 and 12 plants.m^-2) and 2 row spacing (0.4 and 0.8 m) over 2 different sites in southern France. The ALAEM algorithm was validated against in situ annotations of leaves orientation, showing a satisfactory agreement (root mean square [RMSE] error = 0.1, R² = 0.35) in the proportion of leaves oriented perpendicular to rows direction across sowing patterns, genotypes, and sites. The results from ALAEM permitted to identify significant differences in leaves orientation associated to leaves intraspecific competition. In both experiments, a progressive increase in the proportion of leaves oriented perpendicular to the row is observed when the rectangularity of the sowing pattern increases from 1 (6 plants.m^-2, 0.4 m row spacing) towards 8 (12 plants.m^-2, 0.8 m row spacing). Significant differences among the 5 cultivars were found, with 2 hybrids exhibiting, systematically, a more plastic behavior with a significantly higher proportion of leaves oriented perpendicularly to avoid overlapping with neighbor plants at high rectangularity. Differences in leaves orientation were also found between experiments in a squared sowing pattern (6 plants.m^-2, 0.4 m row spacing), indicating a possible contribution of illumination conditions inducing a preferential orientation toward east-west direction when intraspecific competition is low.

Hormonal control of medial-lateral growth and vein formation in the maize leaf

Parallel veins are characteristic of monocots, including grasses (Poaceae). Therefore, how parallel veins develop as the leaf grows in the medial-lateral (ML) dimension is a key question in grass leaf development. Using fluorescent protein reporters, we mapped auxin, cytokinin (CK), and gibberellic acid (GA) response patterns in maize (Zea mays) leaf primordia. We further defined the roles of these hormones in ML growth and vein formation through combinatorial genetic analyses and measurement of hormone concentrations. We discovered a novel pattern of auxin response in the adaxial protoderm that we hypothesize has important implications for the orderly formation of 3° veins early in leaf development. In addition, we found an auxin transport and response pattern in the margins that correlate with the transition from ML to proximal-distal growth. We present evidence that auxin efflux precedes CK response in procambial strand development. We also determined that GA plays an early role in the shoot apical meristem as well as a later role in the primordium to restrict ML growth. We propose an integrative model whereby auxin regulates ML growth and vein formation in the maize leaf through control of GA and CK.

Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues

Detecting the simultaneous presence of a microRNA (miRNA) and a mRNA in a specific tissue can provide support for the prediction that the miRNA regulates the mRNA. Although two such methods have been developed for mammalian tissues, they have a low signal-noise ratio and/or poor resolution at the single-cell level. To overcome these drawbacks, we develop a method that uses sequence-specific miRNA-locked nucleic acid (LNA) and mRNA-LNA probes. Moreover, it augments the detection signal by rolling circle amplification, achieving a high signal-noise ratio at the single-cell level. Dot signals are counted for determining the expression levels of mRNA and miRNA molecules in specific cells. We show a high sequence specificity of our miRNA-LNA probe, revealing that it can discriminate single-base mismatches. Numerical quantification by our method is tested in transgenic rice lines with different gene expression levels. We conduct several applications. First, the spatial expression profiling of osa-miR156 and OsSPL12 in rice leaves reveals their specific expression in mesophyll cells. Second, studying rice and its mutant lines with our method reveals opposite expression patterns of miRNA and its target mRNA in tissues. Third, the dynamic expression profiles of ZmGRF8 and zma-miR396 during maize leaf development provide evidence that zma-miR396 regulates the preferential spatial expression of ZmGRF8 in bundle sheath cells. Finally, our method can be scaled up to simultaneously detect multiple miRNAs and mRNAs in a tissue. Thus, it is a sensitive and versatile technique for studying miRNA regulation of plant tissue development.

Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells

The superior photosynthetic efficiency of C₄ leaves over C₃ leaves is owing to their unique Kranz anatomy, in which the vein is surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. Kranz anatomy development starts from three contiguous ground meristem (GM) cells, but its regulators and underlying molecular mechanism are largely unknown. To identify the regulators, we obtained the transcriptomes of 11 maize embryonic leaf cell types from five stages of pre-Kranz cells starting from median GM cells and six stages of pre-M cells starting from undifferentiated cells. Principal component and clustering analyses of transcriptomic data revealed rapid pre-Kranz cell differentiation in the first two stages but slow differentiation in the last three stages, suggesting early Kranz cell fate determination. In contrast, pre-M cells exhibit a more prolonged transcriptional differentiation process. Differential gene expression and coexpression analyses identified gene coexpression modules, one of which included 3 auxin transporter and 18 transcription factor (TF) genes, including known regulators of Kranz anatomy and/or vascular development. In situ hybridization of 11 TF genes validated their expression in early Kranz development. We determined the binding motifs of 15 TFs, predicted TF target gene relationships among the 18 TF and 3 auxin transporter genes, and validated 67 predictions by electrophoresis mobility shift assay. From these data, we constructed a gene regulatory network for Kranz development. Our study sheds light on the regulation of early maize leaf development and provides candidate leaf development regulators for future study.

SCARECROW is deployed in distinct contexts during rice and maize leaf development

The flexible deployment of developmental regulators is an increasingly appreciated aspect of plant development and evolution. The GRAS transcription factor SCARECROW (SCR) regulates the development of the endodermis in Arabidopsis and maize roots, but during leaf development it regulates the development of distinct cell types; bundle-sheath in Arabidopsis and mesophyll in maize. In rice, SCR is implicated in stomatal patterning, but it is unknown whether this function is additional to a role in inner leaf patterning. Here, we demonstrate that two duplicated SCR genes function redundantly in rice. Contrary to previous reports, we show that these genes are necessary for stomatal development, with stomata virtually absent from leaves that are initiated after germination of mutants. The stomatal regulator OsMUTE is downregulated in Osscr1;Osscr2 mutants, indicating that OsSCR acts early in stomatal development. Notably, Osscr1;Osscr2 mutants do not exhibit the inner leaf patterning perturbations seen in Zmscr1;Zmscr1h mutants, and Zmscr1;Zmscr1h mutants do not exhibit major perturbations in stomatal patterning. Taken together, these results indicate that SCR was deployed in different developmental contexts after the divergence of rice and maize around 50 million years ago.

Maize Golden2-like transcription factors boost rice chloroplast development, photosynthesis, and grain yield

Chloroplasts are the sites for photosynthesis, and two Golden2-like factors act as transcriptional activators of chloroplast development in rice (Oryza sativa L.) and maize (Zea mays L.). Rice OsGLK1 and OsGLK2 are orthologous to maize ZmGLK1 (ZmG1) and ZmGLK2 (ZmG2), respectively. However, while rice OsGLK1 and OsGLK2 act redundantly to regulate chloroplast development in mesophyll cells, maize ZmG1 and ZmG2 are functionally specialized and expressed in different cell-specific manners. To boost rice chloroplast development and photosynthesis, we generated transgenic rice plants overexpressing ZmG1 and ZmG2, individually or simultaneously, with constitutive promoters (pZmUbi::ZmG1 and p35S::ZmG2) or maize promoters (pZmG1::ZmG1, pZmG2::ZmG2, and pZmG1::ZmG1/pZmG2::ZmG2). Both ZmG1 and ZmG2 genes were highly expressed in transgenic rice leaves. Moreover, ZmG1 and ZmG2 showed coordinated expression in pZmG1::ZmG1/pZmG2::ZmG2 plants. All Golden2-like (GLK) transgenic plants had higher chlorophyll and protein contents, Rubisco activities and photosynthetic rates per unit leaf area in flag leaves. However, the highest grain yields occurred when maize promoters were used; pZmG1::ZmG1, pZmG2::ZmG2, and pZmG1::ZmG1/pZmG2::ZmG2 transgenic plants showed increases in grain yield by 51%, 47%, and 70%, respectively. In contrast, the pZmUbi::ZmG1 plant produced smaller seeds without yield increases. Transcriptome analysis indicated that maize GLKs act as master regulators promoting the expression of both photosynthesis-related and stress-responsive regulatory genes in both rice shoot and root. Thus, by promoting these important functions under the control of their own promoters, maize GLK1 and GLK2 genes together dramatically improved rice photosynthetic performance and productivity. A similar approach can potentially improve the productivity of many other crops.

The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator

In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress.

Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes

Flowering in maize (Zea mays) is influenced by photoperiod. The CO, CO-like/COL and TOC1 (CCT) domain protein-encoding genes in maize, ZmCCTs, are particularly important for photoperiod sensitivity. However, little is known about CCT protein-encoding gene number across plant species or among maize inbred lines. Therefore, we analysed CCT protein-encoding gene number across plant species, and characterized ZmCCTs in different inbred lines, including structural variations (SVs), copy number variations (CNVs), expression under stresses, dark-dark (DD) and dark-light (DL) cycles, interaction network and associations with maize quantitative trait loci (QTLs) by referring to the latest v4 genome data of B73. Gene number varied greatly across plant species, more in polyploids than in diploids. The numbers of ZmCCTs identified were 58 in B73, 59 in W22, 48 in Mo17, and 57 in Huangzao4 for temperate maize inbred lines, and 68 in tropical maize inbred line SK. Some ZmCCTs underwent duplications and presented chromosome collinearity. Structural variations and CNVs were found but they had no germplasm specificity. Forty-two ZmCCTs responded to stresses. Expression of 37 ZmCCTs in embryonic leaves during seed germination of maize under DD and DL cycles was roughly divided into five patterns of uphill pattern, downhill-pattern, zigzag-pattern, └-pattern and ⅃-pattern, indicating some of them have a potential to perceive dark and/or dark-light transition. Thirty-three ZmCCTs were co-expressed with 218 other maize genes; and 24 ZmCCTs were associated with known QTLs. The data presented in this study will help inform further functions of ZmCCTs.

Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize

The efficiencies offered by C4 photosynthesis have motivated efforts to understand its biochemical, genetic, and developmental basis. Reactions underlying C4 traits in most C4 plants are partitioned between two cell types, bundle sheath (BS), and mesophyll (M) cells. RNA-seq has been used to catalog differential gene expression in BS and M cells in maize (Zea mays) and several other C4 species. However, the contribution of translational control to maintaining the distinct proteomes of BS and M cells has not been addressed. In this study, we used ribosome profiling and RNA-seq to describe translatomes, translational efficiencies, and microRNA abundance in BS- and M-enriched fractions of maize seedling leaves. A conservative interpretation of our data revealed 182 genes exhibiting cell type-dependent differences in translational efficiency, 31 of which encode proteins with core roles in C4 photosynthesis. Our results suggest that non-AUG start codons are used preferentially in upstream open reading frames of BS cells, revealed mRNA sequence motifs that correlate with cell type-dependent translation, and identified potential translational regulators that are differentially expressed. In addition, our data expand the set of genes known to be differentially expressed in BS and M cells, including genes encoding transcription factors and microRNAs. These data add to the resources for understanding the evolutionary and developmental basis of C4 photosynthesis and for its engineering into C3 crops.

MP3RNA-seq: Massively parallel 3' end RNA sequencing for high-throughput gene expression profiling and genotyping

Transcriptome deep sequencing (RNA-seq) has become a routine method for global gene expression profiling. However, its application to large-scale experiments remains limited by cost and labor constraints. Here we describe a massively parallel 3' end RNA-seq (MP3RNA-seq) method that introduces unique sample barcodes during reverse transcription to permit sample pooling immediately following this initial step. MP3RNA-seq allows for handling of hundreds of samples in a single experiment, at a cost of about $6 per sample for library construction and sequencing. MP3RNA-seq is effective for not only high-throughput gene expression profiling, but also genotyping. To demonstrate its utility, we applied MP3RNA-seq to 477 double haploid lines of maize. We identified 19,429 genes expressed in at least 50% of the lines and 35,836 high-quality single nucleotide polymorphisms for genotyping analysis. Armed with these data, we performed expression and agronomic trait quantitative trait locus (QTL) mapping and identified 25,797 expression QTLs for 15,335 genes and 21 QTLs for plant height, ear height, and relative ear height. We conclude that MP3RNA-seq is highly reproducible, accurate, and sensitive for high-throughput gene expression profiling and genotyping, and should be generally applicable to most eukaryotic species.

Transcriptome analysis of Cinnamomum migao seed germination in medicinal plants of Southwest China

BACKGROUND

Cinnamomum migao is an endangered evergreen woody plant species endemic to China. Its fruit is used as a traditional medicine by the Miao nationality of China and has a high commercial value. However, its seed germination rate is extremely low under natural and artificial conditions. As the foundation of plant propagation, seed germination involves a series of physiological, cellular, and molecular changes; however, the molecular events and systematic changes occurring during C. migao seed germination remain unclear.

RESULTS

In this study, combined with the changes in physiological indexes and transcription levels, we revealed the regulation characteristics of cell structures, storage substances, and antioxidant capacity during seed germination. Electron microscopy analysis revealed that abundant smooth and full oil bodies were present in the cotyledons of the seeds. With seed germination, oil bodies and other substances gradually degraded to supply energy; this was consistent with the content of storage substances. In parallel to electron microscopy and physiological analyses, transcriptome analysis showed that 80-90 % of differentially expressed genes (DEGs) appeared after seed imbibition, reflecting important development and physiological changes. The unigenes involved in material metabolism (glycerolipid metabolism, fatty acid degradation, and starch and sucrose metabolism) and energy supply pathways (pentose phosphate pathway, glycolysis pathway, pyruvate metabolism, tricarboxylic acid cycle, and oxidative phosphorylation) were differentially expressed in the four germination stages. Among these DEGs, a small number of genes in the energy supply pathway at the initial stage of germination maintained high level of expression to maintain seed vigor and germination ability. Genes involved in lipid metabolism were firstly activated at a large scale in the LK (seed coat fissure) stage, and then genes involved in carbohydrates (CHO) metabolism were activated, which had their own species specificity.

CONCLUSIONS

Our study revealed the transcriptional levels of genes and the sequence of their corresponding metabolic pathways during seed germination. The changes in cell structure and physiological indexes also confirmed these events. Our findings provide a foundation for determining the molecular mechanisms underlying seed germination.

Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf

BACKGROUND

The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development.

RESULTS

Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. This allows us to generate the first biologically-informed gene expression map of this leaf, with the entire developmental gradient from meristematic to fully differentiated cells captured. We show that the first phase of plastid development begins with organelle proliferation, which extends well beyond cell proliferation, and continues with the establishment and then the build-up of the plastid genetic machinery. The second phase is marked by the development of photosynthetic chloroplasts which occupy the available cellular space. Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages.

CONCLUSIONS

Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, and highlights our very limited knowledge of the earliest drivers of plastid biogenesis, while providing a basis for their future identification.

Transcriptome analysis revealed the regulation of gibberellin and the establishment of photosynthetic system promote rapid seed germination and early growth of seedling in pearl millet

BACKGROUND

Seed germination is the most important stage for the formation of a new plant. This process starts when the dry seed begins to absorb water and ends when the radicle protrudes. The germination rate of seed from different species varies. The rapid germination of seed from species that grow on marginal land allows seedlings to compete with surrounding species, which is also the guarantee of normal plant development and high yield. Pearl millet is an important cereal crop that is used worldwide, and it can also be used to extract bioethanol. Previous germination experiments have shown that pearl millet has a fast seed germination rate, but the molecular mechanisms behind pearl millet are unclear. Therefore, this study explored the expression patterns of genes involved in pearl millet growth from the germination of dry seed to the early growth stages.

RESULTS

Through the germination test and the measurement of the seedling radicle length, we found that pearl millet seed germinated after 24 h of swelling of the dry seed. Using transcriptome sequencing, we characterized the gene expression patterns of dry seed, water imbibed seed, germ and radicle, and found more differentially expressed genes (DEGs) in radicle than germ. Further analysis showed that different genome clusters function specifically at different tissues and time periods. Weighted gene co-expression network analysis (WGCNA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that many genes that positively regulate plant growth and development are highly enriched and expressed, especially the gibberellin signaling pathway, which can promote seed germination. We speculated that the activation of these key genes promotes the germination of pearl millet seed and the growth of seedlings. To verify this, we measured the content of gibberellin and found that the gibberellin content after seed imbibition rose sharply and remained at a high level.

CONCLUSIONS

In this study, we identified the key genes that participated in the regulation of seed germination and seedling growth. The activation of key genes in these pathways may contribute to the rapid germination and growth of seed and seedlings in pearl millet. These results provided new insight into accelerating the germination rate and seedling growth of species with slow germination.

Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

BACKGROUND

Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions.

RESULTS

In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves.

CONCLUSIONS

Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.

Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors

The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex network. In this study, we use large-scale ChIP-seq to reconstruct it in the maize leaf, and train machine-learning models to predict TF binding and co-localization. The resulting network covers 77% of the expressed genes, and shows a scale-free topology and functional modularity like a real-world network. TF binding sequence preferences are conserved within family, while co-binding could be key for their binding specificity. Cross-species comparison shows that core network nodes at the top of the transmission of information being more conserved than those at the bottom. This study reveals the complex and redundant nature of the plant transcription regulatory network, and sheds light on its architecture, organizing principle and evolutionary trajectory.

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.

Maize ANT1 modulates vascular development, chloroplast development, photosynthesis, and plant growth

Arabidopsis AINTEGUMENTA (ANT), an AP2 transcription factor, is known to control plant growth and floral organogenesis. In this study, our transcriptome analysis and in situ hybridization assays of maize embryonic leaves suggested that maize ANT1 (ZmANT1) regulates vascular development. To better understand ANT1 functions, we determined the binding motif of ZmANT1 and then showed that ZmANT1 binds the promoters of millet SCR1, GNC, and AN3, which are key regulators of Kranz anatomy, chloroplast development, and plant growth, respectively. We generated a mutant with a single-codon deletion and two frameshift mutants of the ANT1 ortholog in the C4 millet Setaria viridis by the CRISPR/Cas9 technique. The two frameshift mutants displayed reduced photosynthesis efficiency and growth rate, smaller leaves, and lower grain yields than wild-type (WT) plants. Moreover, their leaves sporadically exhibited distorted Kranz anatomy and vein spacing. Conducting transcriptomic analysis of developing leaves in the WT and the three mutants we identified differentially expressed genes (DEGs) in the two frameshift mutant lines and found many down-regulated DEGs enriched in photosynthesis, heme, tetrapyrrole binding, and antioxidant activity. In addition, we predicted many target genes of ZmANT1 and chose 13 of them to confirm binding of ZmANT1 to their promoters. Based on the above observations, we proposed a model for ANT1 regulation of cell proliferation and leaf growth, vascular and vein development, chloroplast development, and photosynthesis through its target genes. Our study revealed biological roles of ANT1 in several developmental processes beyond its known roles in plant growth and floral organogenesis.

Neurotropin Inhibits Lipid Accumulation by Maintaining Mitochondrial Function in Hepatocytes via AMPK Activation

The accumulation of lipid droplets in the cytoplasm of hepatocytes, known as hepatic steatosis, is a hallmark of non-alcoholic fatty liver disease (NAFLD). Inhibiting hepatic steatosis is suggested to be a therapeutic strategy for NAFLD. The present study investigated the actions of Neurotropin (NTP), a drug used for chronic pain in Japan and China, on lipid accumulation in hepatocytes as a possible treatment for NAFLD. NTP inhibited lipid accumulation induced by palmitate and linoleate, the two major hepatotoxic free fatty acids found in NAFLD livers. An RNA sequencing analysis revealed that NTP altered the expression of mitochondrial genes. NTP ameliorated palmitate-and linoleate-induced mitochondrial dysfunction by reversing mitochondrial membrane potential, respiration, and β-oxidation, suppressing mitochondrial oxidative stress, and enhancing mitochondrial turnover. Moreover, NTP increased the phosphorylation of AMPK, a critical factor in the regulation of mitochondrial function, and induced PGC-1β expression. Inhibition of AMPK activity and PGC-1β expression diminished the anti-steatotic effect of NTP in hepatocytes. JNK inhibition could also be associated with NTP-mediated inhibition of lipid accumulation, but we did not find the association between AMPK and JNK. These results suggest that NTP inhibits lipid accumulation by maintaining mitochondrial function in hepatocytes via AMPK activation, or by inhibiting JNK.

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

The regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent maps of potential transcriptional regulation. Here, we analyzed a large number of publically available maize (Zea mays) transcriptome data sets including >6000 RNA sequencing samples to generate 45 coexpression-based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, and tissue-and-genotype samples). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes. By examining the power of our coexpression-based GRNs to accurately predict covarying TF-target relationships in natural variation data sets, we found that presence/absence changes rather than quantitative changes in TF gene expression are more likely associated with changes in target gene expression. Integrating information from our TF-target predictions and previous expression quantitative trait loci (eQTL) mapping results provided support for 68 TFs underlying 74 previously identified trans-eQTL hotspots spanning a variety of metabolic pathways. This study highlights the utility of developing multiple GRNs within a species to detect putative regulators of important plant pathways and provides potential targets for breeding or biotechnological applications.

Identification of Quantitative Trait Loci Controlling Ethylene Production in Germinating Seeds in Maize (Zea mays L.)

Plant seed germination is a crucial developmental event that has significant effects on seedling establishment and yield production. This process is controlled by multiple intrinsic signals, particularly phytohormones. The gaseous hormone ethylene stimulates seed germination; however, the genetic basis of ethylene production in maize during seed germination remains poorly understood. In this study, we quantified the diversity of germination among 14 inbred lines representing the parental materials corresponding to multiple recombinant inbred line (RIL) mapping populations. Quantitative trait loci (QTLs) controlling ethylene production were then identified in germinating seeds from an RIL population constructed from two parental lines showing differences in both germination speed and ethylene production during germination. To explore the possible genetic correlations of ethylene production with other traits, seed germination and seed weight were evaluated using the same batch of samples. On the basis of high-density single nucleotide polymorphism-based genetic linkage maps, we detected three QTLs for ethylene production in germinating seeds, three QTLs for seed germination, and four QTLs for seed weight, with each QTL explaining 5.8%–13.2% of the phenotypic variation of the trait. No QTLs were observed to be co-localized, suggesting that the genetic bases underlying the three traits are largely different. Our findings reveal three chromosomal regions responsible for ethylene production during seed germination, and provide a valuable reference for the future investigation of the genetic mechanism underlying the role of the stress hormone ethylene in maize germination control under unfavourable external conditions.

Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains

Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation, which is best studied in the mammalian models. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We found that their global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic associated with differential gene expression. Plant domains are largely stable across tissues, while new domain border formations are often associated with transcriptional activation in the region. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian TADs. Although we only observed chromatin loops between gene islands in the large genomes, the maize loop gene pairs' syntenic orthologs have shorter physical distances in small genome monocots, suggesting that loops instead of domains might have conserved biological function. Our study showed that plants' chromatin features might not have conserved biological functions as the mammalian ones.

Comprehensive dynamic transcriptome analysis at two seed germination stages in maize (Zea mays L.)

Seed germination, as an integral stage of crop production, directly affects Zea mays (maize) yield and grain quality. However, the molecular mechanisms of seed germination remain unclear in maize. We performed comparative transcriptome analysis of two maize inbred lines, Yu82 and Yu537A, at two stages of seed germination. Expression profile analysis during seed germination revealed that a total of 3381 and 4560 differentially expressed genes (DEGs) were identified in Yu82 and Yu537A at the two stages. Transcription factors were detected from several families, such as the bZIP, ERF, WRKY, MYB and bHLH families, which indicated that these transcription factor families might be involved in driving seed germination in maize. Prominent DEGs were submitted for KEGG enrichment analysis, which included plant hormones, amino acid mechanism, nutrient reservoir, metabolic pathways and ribosome. Of these pathways, genes associated with plant hormones, especially gibberellins, abscisic acid and auxin may be important for early germination in Yu82. In addition, DEGs involved in amino acid mechanism showed significantly higher expression levels in Yu82 than in Yu537A, which indicated that energy supply from soluble sugars and amino acid metabolism may contribute to early germination in Yu82. This results provide novel insights into transcriptional changes and gene interactions in maize during seed germination.

Jasmonic acid levels decline in advance of the transition to the adult phase in maize

Leaf-derived signals drive the development of the shoot, eventually leading to flowering. In maize, transcripts of genes that facilitate jasmonic acid (JA) signaling are more abundant in juvenile compared to adult leaf primordia; exogenous application of JA both extends the juvenile phase and delays the decline in miR156 levels. To test the hypothesis that JA promotes juvenility, we measured JA and meJA levels using LC-MS in successive stages of leaf one development and in later leaves at stages leading up to phase change in both normal maize and phase change mutants. We concurrently measured gibberellic acid (GA), required for the timely transition to the adult phase. Jasmonic acid levels increased from germination through leaf one differentiation, declining in later formed leaves as the shoot approached phase change. In contrast, levels of GA were low in leaf one after germination and increased as the shoot matured to the adult phase. Multiple doses of exogenous JA resulted in the production of as many as three additional juvenile leaves. We analyzed two transcript expression datasets to investigate when gene regulation by miR156 begins in the context of spatiotemporal patterns of JA and GA signaling. Quantifying these hormones in phase change mutants provided insight into how these two hormones control phase-specific patterns of differentiation. We conclude that the hormone JA is a leaf-provisioned signal that influences the duration, and possibly the initiation, of the juvenile phase of maize by controlling patterns of differentiation in successive leaf primordia.

Morphological changes during juvenile-to-adult phase transition in sorghum

Morphological and genetic markers indicate that in sorghum, the juvenile-to-adult phase transition occurs during the fourth and fifth leaf stages. This timing differs from those reported for other plants. The juvenile-to-adult (JA) phase transition is an important event for optimizing vegetative growth and reproductive success in plants. Among the Poaceae crops, which are a vital food source for humans, studies of the JA phase transition have been restricted to rice and maize. We studied the morphological and genetic changes that occur during the early development of sorghum and found that dramatic changes occur in shoot architecture during the early vegetative stages. Changes were observed in leaf size, leaf shape, numbers of trichomes, and size of the shoot apical meristem. In particular, the length/width ratios of the leaf blades in the fifth and upper leaves were completely different from those of the second to fourth leaves. The fifth and upper leaves have trichomes on their adaxial sides, which were absent on the lower leaves. We also analyzed expression of two microRNAs that are known to be molecular markers of the JA phase transition and found that expression of miR156 was highest in the second to fourth leaves and then was gradually down-regulated, whereas miR172 expression followed the opposite pattern. These results suggest that in sorghum, the second and third leaves represent the juvenile phase, the fourth and fifth leaves are in the transition stage, and the sixth and upper leaves are in the adult phase. Thus, the JA phase transition occurs during the fourth and fifth leaf stages. These findings are expected to be useful for understanding the early development of sorghum.

SWEET Transporters for the Nourishment of Embryonic Tissues during Maize Germination

In maize seed germination, the endosperm and the scutellum nourish the embryo axis. Here, we examined the mRNA relative amount of the SWEET protein family, which could be involved in sugar transport during germination since high [¹⁴-C]-glucose and mainly [¹⁴-C]-sucrose diffusional uptake were found in embryo tissues. We identified high levels of transcripts for SWEETs in the three phases of the germination process: ZmSWEET4c, ZmSWEET6b, ZmSWEET11, ZmSWEET13a, ZmSWEET13b, ZmSWEET14b and ZmSWEET15a, except at 0 h of imbibition where the abundance of each ZmSWEET was low. Despite the major sucrose (Suc) biosynthesis capacity of the scutellum and the high level of transcripts of the Suc symporter SUT1, Suc was not found to be accumulated; furthermore, in the embryo axis, Suc did not decrease but hexoses increased, suggesting an efficient Suc efflux from the scutellum to nourish the embryo axis. The influx of Glc into the scutellum could be mediated by SWEET4c to take up the large amount of transported sugars due to the late hydrolysis of starch. In addition, sugars regulated the mRNA amount of SWEETs at the embryo axis. These results suggest an important role for SWEETs in transporting Suc and hexoses between the scutellum and the embryo axis, and differences in SWEET transcripts between both tissues might occur because of the different sugar requirements and metabolism.

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor

Gibberellins (GA) are key positive regulators of seed germination. Although the GA effects on seed germination have been studied in a number of species, little is known about the transcriptional reprogramming modulated by GA during this phase in species other than Arabidopsis thaliana. Here we report the transcriptome analysis of soybean embryonic axes during germination in the presence of paclobutrazol (PBZ), a GA biosynthesis inhibitor. We found a number of differentially expressed cell wall metabolism genes, supporting their roles in cell expansion during germination. Several genes involved in the biosynthesis and signaling of other phytohormones were also modulated, indicating an intensive hormonal crosstalk at the embryonic axis. We have also found 26 photosynthesis genes that are up-regulated by PBZ at 24 hours after imbibition (HAI) and down-regulated at 36 HAI, which led us to suggest that this is part of a strategy to implement an autotrophic growth program in the absence of GA-driven mobilization of reserves. Finally, 30 transcription factors (mostly from the MYB, bHLH, and bZIP families) were down-regulated by PBZ and are likely downstream GA targets that will drive transcriptional changes during germination.

Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes

Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light-dark cycles and under total darkness and obtained eight time-ordered gene coexpression networks (TO-GCNs), which can be used to predict upstream regulators of any genes in the GCNs. One of the eight TO-GCNs is light-independent and likely includes all genes involved in the development of Kranz anatomy, which is a structure crucial for the high efficiency of photosynthesis in C₄ plants. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade upstream of SHORTROOT1, a key Kranz anatomy regulator. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of maize C₄ enzyme genes and RUBISCO SMALL SUBUNIT2 Our study provides not only a powerful method but also novel insights into the regulatory networks underlying Kranz anatomy development and C₄ photosynthesis.

Getting closer: vein density in C4 leaves

Contents Summary 1260 I. Introduction 1260 II. Molecular and genetic mechanisms of C₄ leaf venation 1262 III. Conclusions and future perspectives 1266 Acknowledgements 1266 References 1266 SUMMARY: C₄ grasses are major contributors to the world's food supply. Their highly efficient method of carbon fixation is a unique adaptation that combines close vein spacing and distinct photosynthetic cell types. Despite its importance, the molecular genetic basis of C₄ leaf development is still poorly understood. Here we summarize current knowledge of leaf venation and review recent progress in understanding molecular and genetic regulation of vascular patterning events in C₄ plants. Evidence points to the interplay of auxin, brassinosteroids, SHORTROOT/SCARECROW and INDETERMINATE DOMAIN transcription factors. Identification and functional characterization of candidate regulators acting early in vascular development will be essential for further progress in understanding the precise regulation of these processes.

Understanding the Genetic Basis of C4 Kranz Anatomy with a View to Engineering C3 Crops

One of the most remarkable examples of convergent evolution is the transition from C₃ to C₄ photosynthesis, an event that occurred on over 60 independent occasions. The evolution of C₄ is particularly noteworthy because of the complexity of the developmental and metabolic changes that took place. In most cases, compartmentalized metabolic reactions were facilitated by the development of a distinct leaf anatomy known as Kranz. C₄ Kranz anatomy differs from ancestral C₃ anatomy with respect to vein spacing patterns across the leaf, cell-type specification around veins, and cell-specific organelle function. Here we review our current understanding of how Kranz anatomy evolved and how it develops, with a focus on studies that are dissecting the underlying genetic mechanisms. This research field has gained prominence in recent years because understanding the genetic regulation of Kranz may enable the C₃-to-C₄ transition to be engineered, an endeavor that would significantly enhance crop productivity.

Anatomy and ultrastructure of embryonic leaves of the C4 species Setaria viridis

BACKGROUND AND AIMS

Setaria viridis is being promoted as a model C4 photosynthetic plant because it has a small genome (~515 Mb), a short life cycle (~60 d) and it can be transformed. Unlike other C4 grasses such as maize, however, there is very little information about how C4 leaf anatomy (Kranz anatomy) develops in S. viridis. As a foundation for future developmental genetic studies, we provide an anatomical and ultrastructural framework of early shoot development in S. viridis, focusing on the initiation of Kranz anatomy in seed leaves.

METHODS

Setaria viridis seeds were germinated and divided into five stages covering development from the dry seed (stage S0) to 36 h after germination (stage S4). Material at each of these stages was examined using conventional light, scanning and transmission electron microscopy.

KEY RESULTS

Dry seeds contained three embryonic leaf primordia at different developmental stages (plastochron 1-3 primordia). The oldest (P3) leaf primordium possessed several procambial centres whereas P2 displayed only ground meristem. At the tip of P3 primordia at stage S4, C4 leaf anatomy typical of the malate dehydrogenase-dependent nicotinamide dinucleotide phosphate (NADP-ME) subtype was evident in that vascular bundles lacked a mestome layer and were surrounded by a single layer of bundle sheath cells that contained large, centrifugally located chloroplasts. Two to three mesophyll cells separated adjacent vascular bundles and one mesophyll cell layer on each of the abaxial and adaxial sides delimited vascular bundles from the epidermis.

CONCLUSIONS

The morphological trajectory reported here provides a foundation for studies of gene regulation during early leaf development in S. viridis and a framework for comparative analyses with other C4 grasses.

Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data

A transcription factor (TF) is a DNA binding protein that targets specific binding-sites (TFBSs) to regulate the transcript levels of its downstream genes. Thus, identifying the TF-TFBS pairs is a pivotal step in understanding the function of TFs and the regulatory network in an organism. Here, we describe two methods for predicting the TFBS of a given TF and for predicting the cognate TF of a given TFBS from a set of strongly co-expressed genes, using time-course transcriptome data of maize developing leaves.

Transcriptomic Analysis of Long Non-Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development

Long non-coding RNAs (lncRNAs) have been reported to be involved in the development of maize plant. However, few focused on seed development of maize. Here, we identified 753 lncRNA candidates in maize genome from six seed samples. Similar to the mRNAs, lncRNAs showed tissue developmental stage specific and differential expression, indicating their putative role in seed development. Increasing evidence shows that crosstalk among RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in plant development. Functional roles and regulatory mechanisms of lncRNAs as competing endogenous RNAs (ceRNA) in plants, particularly in maize seed development, are unclear. We combined analyses of consistently altered 17 lncRNAs, 840 mRNAs and known miRNA to genome-wide investigate potential lncRNA-mediated ceRNA based on “ceRNA hypothesis”. The results uncovered seven novel lncRNAs as potential functional ceRNAs. Functional analyses based on their competitive coding-gene partners by Gene Ontology (GO) and KEGG biological pathway demonstrated that combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in maize seed. These findings provided a useful platform for uncovering novel mechanisms of maize seed development and may provide opportunities for the functional characterization of individual lncRNA in future studies.

Enhancing crop yield by optimizing plant developmental features

A number of plant features and traits, such as overall plant architecture, leaf structure and morphological features, vascular architecture and flowering time are important determinants of photosynthetic efficiency and hence the overall performance of crop plants. The optimization of such developmental traits thus has great potential to increase biomass and crop yield. Here, we provide a comprehensive review of these developmental traits in crop plants, summarizing their genetic regulation and highlighting the potential of manipulating these traits for crop improvement. We also briefly review the effects of domestication on the developmental features of crop plants. Finally, we discuss the potential of functional genomics-based approaches to optimize plant developmental traits to increase yield.

Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves

High vein density, a distinctive trait of C4 leaves, is central to both C3-to-C4 evolution and conversion of C3 to C4-like crops. We tested the hypothesis that high vein density in C4 leaves is due to elevated auxin biosynthesis and transport in developing leaves. Up-regulation of genes in auxin biosynthesis pathways and higher auxin content were found in developing C4 leaves compared with developing C3 leaves. The same observation held for maize foliar (C4) and husk (C3) leaf primordia. Moreover, auxin content and vein density were increased in loss-of-function mutants of Arabidopsis MYC2, a suppressor of auxin biosynthesis. Treatment with an auxin biosynthesis inhibitor or an auxin transport inhibitor led to much fewer veins in new leaves. Finally, both Arabidopsis thaliana auxin efflux transporter pin1 and influx transporter lax2 mutants showed reduced vein numbers. Thus, development of high leaf vein density requires elevated auxin biosynthesis and transport.

Spatial Mapping and Profiling of Metabolite Distributions during Germination

Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this study, we utilize a combination of gas chromatography-mass spectrometry, liquid chromatography-fluorescence, and mass spectrometry imaging approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize (Zea mays) seeds, B73 and Mo17. Gas chromatography and liquid chromatography analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by gas chromatography-mass spectrometry analysis of polar metabolites also revealed that many compounds were highly sequestered among the various seed tissue types. To further localize compounds, matrix-assisted laser desorption/ionization mass spectrometry imaging was utilized to visualize compounds in fine detail in their native environments over the course of germination. Most notably, the fatty acyl chain-dependent differential localization of phospholipids and triacylglycerols was observed within the embryo and radicle, showing correlation with the heterogeneous distribution of fatty acids. Other interesting observations include unusual localization of ceramides on the endosperm/scutellum boundary and subcellular localization of ferulate in the aleurone.

Candidate regulators of Early Leaf Development in Maize Perturb Hormone Signalling and Secondary Cell Wall Formation When Constitutively Expressed in Rice

All grass leaves are strap-shaped with a series of parallel veins running from base to tip, but the distance between each pair of veins, and the cell-types that develop between them, differs depending on whether the plant performs C₃ or C₄ photosynthesis. As part of a multinational effort to introduce C₄ traits into rice to boost crop yield, candidate regulators of C₄ leaf anatomy were previously identified through an analysis of maize leaf transcriptomes. Here we tested the potential of 60 of those candidate genes to alter leaf anatomy in rice. In each case, transgenic rice lines were generated in which the maize gene was constitutively expressed. Lines grouped into three phenotypic classes: (1) indistinguishable from wild-type; (2) aberrant shoot and/or root growth indicating possible perturbations to hormone homeostasis; and (3) altered secondary cell wall formation. One of the genes in class 3 defines a novel monocot-specific family. None of the genes were individually sufficient to induce C₄-like vein patterning or cell-type differentiation in rice. A better understanding of gene function in C₄ plants is now needed to inform more sophisticated engineering attempts to alter leaf anatomy in C₃ plants.

Metabolomic and Proteomic Analysis of Maize Embryonic Callus induced from immature embryo

The low ratio of embryonic callus (EC) induction has inhibited the rapid development of maize genetic engineering. Still, little is known to explain the genotype-dependence of EC induction. Here, we performed a large-scale, quantitative analysis of the maize EC metabolome and proteome at three typical induction stages in two inbred lines with a range of EC induction capabilities. Comparison of the metabolomes and proteomes suggests that the differential molecular responses begin at an early stage of development and continue throughout the process of EC formation. The two inbred lines show different responses under various conditions, such as metal ion binding, cell enlargement, stem cell formation, meristematic activity maintenance, somatic embryogenesis, cell wall synthesis, and hormone signal transduction. Furthermore, the differences in hormone (auxin, cytokinin, gibberellin, salicylic acid, jasmonic acid, brassinosteroid and ethylene) synthesis and transduction ability could partially explain the higher EC induction ratio in the inbred line 18-599R. During EC formation, repression of the "histone deacetylase 2 and ERF transcription factors" complex in 18-599R activated the expression of downstream genes, which further promoted EC induction. Together, our data provide new insights into the molecular regulatory mechanism responsible for efficient EC induction in maize.

Identification and evolutionary analysis of long non-coding RNAs in zebra finch

Background

Long non-coding RNAs (lncRNAs) are important in various biological processes, but very few studies on lncRNA have been conducted in birds. To identify IncRNAs expressed during feather development, we analyzed single-stranded RNA-seq (ssRNA-seq) data from the anterior and posterior dorsal regions during zebra finch (Taeniopygia guttata) embryonic development. Using published transcriptomic data, we further analyzed the evolutionary conservation of IncRNAs in birds and amniotes.

Results

A total of 1,081 lncRNAs, including 965 intergenic lncRNAs (lincRNAs), 59 intronic lncRNAs, and 57 antisense lncRNAs (lncNATs), were identified using our newly developed pipeline. These avian IncRNAs share similar characteristics with lncRNAs in mammals, such as shorter transcript length, lower exon number, lower average expression level and less sequence conservation than mRNAs. However, the proportion of lncRNAs overlapping with transposable elements in birds is much lower than that in mammals. We predicted the functions of IncRNAs based on the enriched functions of co-expressed protein-coding genes. Clusters of lncRNAs associated with natal down development were identified. The sequences and expression levels of candidate lncRNAs that shared conserved sequences among birds were validated by qPCR in both zebra finch and chicken. Finally, we identified three highly conserved lncRNAs that may be associated with natal down development.

Conclusions

Our study provides the first systematical identification of avian lncRNAs using ssRNA-seq analysis and offers a resource of embryonically expressed lncRNAs in zebra finch. We also predicted the biological function of identified lncRNAs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3506-z) contains supplementary material, which is available to authorized users.

Transcriptome Analysis of Chilling-Imbibed Embryo Revealed Membrane Recovery Related Genes in Maize

The delayed seed germination and poor seedling growth caused by imbibitional chilling injury was common phenomenon in maize seedling establishment. In this study, RNA sequencing technology was used to comprehensively investigate the gene expressions in chilling-imbibed maize embryo and to reveal the underlying mechanism of chilling injury at molecular level. Imbibed seeds for 2 h at 5°C (LT2) were selected and transcriptomic comparative analysis was performed. Among 327 DEGs indentified between dry seed (CK0) and LT2, 15 specific genes with plasma membrane (PM) relevant functions belonging to lipid metabolism, stress, signaling and transport were characterized, and most of them showed down-regulation pattern under chilling stress. When transferred to 25°C for recovery (LT3), remarkable changes occurred in maize embryo. There were 873 DEGs including many PM related genes being identified between LT2 and LT3, some of which showing significant increase after 1 h recovery. Moreover, 15 genes encoding intracellular vesicular trafficking proteins were found to be exclusively differential expressed at recovery stage. It suggested that the intracellular vesicle trafficking might be essential for PM recovery through PM turnover. Furthermore, transcriptome analyses on imbibed embryos under normal condition (25°C) were also made as a contrast. A total of 651 DEGs were identified to mainly involved in protein metabolism, transcriptional regulation, signaling, and energy productions. Overall, the RNA-Seq results provided us a deep knowledge of imbibitional chilling injury on plasma membrane and a new view on PM repaired mechanism during early seed imbibition at transcriptional level. The DEGs identified in this work would be useful references in future seed germination research.

Transcriptome and Degradome Sequencing Reveals Dormancy Mechanisms of Cunninghamia lanceolata Seeds

Seeds with physiological dormancy usually experience primary and secondary dormancy in the nature; however, little is known about the differential regulation of primary and secondary dormancy. We combined multiple approaches to investigate cytological changes, hormonal levels, and gene expression dynamics in Cunninghamia lanceolata seeds during primary dormancy release and secondary dormancy induction. Light microscopy and transmission electron microscopy revealed that protein bodies in the embryo cells coalesced during primary dormancy release and then separated during secondary dormancy induction. Transcriptomic profiling demonstrated that expression of genes negatively regulating gibberellic acid (GA) sensitivity reduced specifically during primary dormancy release, whereas the expression of genes positively regulating abscisic acid (ABA) biosynthesis increased during secondary dormancy induction. Parallel analysis of RNA ends revealed uncapped transcripts for ∼55% of all unigenes. A negative correlation between fold changes in expression levels of uncapped versus capped mRNAs was observed during primary dormancy release. However, this correlation was loose during secondary dormancy induction. Our analyses suggest that the reversible changes in cytology and gene expression during dormancy release and induction are related to ABA/GA balance. Moreover, mRNA degradation functions as a critical posttranscriptional regulator during primary dormancy release. These findings provide a mechanistic framework for understanding physiological dormancy in seeds.

Hybrid-Cut: An Improved Sectioning Method for Recalcitrant Plant Tissue Samples

Maintaining plant section integrity is essential for studying detailed anatomical structures at the cellular, tissue, or even organ level. However, some plant cells have rigid cell walls, tough fibers and crystals (calcium oxalate, silica, etc.), and high water content that often disrupt tissue integrity during plant tissue sectioning. This study establishes a simple Hybrid-Cut tissue sectioning method. This protocol modifies a paraffin-based sectioning technique and improves the integrity of tissue sections from different plants. Plant tissues were embedded in paraffin before sectioning in a cryostat at -16 °C. Sectioning under low temperature hardened the paraffin blocks, reduced tearing and scratching, and improved tissue integrity significantly. This protocol was successfully applied to calcium oxalate-rich Phalaenopsis orchid tissues as well as recalcitrant tissues such as reproductive organs and leaves of rice, maize, and wheat. In addition, the high quality of tissue sections from Hybrid-Cut could be used in combination with in situ hybridization (ISH) to provide spatial expression patterns of genes of interest. In conclusion, this protocol is particularly useful for recalcitrant plant tissue containing high crystal or silica content. Good quality tissue sections enable morphological and other biological studies.

iTRAQ-based analysis of developmental dynamics in the soybean leaf proteome reveals pathways associated with leaf photosynthetic rate

Photosynthetic rate which acts as a vital limiting factor largely affects the potential of soybean production, especially during the senescence phase. However, the physiological and molecular mechanisms that underlying the change of photosynthetic rate during the developmental process of soybean leaves remain unclear. In this study, we compared the protein dynamics during the developmental process of leaves between the soybean cultivar Hobbit and the high-photosynthetic rate cultivar JD 17 using the iTRAQ (isobaric tags for relative and absolute quantification) method. A total number of 1269 proteins were detected in the leaves of these two cultivars at three different developmental stages. These proteins were classified into nine expression patterns depending on the expression levels at different developmental stages, and the proteins in each pattern were also further classified into three large groups and 20 small groups depending on the protein functions. Only 3.05-6.53 % of the detected proteins presented a differential expression pattern between these two cultivars. Enrichment factor analysis indicated that proteins involved in photosynthesis composed an important category. The expressions of photosynthesis-related proteins were also further confirmed by western blotting. Together, our results suggested that the reduction in photosynthetic rate as well as chloroplast activity and composition during the developmental process was a highly regulated and complex process which involved a serial of proteins that function as potential candidates to be targeted by biotechnological approaches for the improvement of photosynthetic rate and production.

The Juvenile Phase of Maize Sees Upregulation of Stress-Response Genes and Is Extended by Exogenous Jasmonic Acid

As maize (Zea mays) plants undergo vegetative phase change from juvenile to adult, they both exhibit heteroblasty, an abrupt change in patterns of leaf morphogenesis, and gain the ability to produce flowers. Both processes are under the control of microRNA156 (miR156), whose levels decline at the end of the juvenile phase. Gain of the ability to flower is conferred by the expression of miR156 targets that encode SQUAMOSA PROMOTER-BINDING transcription factors, which, when derepressed in the adult phase, induce the expression of MADS box transcription factors that promote maturation and flowering. How gene expression, including targets of those microRNAs, differs between the two phases remains an open question. Here, we compare transcript levels in primordia that will develop into juvenile or adult leaves to identify genes that define these two developmental states and may influence vegetative phase change. In comparisons among successive leaves at the same developmental stage, plastochron 6, three-fourths of approximately 1,100 differentially expressed genes were more highly expressed in primordia of juvenile leaves. This juvenile set was enriched in photosynthetic genes, particularly those associated with cyclic electron flow at photosystem I, and in genes involved in oxidative stress and retrograde redox signaling. Pathogen- and herbivory-responsive pathways including salicylic acid and jasmonic acid also were up-regulated in juvenile primordia; indeed, exogenous application of jasmonic acid delayed both the appearance of adult traits and the decline in the expression of miR156-encoding loci in maize seedlings. We hypothesize that the stresses associated with germination promote juvenile patterns of differentiation in maize.

Engineering C4 photosynthesis into C3 chassis in the synthetic biology age

C4 photosynthetic plants outperform C3 plants in hot and arid climates. By concentrating carbon dioxide around Rubisco C4 plants drastically reduce photorespiration. The frequency with which plants evolved C4 photosynthesis independently challenges researchers to unravel the genetic mechanisms underlying this convergent evolutionary switch. The conversion of C3 crops, such as rice, towards C4 photosynthesis is a long-standing goal. Nevertheless, at the present time, in the age of synthetic biology, this still remains a monumental task, partially because the C4 carbon-concentrating biochemical cycle spans two cell types and thus requires specialized anatomy. Here we review the advances in understanding the molecular basis and the evolution of the C4 trait, advances in the last decades that were driven by systems biology methods. In this review we emphasise essential genetic engineering tools needed to translate our theoretical knowledge into engineering approaches. With our current molecular understanding of the biochemical C4 pathway, we propose a simplified rational engineering model exclusively built with known C4 metabolic components. Moreover, we discuss an alternative approach to the progressing international engineering attempts that would combine targeted mutagenesis and directed evolution.

RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus

Background

Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression.

Results

RNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson’s correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches.

Conclusions

Dynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important in clarifying the molecular mechanisms associated with the development of SUS in sea cucumber.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2810-3) contains supplementary material, which is available to authorized users.

Finding the genes to build C4 rice

Rice, a C3 crop, is a staple food for more than half of the world's population, with most consumers living in developing countries. Engineering C4 photosynthetic traits into rice is increasingly suggested as a way to meet the 50% yield increase that is predicted to be needed by 2050. Advances in genome-wide deep-sequencing, gene discovery and genome editing platforms have brought the possibility of engineering a C3 to C4 conversion closer than ever before. Because C4 plants have evolved independently multiple times from C3 origins, it is probably that key genes and gene regulatory networks that regulate C4 were recruited from C3 ancestors. In the past five years there have been over 20 comparative transcriptomic studies published that aimed to identify these recruited C4 genes and regulatory mechanisms. Here we present an overview of what we have learned so far and preview the efforts still needed to provide a practical blueprint for building C4 rice.