Genetic and biochemical evidence for involvement of HOTHEAD in the biosynthesis of long-chain alpha-,omega-dicarboxylic fatty acids and formation of extracellular matrix

The Arabidopsis cytochrome P450 enzyme CYP96A4 is involved in the wound-induced biosynthesis of cuticular wax and cutin monomers

The plant cuticle is composed of cuticular wax and cutin polymers and plays an essential role in plant tolerance to diverse abiotic and biotic stresses. Several stresses, including water deficit and salinity, regulate the synthesis of cuticular wax and cutin monomers. However, the effect of wounding on wax and cutin monomer production and the associated molecular mechanisms remain unclear. In this study, we determined that the accumulation of wax and cutin monomers in Arabidopsis leaves is positively regulated by wounding primarily through the jasmonic acid (JA) signaling pathway. Moreover, we observed that a wound- and JA-responsive gene (CYP96A4) encoding an ER-localized cytochrome P450 enzyme was highly expressed in leaves. Further analyses indicated that wound-induced wax and cutin monomer production was severely inhibited in the cyp96a4 mutant. Furthermore, CYP96A4 interacted with CER1 and CER3, the core enzymes in the alkane-forming pathway associated with wax biosynthesis, and modulated CER3 activity to influence aldehyde production in wax synthesis. In addition, transcripts of MYC2 and JAZ1, key genes in JA signaling pathway, were significantly reduced in cyp96a4 mutant. Collectively, these findings demonstrate that CYP96A4 functions as a cofactor of the alkane synthesis complex or participates in JA signaling pathway that contributes to cuticular wax biosynthesis and cutin monomer formation in response to wounding.

La2O3 Nanoparticles Can Cause Cracking of Tomato Fruit through Genetic Reconstruction

La2O3 nanoparticles (NPs) have shown great potential in agriculture, but cracking of plant sensitive tissue could occur during application, resulting in a poor appearance, facilitating entry for insects and fungi, and increasing economic losses. Herein, exocarp cracking mechanisms of tomato (Solanum lycopersicum L.) fruit in response to La2O3 NPs were investigated. Tomato plants were exposed to La2O3 NPs (0-40 mg/L, 90 days) by a split-root system under greenhouse condition. La2O3 NPs with high concentrations (25 and 40 mg/L) increased the obvious cracking of the fruit exocarp by 20.0 and 22.7%, respectively. After exposure to 25 mg/L La2O3 NPs, decreased thickness of the cuticle and cell wall and lower wax crystallization patterns of tomato fruit exocarp were observed. Biomechanical properties (e.g., firmness and stiffness) of fruit exocarp were decreased by 34.7 and 25.9%, respectively. RNA-sequencing revealed that the thinner cuticle was caused by the downregulation of cuticle biosynthesis related genes; pectin remodeling, including the reduction in homogalacturonan (e.g., LOC101264880) and rhamnose (e.g., LOC101248505), was responsible for the thinner cell wall. Additionally, genes related to water and abscisic acid homeostasis were significantly upregulated, causing the increases of water and soluble solid content of fruit and elevated fruit inner pressure. Therefore, the thinner fruit cuticle and cell wall combined with the higher inner pressure caused fruit cracking. This study improves our understanding of nanomaterials on important agricultural crops, including the structural reconstruction of fruit exocarp contributing to NPs-induced cracking at the molecular level.

Comparative morphoanatomy and transcriptomic analyses reveal key factors controlling floral trichome development in Aristolochia (Aristolochiaceae)

Trichomes are specialized epidermal cells in aerial plant parts. Trichome development proceeds in three stages, determination of cell fate, specification, and morphogenesis. Most genes responsible for these processes have been identified in the unicellular branched leaf trichomes from the model Arabidopsis thaliana. Less is known about the molecular basis of multicellular trichome formation across flowering plants, especially those formed in floral organs of early diverging angiosperms. Here, we aim to identify the genetic regulatory network (GRN) underlying multicellular trichome development in the kettle-shaped trap flowers of Aristolochia (Aristolochiaceae). We selected two taxa for comparison, A. fimbriata, with trichomes inside the perianth, which play critical roles in pollination, and A. macrophylla, lacking specialized trichomes in the perianth. A detailed morphoanatomical characterization of floral epidermis is presented for the two species. We compared transcriptomic profiling at two different developmental stages in the different perianth portions (limb, tube, and utricle) of the two species. Moreover, we present a comprehensive expression map for positive regulators and repressors of trichome development, as well as cell cycle regulators. Our data point to extensive modifications in gene composition, expression, and putative roles in all functional categories when compared with model species. We also record novel differentially expressed genes (DEGs) linked to epidermis patterning and trichome development. We thus propose the first hypothetical genetic regulatory network (GRN) underlying floral multicellular trichome development in Aristolochia, and pinpoint key factors responsible for the presence and specialization of floral trichomes in phylogenetically distant species of the genus.

Secretome analysis revealed that cell wall remodeling and starch catabolism underlie the early stages of somatic embryogenesis in Pinus nigra

Somatic embryogenesis is an efficient mean for rapid micropropagation and preservation of the germplasm of valuable coniferous trees. Little is known about how the composition of secretome tracks down the level of embryogenic capacity. Unlike embryogenic tissue on solid medium, suspension cell cultures enable the study of extracellular proteins secreted into a liquid cultivation medium, avoiding contamination from destructured cells. Here, we present proteomic data of the secretome of Pinus nigra cell lines with contrasting embryogenic capacity, accounting for variability between genotypes. Our results showed that cell wall-related and carbohydrate-acting proteins were the most differentially accumulated. Peroxidases, extensin, α-amylase, plant basic secretory family protein (BSP), and basic secretory protease (S) were more abundant in the medium from the lines with high embryogenic capacity. In contrast, the medium from the low embryogenic capacity cell lines contained a higher amount of polygalacturonases, hothead protein, and expansin, which are generally associated with cell wall loosening or softening. These results corroborated the microscopic findings in cell lines with low embryogenic capacity-long suspensor cells without proper assembly. Furthermore, proteomic data were subsequently validated by peroxidase and α-amylase activity assays, and hence, we conclude that both tested enzyme activities can be considered potential markers of high embryogenic capacity.

Microscopic and metabolic investigations disclose the factors that lead to skin cracking in chili-type pepper fruit varieties

The hydrophobic cuticle encasing the fruit skin surface plays critical roles during fruit development and post-harvest. Skin failure often results in the fruit surface cracking and forming a wound-periderm tissue made of suberin and lignin. The factors that make the fruit skin susceptible to cracking have yet to be fully understood. Herein, we investigated two varieties of chili peppers (Capsicum annuum L.), Numex Garnet, whose fruit has intact skin, and Vezena Slatka, whose fruit has cracked skin. Microscopical observations, gas chromatography-mass spectrometry, biochemical and gene expression assays revealed that Vezena Slatka fruit form a thicker cuticle with greater levels of cutin monomers and hydroxycinnamic acids, and highly express key cutin-related genes. The skin of these fruit also had a lower epidermal cell density due to cells with very large perimeters, and highly express genes involved in epidermal cell differentiation. We demonstrate that skin cracking in the Vezena Slatka fruit is accompanied by a spatial accumulation of lignin-like polyphenolic compounds, without the formation of a typical wound-periderm tissues made of suberized cells. Lastly, we establish that skin cracking in chili-type pepper significantly affects fruit quality during post-harvest storage in a temperature-dependent manner. In conclusion, our data highlight cuticle thickness and epidermal cell density as two critical factors determining fruit skin susceptibility to cracking in chili-type pepper fruit.

Whole-transcriptome profiles of Chrysanthemum seticuspe improve genome annotation and shed new light on mRNA-miRNA-lncRNA networks in ray florets and disc florets

BACKGROUND

Chrysanthemum seticuspe has emerged as a model plant species of cultivated chrysanthemums, especially for studies involving diploid and self-compatible pure lines (Gojo-0). Its genome was sequenced and assembled into chromosomes. However, the genome annotation of C. seticuspe still needs to be improved to elucidate the complex regulatory networks in this species.

RESULTS

In addition to the 74,259 mRNAs annotated in the C. seticuspe genome, we identified 18,265 novel mRNAs, 51,425 novel lncRNAs, 501 novel miRNAs and 22,065 novel siRNAs. Two C-class genes and YABBY family genes were highly expressed in disc florets, while B-class genes were highly expressed in ray florets. A WGCNA was performed to identify the hub lncRNAs and mRNAs in ray floret- and disc floret-specific modules, and CDM19, BBX22, HTH, HSP70 and several lncRNAs were identified. ceRNA and lncNAT networks related to flower development were also constructed, and we found a latent functional lncNAT-mRNA combination, LXLOC_026470 and MIF2.

CONCLUSIONS

The annotations of mRNAs, lncRNAs and small RNAs in the C. seticuspe genome have been improved. The expression profiles of flower development-related genes, ceRNA networks and lncNAT networks were identified, laying a foundation for elucidating the regulatory mechanisms underlying disc floret and ray floret formation.

ALDH2C4 regulates cuticle thickness and reduces water loss to promote drought tolerance

In Arabidopsis thaliana, ALDH2C4 encodes coniferaldehyde dehydrogenase, which oxidizes coniferaldehyde to ferulic acid. Drought stress is one of the important abiotic stresses affecting plant growth. However, the role of ferulic acid in drought resistance is unknown. To investigate the contribution of ferulic acid to cuticle composition and drought resistance, we used two Arabidopsis aldh2c4 mutant lines. Compared with wild-type (WT) leaves, ferulic acid contents were significantly lower (by more than 50 %) in mutants. The mutants also had lower amounts of cutin and wax, primarily due to reductions in C_18:2 dioic acid and alkanes, respectively. Furthermore, the leaves of the mutant plants exhibited greater rates of water loss and released chlorophyll faster than WT leaves when immersed in 80 % ethanol, indicating a defective cuticle barrier. The growth of aldh2c4 mutants was severely inhibited, and their leaves showed a higher degree of wilting relative to the WT plants under drought conditions. In aldh2c4 complementation lines, the growth inhibition of the mutant plants under drought stress was alleviated. Taken together, our results demonstrate that ferulic acid plays an important role in the composition and structural properties of the cuticle and that a ferulic acid deficiency in the cutin leads to reduced drought tolerance.

Mutation of glucose-methanol-choline oxidoreductase leads to thermosensitive genic male sterility in rice and Arabidopsis

Thermosensitive genic male sterility (TGMS) lines serve as the major genetic resource for two-line hybrid breeding in rice. However, their unstable sterility under occasional low temperatures in summer highly limits their application. In this study, we identified a novel rice TGMS line, ostms18, of cultivar ZH11 (Oryza sativa ssp. japonica). ostms18 sterility is more stable in summer than the TGMS line carrying the widely used locus tms5 in the ZH11 genetic background, suggesting its potential application for rice breeding. The ostms18 TGMS trait is caused by the point mutation from Gly to Ser in a glucose-methanol-choline (GMC) oxidoreductase; knockout of the oxidoreductase was previously reported to cause complete male sterility. Cellular analysis revealed the pollen wall of ostms18 to be defective, leading to aborted pollen under high temperature. Further analysis showed that the tapetal transcription factor OsMS188 directly regulates OsTMS18 for pollen wall formation. Under low temperature, the flawed pollen wall in ostms18 is sufficient to protect its microspore, allowing for development of functional pollen and restoring fertility. We identified the orthologous gene in Arabidopsis. Although mutants for the gene were fertile under normal conditions (24°C), fertility was significantly reduced under high temperature (28°C), exhibiting a TGMS trait. A cellular mechanism integrated with genetic mutations and different plant species for fertility restoration of TGMS lines is proposed.

Impact of water deficiency on leaf cuticle lipids and gene expression networks in cotton (Gossypium hirsutum L.)

BACKGROUND

Water deficit (WD) has serious effect on the productivity of crops. Formation of cuticular layer with increased content of wax and cutin on leaf surfaces is closely related to drought tolerance. Identification of drought tolerance associated wax components and cutin monomers and the genes responsible for their biosynthesis is essential for understanding the physiological and genetic mechanisms underlying drought tolerance and improving crop drought resistance.

RESULT

In this study, we conducted comparative phenotypic and transcriptomic analyses of two Gossypium hirsutum varieties that are tolerant (XL22) or sensitive (XL17) to drought stress. XL17 consumed more water than XL22, particularly under the WD conditions. WD significantly induced accumulation of most major wax components (C29 and C31 alkanes) and cutin monomers (palmitic acid and stearic acid) in leaves of both XL22 and XL17, although accumulation of the major cutin monomers, i.e., polyunsaturated linolenic acid (C18:3n-3) and linoleic acid (C18:2n-6), were significantly repressed by WD in both XL22 and XL17. According to the results of transcriptome analysis, although many genes and their related pathways were commonly induced or repressed by WD in both XL22 and XL17, WD-induced differentially expressed genes specific to XL22 or XL17 were also evident. Among the genes that were commonly induced by WD were the GhCER1 genes involved in biosynthesis of alkanes, consistent with the observation of enhanced accumulation of alkanes in cotton leaves under the WD conditions. Interestingly, under the WD conditions, several GhCYP86 genes, which encode enzymes catalyzing the omega-hydroxylation of fatty acids and were identified to be the hub genes of one of the co-expression gene modules, showed a different expression pattern between XL22 and XL17 that was in agreement with the WD-induced changes of the content of hydroxyacids or fatty alcohols in these two varieties.

CONCLUSION

The results contribute to our comprehending the physiological and genetic mechanisms underlying drought tolerance and provide possible solutions for the difference of drought resistance of different cotton varieties.

The making of suberin

Outer protective barriers of animals use a variety of bio-polymers, based on either proteins (e.g. collagens), or modified sugars (e.g. chitin). Plants, however, have come up with a particular solution, based on the polymerisation of lipid-like precursors, giving rise to cutin and suberin. Suberin is a structural lipophilic polyester of fatty acids, glycerol and some aromatics found in cell walls of phellem, endodermis, exodermis, wound tissues, abscission zones, bundle sheath and other tissues. It deposits as a hydrophobic layer between the (ligno)cellulosic primary cell wall and plasma membrane. Suberin is highly protective against biotic and abiotic stresses, shows great developmental plasticity and its chemically recalcitrant nature might assist the sequestration of atmospheric carbon by plants. The aim of this review is to integrate the rapidly accelerating genetic and cell biological discoveries of recent years with the important chemical and structural contributions obtained from very diverse organisms and tissue layers. We critically discuss the order and localisation of the enzymatic machinery synthesising the presumed substrates for export and apoplastic polymerisation. We attempt to explain observed suberin linkages by diverse enzyme activities and discuss the spatiotemporal relationship of suberin with lignin and ferulates, necessary to produce a functional suberised cell wall.

Fatty alcohol oxidase 3 (FAO3) and FAO4b connect the alcohol- and alkane-forming pathways in Arabidopsis stem wax biosynthesis

The alcohol- and alkane-forming pathways in cuticular wax biosynthesis are well characterized in Arabidopsis. However, potential interactions between the two pathways remain unclear. Here, we reveal that mutation of CER4, the key gene in the alcohol-forming pathway, also led to a deficiency in the alkane-forming pathway in distal stems. To trace the connection between the two pathways, we characterized two homologs of fatty alcohol oxidase (FAO), FAO3 and FAO4b, which were highly expressed in distal stems and localized to the endoplasmic reticulum. The amounts of waxes from the alkane-forming pathway were significantly decreased in stems of fao4b and much lower in fao3 fao4b plants, indicative of an overlapping function for the two proteins in wax synthesis. Additionally, overexpression of FAO3 and FAO4b in Arabidopsis resulted in a dramatic reduction of primary alcohols and significant increases of aldehydes and related waxes. Moreover, expressing FAO3 or FAO4b led to significantly decreased amounts of C18-C26 alcohols in yeast co-expressing CER4 and FAR1. Collectively, these findings demonstrate that FAO3 and FAO4b are functionally redundant in suppressing accumulation of primary alcohols and contributing to aldehyde production, which provides a missing and long-sought-after link between these two pathways in wax biosynthesis.

Stocky1, a Novel Gene Involved in Maize Seedling Development and Cuticle Integrity

The cuticle is the plant’s outermost layer that covers the surfaces of aerial parts. This structure is composed of a variety of aliphatic molecules and is well-known for its protective role against biotic and abiotic stresses in plants. Mutants with a permeable cuticle show developmental defects such as organ fusions and altered seed germination and viability. In this study, we identified a novel maize mutant, stocky1, with unique features: lethal at the seedling stage, and showing a severely dwarfed phenotype, due to a defective cuticle. For the first time, the mutant was tentatively mapped to chromosome 5, bin 5.04. The mutant phenotype investigated in this work has the potential to contribute to the elucidation of the role of the cuticle during plant development. The possibility of controlling this trait is of relevance in the context of climate change, as it may contribute to tolerance to abiotic stresses.

Transcriptomic Insights on the Preventive Action of Apple (cv Granny Smith) Skin Wounding on Superficial Scald Development

Superficial scald is a post-harvest chilling storage injury leading to browning of the surface of the susceptible cv Granny Smith apples. Wounding of skins has been reported to play a preventive role on scald development however its underlying molecular factors are unknown. We have artificially wounded the epidermal and sub-epidermal layers of apple skins consistently obtaining the prevention of superficial scald in the surroundings of the wounds during two independent vintages. Time course RNA-Seq analyses of the transcriptional changes in wounded versus unwounded skins revealed that two transcriptional waves occurred. An early wave included genes up-regulated by wounding already after 6 h, highlighting a specific transcriptional rearrangement of genes connected to the biosynthesis and signalling of JA, ethylene and ABA. A later transcriptional wave, occurring after three months of cold storage, included genes up-regulated exclusively in unwounded skins and was prevented from its occurrence in wounded skins. A significant portion of these genes was related to decay of tissues and to the senescence hormones ABA, JA and ethylene. Such changes suggest a wound-inducible reversed hormonal balance during post-harvest storage which may explain the local inhibition of scald in wounded tissues, an aspect that will need further studies for its mechanistic explanation.

The jojoba genome reveals wide divergence of the sex chromosomes in a dioecious plant

Most flowering plants are hermaphrodites, but around 6% of species are dioecious, having separate male and female plants. Sex chromosomes and some sex-specific genes have been reported in plants, but the genome sequences have not been compared. We now report the genome sequence of male and female jojoba (Simmondsia chinensis) plants, revealing a very large difference in the sex chromosomes. The male genome assembly was 832 Mb and the female 822 Mb. This was explained by the large size differences in the Y chromosome (37.6 Mb) compared with the X chromosome (26.9 Mb). Relative to the X chromosome, the Y chromosome had two large insertions each of more than 5 Mb containing more than 400 genes. Many of the genes in the chromosome-specific regions were novel. These male-specific regions included many flowering-related and stress response genes. Smaller insertions found only in the X chromosome totalled 877 kb. The wide divergence of the sex chromosomes suggests a long period of adaptation to diverging sex-specific roles. Male and female plants may have evolved to accommodate factors such as differing reproductive resource allocation requirements under the stress of the desert environment in which the plants are found. The sex-determining regions accumulate genes beneficial to each sex. This has required the evolution of many more novel sex-specific genes than has been reported for other organisms. This suggest that dioecious plants provide a novel source of genes for manipulation of reproductive performance and environmental adaptation in crops.

The bHLH transcription factor regulated gene OsWIH2 is a positive regulator of drought tolerance in rice

Drought is a major abiotic stress limiting crop growth and yield. In this study, we characterized a novel drought tolerance induced WIH gene in rice, OsWIH2. Overexpression of OsWIH2 in rice resulted in significantly higher drought tolerance, probably due to the decreased water loss rate and reactive oxygen species (ROS) accumulation under drought stress. We identified a long-chain fatty acid HOTHEAD (HTH) that interacted with OsWIH2 using yeast two-hybrid screening. OsWIH2 is an enzyme which is involved in fatty acid synthesis. We further demonstrated that the drought-inducible bHLH transcription factor OsbHLH130 could activate the expression of OsWIH2. Overall, our results suggest that drought stress may induce OsbHLH130 accumulation, which in turn activates OsWIH2 expression, and the latter improves rice drought tolerance by participating in cuticular wax biosynthesis and reducing the water loss rate as well as ROS accumulation. This research provides new genes for crop improvement.

Evolutionary insight of plant cuticle biosynthesis in bryophytes

As an adaptive innovation in plant terrestrialization, cuticle covers the plant surface and greatly contributes to the development and stress tolerance in land plants. Although past decades have seen great progress in understanding the molecular mechanism of cuticle biosynthesis in flowering plants with the contribution of cuticle biosynthesis mutants and advanced cuticle composition profiling techniques, origins and evolution of cuticle biosynthesis are poorly understood. Recent chemical, phylogenomic, and molecular genetic studies on cuticle biosynthesis in early-diverging extant land plant lineages, the bryophytes, shed novel light on the origins and evolution of plant cuticle biosynthesis. In this mini-review, we highlighted these recent advances in the molecular biology of cuticle biosynthesis in bryophytes, and provided evolutionary insights into plant cuticle biosynthesis.

High-resolution spatiotemporal transcriptome analyses during cellularization of rice endosperm unveil the earliest gene regulation critical for aleurone and starchy endosperm cell fate specification

The major tissues of the cereal endosperm are the starchy endosperm (SE) in the inner and the aleurone layer (AL) at the outer periphery. The fates of the cells that comprise these tissues are determined according to positional information; however, our understanding of the underlying molecular mechanisms remains limited. Here, we conducted a high-resolution spatiotemporal analysis of the rice endosperm transcriptome during early cellularization. In rice, endosperm cellularization proceeds in a concentric pattern from a primary alveolus cell layer, such that developmental progression can be defined by the number of cell layers. Using laser-capture microdissection to obtain precise tissue sections, transcriptomic changes were followed through five histologically defined stages of cellularization from the syncytial to 3-cell layer (3 L) stage. In addition, transcriptomes were compared between the inner and the outermost peripheral cell layers. Large differences in the transcriptomes between stages and between the inner and the peripheral cells were found. SE attributes were expressed at the alveolus-cell-layer stage but were preferentially activated in the inner cell layers that resulted from periclinal division of the alveolus cell layer. Similarly, AL attributes started to be expressed only after the 2 L stage and were localized to the outermost peripheral cell layer. These results indicate that the first periclinal division of the alveolus cell layer is asymmetric at the transcriptome level, and that the cell-fate-specifying positional cues and their perception system are already operating before the first periclinal division. Several genes related to epidermal identity (i.e., type IV homeodomain-leucine zipper genes and wax biosynthetic genes) were also found to be expressed at the syncytial stage, but their expression was localized to the outermost peripheral cell layer from the 2 L stage onward. We believe that our findings significantly enhance our knowledge of the mechanisms underlying cell fate specification in rice endosperm.

Dual species dynamic transcripts reveal the interaction mechanisms between Chrysanthemum morifolium and Alternaria alternata

BACKGROUND

Chrysanthemum (Chrysanthemum morifolium) black spot disease caused by Alternaria alternata is one of the plant's most destructive diseases. Dual RNA-seq was performed to simultaneously assess their transcriptomes to analyze the potential interaction mechanism between the two species, i.e., host and pathogen.

RESULTS

C. morifolium and A. alternata were subjected to dual RNA-seq at 1, 12, and 24 h after inoculation, and differential expression genes (DEGs) in both species were identified. This analysis confirmed 153,532 DEGs in chrysanthemum and 14,932 DEGs in A. alternata, which were involved in plant-fungal interactions and phytohormone signaling. Fungal DEGs such as toxin synthesis related enzyme and cell wall degrading enzyme genes played important roles during chrysanthemum infection. Moreover, a series of key genes highly correlated with the early, middle, or late infection stage were identified, together with the regulatory network of key genes annotated in the Plant Resistance Genes database (PRGdb) or Pathogen-Host Interactions database (PHI-base). Highly correlated genes were identified at the late infection stage, expanding our understanding of the interplay between C. morifolium and A. alternata. Additionally, six DEGs each from chrysanthemum and A. alternata were selected for quantitative real-time PCR (qRT-PCR) assays to validate the RNA-seq output.

CONCLUSIONS

Collectively, data obtained in this study enriches the resources available for research into the interactions that exist between chrysanthemum and A. alternata, thereby providing a theoretical basis for the development of new chrysanthemum cultivars with resistance to pathogen.

The Plant Cuticle: An Ancient Guardian Barrier Set Against Long-Standing Rivals

The aerial surfaces of plants are covered by a protective barrier formed by the cutin polyester and waxes, collectively referred to as the cuticle. Plant cuticles prevent the loss of water, regulate transpiration, and facilitate the transport of gases and solutes. As the cuticle covers the outermost epidermal cell layer, it also acts as the first line of defense against environmental cues and biotic stresses triggered by a large array of pathogens and pests, such as fungi, bacteria, and insects. Numerous studies highlight the cuticle interface as the site of complex molecular interactions between plants and pathogens. Here, we outline the multidimensional roles of cuticle-derived components, namely, epicuticular waxes and cutin monomers, during plant interactions with pathogenic fungi. We describe how certain wax components affect various pre-penetration and infection processes of fungi with different lifestyles, and then shift our focus to the roles played by the cutin monomers that are released from the cuticle owing to the activity of fungal cutinases during the early stages of infection. We discuss how cutin monomers can activate fungal cutinases and initiate the formation of infection organs, the significant impacts of cuticle defects on the nature of plant-fungal interactions, along with the possible mechanisms raised thus far in the debate on how host plants perceive cutin monomers and/or cuticle defects to elicit defense responses.

Tomato protein phosphatase 2C influences the onset of fruit ripening and fruit glossiness

Abscisic acid (ABA) plays a vital role in coordinating physiological processes during fresh fruit ripening. Binding of ABA to receptors facilitates the interaction and inhibition of type 2C phosphatase (PP2C) co-receptors. However, the exact mechanism of PP2C during fruit ripening is unclear. In this study, we determined the role of the tomato ABA co-receptor type 2C phosphatase SlPP2C3, a negative regulator of ABA signaling and fruit ripening. SlPP2C3 selectively interacted with monomeric ABA receptors and SlSnRK2.8 kinase in both yeast and tobacco epidermal cells. Expression of SlPP2C3 was ABA-inducible, which was negatively correlated with fruit ripening. Tomato plants with suppressed SlPP2C3 expression exhibited enhanced sensitivity to ABA, while plants overexpressing SlPP2C3 were less sensitive to ABA. Importantly, lack of SlPP2C3 expression accelerated the onset of fruit ripening and affected fruit glossiness by altering the outer epidermis structure. There was a significant difference in the expression of cuticle-related genes in the pericarp between wild-type and SlPP2C3-suppressed lines based on RNA sequencing (RNA-seq) analysis. Taken together, our findings demonstrate that SlPP2C3 plays an important role in the regulation of fruit ripening and fruit glossiness in tomato.

Differential expression of SlKLUH controlling fruit and seed weight is associated with changes in lipid metabolism and photosynthesis-related genes

The sizes of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the locus fw3.2, an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affect organ size is poorly understood. We found that higher expression of SlKLUH increased cell proliferation in the pericarp within 5 d post-anthesis in tomato near-isogenic lines. Differential gene expression analyses showed that lower expression of SlKLUH was associated with increased expression of genes involved in lipid metabolism. Lipidomic analysis revealed that repression of SlKLUH mainly increased the contents of certain non-phosphorus glycerolipids and phospholipids and decreased the contents of four unknown lipids. Co-expression network analyses revealed that lipid metabolism was possibly associated with but not directly controlled by SlKLUH, and that this gene instead controls photosynthesis-related processes. In addition, many transcription factors putatively involved in the KLUH pathway were identified. Collectively, we show that SlKLUH regulates fruit and seed weight which is associated with altered lipid metabolism. The results expand our understanding of fruit and seed weight regulation and offer a valuable resource for functional studies of candidate genes putatively involved in regulation of organ size in tomato and other crops.

The kinase module of the Mediator complex: an important signalling processor for the development and survival of plants

Mediator, a multisubunit protein complex, is a signal processor that conveys regulatory information from transcription factors to RNA polymerase II and therefore plays an important role in the regulation of gene expression. This megadalton complex comprises four modules, namely, the head, middle, tail, and kinase modules. The first three modules form the core part of the complex, whereas association of the kinase module is facultative. The kinase module is able to alter the function of Mediator and has been established as a major transcriptional regulator of numerous developmental and biochemical processes. The kinase module consists of MED12, MED13, CycC, and kinase CDK8. Upon association with Mediator, the kinase module can alter its structure and function dramatically. In the past decade, research has established that the kinase module is very important for plant growth and development, and in the fight against biotic and abiotic challenges. However, there has been no comprehensive review discussing these findings in detail and depth. In this review, we survey the regulation of kinase module subunits and highlight their many functions in plants. Coordination between the subunits to process different signals for optimum plant growth and development is also discussed.

Study of micro-trichome (mict) reveals novel connections between transcriptional regulation of multicellular trichome development and specific metabolism in cucumber

Trichomes that cover the epidermis of aerial plant organs play multiple roles in plant protection. Compared with a unicellular trichome in model plants, the development mechanism of the multicellular trichome is largely unclear. Notably, variations in trichome development are often accompanied by defects in the biosynthesis of cuticle and secondary metabolites; however, major questions about the interactions between developmental differences in trichomes and defects in metabolic pathways remain unanswered. Here, we characterized the glabrous mutant mict/csgl1/cstbh via combined metabolomic and transcriptomic analyses to extend our limited knowledge regarding multicellular trichome development and metabolism in cucumber. Mict was found to be explicitly expressed within trichome cells. Transcriptomic analysis indicated that genes involved in flavonoid and cuticle metabolism are significantly downregulated in mict mutants. Further metabolomic analysis confirmed that flavonoids, lipids, and cuticle compositions are dramatically altered in mict mutants. Additional studies revealed that Mict regulates flavonoid, lipid, and cuticle biosynthesis by likely directly binding to downstream functional genes, such as CsTT4, CsFLS1, CsCER26, and CsMYB36. These findings suggest that specific metabolic pathways (e.g., flavonoids and cuticle components) are co-regulated by Mict and provide insights into transcriptional regulation mechanisms of multicellular trichome development and its specific metabolism in cucumber.

The FUSED LEAVES1-ADHERENT1 regulatory module is required for maize cuticle development and organ separation

All aerial epidermal cells in land plants are covered by the cuticle, an extracellular hydrophobic layer that provides protection against abiotic and biotic stresses and prevents organ fusion during development. Genetic and morphological analysis of the classic maize adherent1 (ad1) mutant was combined with genome-wide binding analysis of the maize MYB transcription factor FUSED LEAVES1 (FDL1), coupled with transcriptional profiling of fdl1 mutants. We show that AD1 encodes an epidermally-expressed 3-KETOACYL-CoA SYNTHASE (KCS) belonging to a functionally uncharacterized clade of KCS enzymes involved in cuticular wax biosynthesis. Wax analysis in ad1 mutants indicates that AD1 functions in the formation of very-long-chain wax components. We demonstrate that FDL1 directly binds to CCAACC core motifs present in AD1 regulatory regions to activate its expression. Over 2000 additional target genes of FDL1, including many involved in cuticle formation, drought response and cell wall organization, were also identified. Our results identify a regulatory module of cuticle biosynthesis in maize that is conserved across monocots and eudicots, and highlight previously undescribed factors in lipid metabolism, transport and signaling that coordinate organ development and cuticle formation.

A comparative UHPLC-Q/TOF-MS-based eco-metabolomics approach reveals temperature adaptation of four Nepenthes species

Nepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifically in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the different Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco-metabolomics approach to identify temperature stressed individual metabolic fingerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafflesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards different geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fingerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecific responses and adaptation of N. rafflesiana and N. northiana likely reflected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafflesiana, to produce metabolites needed to deal with increased temperatures, offering hope for the plant genus and future adaption in times of changing climate.

Phylogeny and Structure of Fatty Acid Photodecarboxylases and Glucose-Methanol-Choline Oxidoreductases

Glucose-methanol-choline (GMC) oxidoreductases are a large and diverse family of flavin-binding enzymes found in all kingdoms of life. Recently, a new related family of proteins has been discovered in algae named fatty acid photodecarboxylases (FAPs). These enzymes use the energy of light to convert fatty acids to the corresponding Cn-1 alkanes or alkenes, and hold great potential for biotechnological application. In this work, we aimed at uncovering the natural diversity of FAPs and their relations with other GMC oxidoreductases. We reviewed the available GMC structures, assembled a large dataset of GMC sequences, and found that one active site amino acid, a histidine, is extremely well conserved among the GMC proteins but not among FAPs, where it is replaced with alanine. Using this criterion, we found several new potential FAP genes, both in genomic and metagenomic databases, and showed that related bacterial, archaeal and fungal genes are unlikely to be FAPs. We also identified several uncharacterized clusters of GMC-like proteins as well as subfamilies of proteins that lack the conserved histidine but are not FAPs. Finally, the analysis of the collected dataset of potential photodecarboxylase sequences revealed the key active site residues that are strictly conserved, whereas other residues in the vicinity of the flavin adenine dinucleotide (FAD) cofactor and in the fatty acid-binding pocket are more variable. The identified variants may have different FAP activity and selectivity and consequently may prove useful for new biotechnological applications, thereby fostering the transition from a fossil carbon-based economy to a bio-economy by enabling the sustainable production of hydrocarbon fuels.

Occurrence of land-plant-specific glycerol-3-phosphate acyltransferases is essential for cuticle formation and gametophore development in Physcomitrella patens

During the evolution of land plants from aquatic to terrestrial environments, their aerial surfaces were surrounded by cuticle composed of cutin and cuticular waxes to protect them from environmental stresses. Glycerol-3-phosphate acyltransferase (GPAT) harboring bifunctional sn-2 acyltransferase/phosphatase activity produces 2-monoacylglycerol, a precursor for cutin synthesis. Here, we report that bifunctional sn-2 GPATs play roles in cuticle biosynthesis and gametophore development of Physcomitrella patens. Land plant-type cuticle was observed in gametophores but not in protonema. The expression of endoplasmic reticulum-localized PpGPATs was significantly upregulated in gametophores compared with protonema. Floral organ fusion and permeable cuticle phenotypes of Arabidopsis gpat6-2 petals were rescued to the wild type (WT) by the expression of PpGPAT2 or PpGPAT4. Disruption of PpGPAT2 and PpGPAT4 caused a significant reduction of total cutin loads, and a prominent decrease in the levels of palmitic and 10,16-dihydroxydecanoic acids, which are major cutin monomers in gametophores. Δppgpat2 mutants displayed growth retardation, delayed gametophore development, increased cuticular permeability, and reduced tolerance to drought, osmotic and salt stresses compared to the WT. Genome-wide analysis of genes encoding acyltransferase or phosphatase domains suggested that the occurrence of sn-2 GPATs with both domains may be a key event in cuticle biogenesis of land plants.

The quality of barley husk-caryopsis adhesion is not correlated with caryopsis cuticle permeability

Adhesion of the barley husk to the underlying caryopsis requires the development of a cuticular cementing layer on the caryopsis surface. Differences in adhesion quality among genotypes have previously been correlated with cementing layer composition, which is thought to influence caryopsis cuticle permeability, the hypothesised mechanism of adhesion mediation. It is not yet known whether differences in adhesion quality among genotypes are determined by changes in caryopsis cuticle permeability. We examined changes in candidate cementing layer biosynthetic and regulatory genes to investigate the genetic mechanisms behind husk adhesion quality. We used both commercially relevant UK malting cultivars and older European lines to ensure phenotypic diversity in adhesion quality. An ethylene responsive transcription factor (NUD) is required for the development of the cementing layer. To examine correlations between gene expression, cementing layer permeability and husk adhesion quality we also treated cultivars with ethephon (2-chloroethylphosphonic acid) which breaks down to ethylene, and silver thiosulphate which inhibits ethylene reception, and measured caryopsis cuticle permeability. Differential adhesion qualities among genotypes are not determined by NUD expression during development of the cementing material alone, but could result from differences in biosynthetic gene expression during cementing layer development in response to longer-term NUD expression patterns. Altered caryopsis cuticle permeability does result in altered adhesion quality, but the correlation is not consistently positive or negative. Cuticle permeability is therefore not the mechanism that determines husk adhesion quality, but is likely a consequence of the required cuticular compositional changes that determine adhesion.

Comparative Analysis of Proteomics and Transcriptomics during Fertility Transition in a Two-Line Hybrid Rice Line Wuxiang S

The two-line hybrid rice is an important factor of a global crop, but its fertility transition mechanism is unclear. Here, a comparative proteomics and transcriptomics analysis was completed on the two-line hybrid rice line Wuxiang S (WXS) to explore its molecular mechanism and protein regulation during fertility transition. A total of 340 differentially abundant proteins (DAPs) were identified using iTRAQ between the pollen mother cell formation stage (P2) and the meiosis stage (P3). There were 3541 and 4247 differentially expressed genes (DEGs) in P2 and P3 between WXS (Sterile, S)-WXS(S) and WXS (Fertile, F)-WXS(F), respectively, of which 92 and 71 DEGs had corresponding DAPs. Among the DAPs and DEGs, 65 (SP2 vs. FP2) and 55 (SP3 vs. FP3) corresponding DEGs and DAPs (cor-DEGs-DAPs) showed the same expression trend, indicating the cor-DEGs-DAPs genes might play vital roles in WXS fertility transition. Further analysis indicated that cor-DEGs-DAPs proteins were related to energy metabolism-related proteins in anther development and were accompanied by the activation of the stress response pathway and modifications to the cell wall, which ultimately affected the fertility transition of the PTGMS rice line WXS.

Development and Quality of Barley Husk Adhesion Correlates With Changes in Caryopsis Cuticle Biosynthesis and Composition

The caryopses of barley become firmly adhered to the husk during grain development through a cuticular cementing layer on the caryopsis surface. The degree of this attachment varies among cultivars, with poor quality adhesion causing "skinning", an economically significant grain quality defect for the malting industry. Malting cultivars encompassing a range of husk adhesion qualities were grown under a misting treatment known to induce skinning. Development of the cementing layer was examined by electron microscopy and compositional changes of the cementing layer were investigated with gas-chromatography followed by mass spectroscopy. Changes in gene expression during adhesion development were examined with a custom barley microarray. The abundance of transcripts involved early in cuticular lipid biosynthesis, including those encoding acetyl-CoA carboxylase, and all four members of the fatty acid elongase complex of enzymes, was significantly higher earlier in caryopsis development than later. Genes associated with subsequent cuticular lipid biosynthetic pathways were also expressed higher early in development, including the decarbonylation and reductive pathways, and sterol biosynthesis. Changes in cuticular composition indicate that lowered proportions of alkanes and higher proportions of fatty acids are associated with development of good quality husk adhesion, in addition to higher proportions of sterols.

Arabidopsis HSP70-16 is required for flower opening under normal or mild heat stress temperatures

Sepals play important roles in protecting inner floral organs from various stresses and in guaranteeing timely flower opening. However, the exact role of sepals in coordinating interior and exterior signals remains elusive. In this study, we functionally characterized a heat shock protein gene, Arabidopsis HSP70-16, in flower opening and mild heat stress response, using combined genetics with anatomic, physiological, chemical, and molecular analyses. We showed that HSP70-16 is required for flower opening and mild heat response. Mutation of HSP70-16 led to a significant reduction in seed setting rate under 22°C, which was more severe at 27°C. Mutation of HSP70-16 also caused postgenital fusion at overlapping tips of two lateral sepals, leading to failed flower opening, abnormal floral organ formation, and impaired fertilization and seed setting. Chemical and anatomic analyses confirmed specific chemical and morphological changes of cuticle property in mutant lateral sepals, and qRT-PCR data indicated that expression levels of different sets of cuticle regulatory and biosynthetic genes were altered in mutants grown at both 22°C and 27°C temperatures. This study provides a link between thermal and developmental perception signals and expands the understanding of the roles of sepal in plant development and heat response.

Map-Based Cloning, Phylogenetic, and Microsynteny Analyses of ZmMs20 Gene Regulating Male Fertility in Maize

Genic male sterility (GMS) mutant is a useful germplasm resource for both theory research and production practice. The identification and characterization of GMS genes, and assessment of male-sterility stability of GMS mutant under different genetic backgrounds in Zea may (maize) have (1) deepened our understanding of the molecular mechanisms controlling anther and pollen development, and (2) enabled the development and efficient use of many biotechnology-based male-sterility (BMS) systems for hybrid breeding. Here, we reported a complete GMS mutant (ms20), which displays abnormal anther cuticle and pollen development. Its fertility restorer gene ZmMs20 was found to be a new allele of IPE1 encoding a glucose methanol choline (GMC) oxidoreductase involved in lipid metabolism in anther. Phylogenetic and microsynteny analyses showed that ZmMs20 was conserved among gramineous species, which provide clues for creating GMS materials in other crops. Additionally, among the 17 maize cloned GMS genes, ZmMs20 was found to be similar to the expression patterns of Ms7, Ms26, Ms6021, APV1, and IG1 genes, which will give some clues for deciphering their functional relationships in regulating male fertility. Finally, two functional markers of ZmMs20/ms20 were developed and tested for creating maize ms20 male-sterility lines in 353 genetic backgrounds, and then an artificial maintainer line of ms20 GMS mutation was created by using ZmMs20 gene, ms20 mutant, and BMS system. This work will promote our understanding of functional mechanisms of male fertility and facilitate molecular breeding of ms20 male-sterility lines for hybrid seed production in maize.

Compositional and transcriptomic analysis associated with cuticle lipid production on rosette and inflorescence stem leaves in the extremophyte Thellungiella salsuginea

The plant cuticle is a complex structure composed primarily of wax and cutin, but also contains cutan, glycerolipids, phenolics, polysaccharides and proteins. The cuticle plays an important protective role as barrier between plants and their environment. In this paper, 4-week-old leaves produced either on the rosette or on the inflorescence stem of the model extremophyte Thellungiella salsuginea were examined using scanning electron microscopy, cuticle permeability assays and chemical composition analysis. Results showed that stem leaves (SL) had more abundant cuticle lipids and lower cuticle permeability than rosette leaves (RL). SL were dominated by alkanes, especially the C29 and C31 homologs, whereas in RL the most abundant wax class was free very long-chain acids. The major cutin monomers for both leaf types were C18:2 dioic acids and 18-OH C18:2 acids. We performed Illumina high-throughput sequencing for SL and RL, and 3577 differentially expressed genes were identified. Sixty-five genes possibly involved in cuticular lipid biosynthesis, transport, or regulation was selected for further analysis. Many cuticle-associated genes exhibited differential expression levels that could be associated with compositional differences between these two leaf types. Furthermore, transcription factors and other regulatory proteins previously associated with cuticle production were expressed at higher levels in SL than in RL. The associations between gene expression and characteristics of this extremophile's leaf cuticles sheds new light on cuticle as an adaptive trait in extreme environments, and contributes new information that may guide efforts to modify crop cuticles for improved stress tolerance.

Cytological, Biochemical and Molecular Events of the Embryogenic State in Douglas-fir (Pseudotsuga menziesii [Mirb.])

Somatic embryogenesis techniques have been developed for most coniferous species, but only using very juvenile material. To extend the techniques' scope, better integrated understanding of the key biological, physiological and molecular characteristics of embryogenic state is required. Therefore, embryonal masses (EMs) and non-embryogenic calli (NECs) have been compared during proliferation at multiple levels. EMs and NECs originating from a single somatic embryo (isogenic lines) of each of three unrelated genotypes were used in the analyses, which included comparison of the lines' anatomy by transmission light microscopy, transcriptomes by RNAseq Illumina sequencing, proteomes by free-gel analysis, contents of endogenous phytohormones (indole-3-acetic acid, cytokinins and ABA) by LC-MS analysis, and soluble sugar contents by HPLC. EMs were characterized by upregulation (relative to levels in NECs) of transcripts, proteins, transcription factors and active cytokinins associated with cell differentiation accompanied by histological, carbohydrate content and genetic markers of cell division. In contrast, NECs were characterized by upregulation (relative to levels in EMs) of transcripts, proteins and products associated with responses to stimuli (ABA, degradation forms of cytokinins, phenols), oxidative stress (reactive oxygen species) and carbohydrate storage (starch). Sub-Network Enrichment Analyses that highlighted functions and interactions of transcripts and proteins that significantly differed between EMs and NECs corroborated these findings. The study shows the utility of a novel approach involving integrated multi-scale transcriptomic, proteomic, biochemical, histological and anatomical analyses to obtain insights into molecular events associated with embryogenesis and more specifically to the embryogenic state of cell in Douglas-fir.

Disruption of glycosylphosphatidylinositol-anchored lipid transfer protein 15 affects seed coat permeability in Arabidopsis

The hydrophobic biopolymer suberin, which is deposited in the root endodermis and seed coats, functions as an extracellular barrier against uncontrolled water, gas, and ion loss. Suberin monomers synthesized in the endoplasmic reticulum (ER) are exported through the plasma membrane to the apoplast. However, limited information is available about the molecular mechanisms underlying suberin monomer export and assembly. In this study, we investigated the in planta role of LTPG15 encoding a glycosylphosphatidylinositol (GPI)-anchored lipid transfer protein. LTPG15 was predominantly expressed in the root endodermis and seed coat. Fluorescent signals from LTPG15:eYFP were detected in the plasma membrane in tobacco epidermis. Disruption of LTPG15 caused a significant decrease in the levels of fatty acids (C20-C24), primary alcohols (C20 and C22), ω-hydroxy fatty acids (C22 and C24), and α,ω-alkanediols (C20 and C22), but an increase in the amounts of primary alcohols and hydroxy fatty acids with C16 and C18 in seed coats. The mutant phenotype was restored to that of the wild type (WT) by the expression of LTPG15 driven by its own promoter. Seed coats of ltpg15 had an increase in permeability to tetrazolium salts compared with WT seed coats. ltpg15 seeds were more sensitive than WT seeds to inhibition of germination and seedling establishment by salt and osmotic stress treatments. Taken together, our results indicate that LTPG15 is involved in suberin monomer export in seed coats, and this highlights the role of Type G non-specific lipid transfer proteins (LTPGs) in very-long-chain fatty acids and their derivatives' export for suberin polyester formation.

A versatile and robust Agrobacterium-based gene stacking system generates high-quality transgenic Arabidopsis plants

Biotechnology provides a means for the rapid genetic improvement of plants. Although single genes have been important in engineering herbicide and pest tolerance traits in crops, future improvements of complex traits like yield and nutritional quality will likely require the introduction of multiple genes. This research reports a system (GAANTRY; Gene Assembly in Agrobacterium by Nucleic acid Transfer using Recombinase technologY) for the flexible, in vivo stacking of multiple genes within an Agrobacterium virulence plasmid Transfer-DNA (T-DNA). The GAANTRY system utilizes in vivo transient expression of unidirectional site-specific recombinases and an alternating selection scheme to sequentially assemble multiple genes into a single transformation construct. To demonstrate GAANTRY's capabilities, 10 cargo sequences were sequentially stacked together to produce a 28.5-kbp T-DNA, which was used to generate hundreds of transgenic events. Approximately 90% of the events identified using a dual antibiotic selection screen exhibited all of the introduced traits. A total of 68% of the tested lines carried a single copy of the selection marker transgene located near the T-DNA left border, and only 8% contained sequence from outside the T-DNA. The GAANTRY system can be modified to easily accommodate any method of DNA assembly and generate high-quality transgenic plants, making it a powerful, yet simple to use tool for plant genetic engineering.

The β-Ketoacyl-CoA Synthase HvKCS1, Encoded by Cer-zh, Plays a Key Role in Synthesis of Barley Leaf Wax and Germination of Barley Powdery Mildew

The cuticle coats the primary aerial surfaces of land plants. It consists of cutin and waxes, which provide protection against desiccation, pathogens and herbivores. Acyl cuticular waxes are synthesized via elongase complexes that extend fatty acyl precursors up to 38 carbons for downstream modification pathways. The leaves of 21 barley eceriferum (cer) mutants appear to have less or no epicuticular wax crystals, making these mutants excellent tools for identifying elongase and modification pathway biosynthetic genes. Positional cloning of the gene mutated in cer-zh identified an elongase component, β-ketoacyl-CoA synthase (CER-ZH/HvKCS1) that is one of 34 homologous KCSs encoded by the barley genome. The biochemical function of CER-ZH was deduced from wax and cutin analyses and by heterologous expression in yeast. Combined, these experiments revealed that CER-ZH/HvKCS1 has a substrate specificity for C16-C20, especially unsaturated, acyl chains, thus playing a major role in total acyl chain elongation for wax biosynthesis. The contribution of CER-ZH to water barrier properties of the cuticle and its influence on the germination of barley powdery mildew fungus were also assessed.

Integrated analysis of transcriptome and proteome changes related to the Ogura cytoplasmic male sterility in cabbage

Cabbage (Brassica oleracea L. var. capitata), an important vegetable crop in the Brassicaceae family, is economically important worldwide. In the process of hybrid seed production, Ogura cytoplasmic male sterility (OguCMS), controlled by the mitochondrial gene orf138, has been extensively used for cabbage hybrid production with complete and stable male sterility. To identify the critical genes and pathways involved in the sterility and to better understand the underlying molecular mechanisms, the anther of OguCMS line R2P2CMS and the fertile line R2P2 were used for RNA-seq and iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) proteome analysis. RNA-seq analysis generated 13,037,109 to 13,066,594 SE50-clean reads, from the sterile and fertile lines, which were assembled into 36,890 unigenes. Among them, 1,323 differentially expressed genes (DEGs) were identified, consisting of 307 up- and 1016 down-regulated genes. For ITRAQ analysis, a total of 7,147 unique proteins were identified, and 833 were differentially expressed including 538 up- and 295 down-regulated proteins. These were mainly annotated to the ribosome, spliceosome and mRNA surveillance pathways. Combined transcriptomic and proteomic analyses identified 22 and 70 genes with the same and opposite expression profiles, respectively. Using KEGG analysis of DEGs, gibberellin mediated signaling pathways regulating tapetum programmed cell death and four different pathways involved in sporopollenin synthesis were identified. Secretion and translocation of the sporopollenin precursors were identified, and the key genes participating in these pathways were all significantly down-regulated in R2P2CMS. Light and transmission electron (TE) microscopy revealed fat abnormal tapetum rather than vacuolization and degradation at the tetrad and microspore stages of the OguCMS line. This resulted in the failed deposition of sporopollenin on the pollen resulting in sterility. This study provides a comprehensive understanding of the mechanism underlying OguCMS in cabbage.

The intimate talk between plants and microorganisms at the leaf surface

The plant epidermis or cuticle is constantly exposed to external and internal environmental factors, including an enriched and diverse community of bacteria, yeast, fungi, viruses, and mites. It is not only where the plant has its first physical barrier, but also where organisms can be recognized and potentially where the plant defense responses can be triggered. The plant cuticle is a polymeric composite formed by an array of structurally and chemically heterogeneous compounds, including cutin and wax. A few studies have shown that cuticular components are essential and important drivers of the structure and size of the bacterial community. On the other hand, cuticular components are also important for both pathogens and plants, to initiate the pre-invasion and infection process and to activate the innate immune response, respectively. In this review, we explore current knowledge on the role of the cuticle during the intimate interactions between plants and microorganisms, in particular pathogenic and non-pathogenic bacteria and fungi. Finally, we propose new perspectives on the potential use of this information for agriculture.

The roles of the cuticle in plant development: organ adhesions and beyond

Cuticles, which are composed of a variety of aliphatic molecules, impregnate epidermal cell walls forming diffusion barriers that cover almost all the aerial surfaces in higher plants. In addition to revealing important roles for cuticles in protecting plants against water loss and other environmental stresses and aggressions, mutants with permeable cuticles show major defects in plant development, such as abnormal organ formation as well as altered seed germination and viability. However, understanding the mechanistic basis for these developmental defects represents a significant challenge due to the pleiotropic nature of phenotypes and the altered physiological status/viability of some mutant backgrounds. Here we discuss both the basis of developmental phenotypes associated with defects in cuticle function and mechanisms underlying developmental processes that implicate cuticle modification. Developmental abnormalities in cuticle mutants originate at early developmental time points, when cuticle composition and properties are very difficult to measure. Nonetheless, we aim to extract principles from existing data in order to pinpoint the key cuticle components and properties required for normal plant development. Based on our analysis, we will highlight several major questions that need to be addressed and technical hurdles that need to be overcome in order to advance our current understanding of the developmental importance of plant cuticles.

Husk to caryopsis adhesion in barley is influenced by pre- and post-anthesis temperatures through changes in a cuticular cementing layer on the caryopsis

BACKGROUND

At ripeness, the outer husk of "covered" barley grains firmly adheres to the underlying caryopsis. A cuticular cementing layer on the caryopsis is required for husk adhesion, however the quality of adhesion varies significantly among cultivars which produce the cementing layer, resulting in the economically important malting defect, grain skinning. The composition of the cementing layer, and grain organ development have been hypothesised to influence the quality of husk adhesion. Plants of Hordeum vulgare 'Concerto' were grown at different temperatures pre- and post-anthesis to effect changes in the development of the husk, caryopsis and cuticular cementing layer, to determine how these variables influence the quality of husk-to-caryopsis adhesion.

RESULTS

Warm conditions pre-anthesis decreased the quality of husk adhesion, and consequently increased the incidence of grain skinning. Cool post-anthesis conditions further decreased the quality of husk adhesion. The composition of the cementing layer, rather than its structure, differed with respect to husk adhesion quality. This cementing layer was produced at the late milk stage, occurring between nine and 29 days post-anthesis, conditional on the temperature-dependent growth rate. The compounds octadecanol, tritriacontane, campesterol and β-sitosterol were most abundant in caryopses with high-quality husk adhesion. The differences in adhesion quality were not due to incompatible husk and caryopsis dimensions affecting organ contact.

CONCLUSIONS

This study shows that husk-to-caryopsis adhesion is dependent on cementing layer composition, and implies that this composition is regulated by temperature before, and during grain development. Understanding this regulation will be key to improving husk-to-caryopsis adhesion.

Fine Mapping of a Gene (ER4.1) that Causes Epidermal Reticulation of Tomato Fruit and Characterization of the Associated Transcriptome

The hydrophobic cuticle that covers the surface of tomato (Solanum lycopersicum) fruit plays key roles in development and protection against biotic and abiotic stresses, including water loss, mechanical damage, UV radiation, pathogens, and pests. However, many details of the genes and regulatory mechanisms involved in cuticle biosynthesis in fleshy fruits are not well understood. In this study, we describe a novel tomato fruit phenotype, characterized by epidermal reticulation (ER) of green fruit and a higher water loss rate than wild type (WT) fruit. The ER phenotype is controlled by a single gene, ER4.1, derived from an introgressed chromosomal segment from the wild tomato species S. pennellii (LA0716). We performed fine mapping of the single dominant gene to an ~300 kb region and identified Solyc04g082540, Solyc04g082950, Solyc04g082630, and Solyc04g082910as potential candidate genes for the ER4.1 locus, based on comparative RNA-seq analysis of ER and WT fruit peels. In addition, the transcriptome analysis revealed that the expression levels of genes involved in cutin, wax and flavonoid biosynthesis were altered in the ER fruit compared with WT. This study provides new insights into the regulatory mechanisms and metabolism of the fruit cuticle.

HOTHEAD-Like HTH1 is Involved in Anther Cutin Biosynthesis and is Required for Pollen Fertility in Rice

The cuticle covering the outer surface of anthers is essential for male reproductive development in plants. However, the mechanism underlying the synthesis of these lipidic polymers remains unclear. HOTHEAD (HTH) in Arabidopsis thaliana is a presumptive glucose-methanol-choline (GMC) oxidoreductase involved in the biosynthesis of long-chain α-,ω-dicarboxylic fatty acids. In this study, we characterized the function of an anther-specific gene HTH1 in rice. HTH1 contains a conserved GMC oxidoreductase-like domain, and the sequence of HTH1 was highly similar to that of HTH in A. thaliana. Quantitative real-time PCR (qRT-PCR) and in situ hybridization analyses showed that HTH1 was highly expressed in epidermal cells of anthers. Rice plants with HTH1 suppression through CRISPR (clustered regularly interspaced short palindromic repeats) and RNA interference (RNAi) displayed defective anther wall and aborted pollen. Disorganized cuticle layers in anthers and shriveled pollen grains were observed in HTH1-RNAi lines. The total amounts of long-chain fatty acids and cutin monomers in anthers of HTH1-RNAi lines were significantly reduced compared with the wild type. Our results suggested that HTH1 is involved in cutin biosynthesis and is required for anther development and pollen fertility in rice.

Rice No Pollen 1 (NP1) is required for anther cuticle formation and pollen exine patterning

Angiosperm male reproductive organs (anthers and pollen grains) have complex and interesting morphological features, but mechanisms that underlie their patterning are poorly understood. Here we report the isolation and characterization of a male sterile mutant of No Pollen 1 (NP1) in rice (Oryza sativa). The np1-4 mutant exhibited smaller anthers with a smooth cuticle surface, abnormal Ubisch bodies, and aborted pollen grains covered with irregular exine. Wild-type exine has two continuous layers; but np1-4 exine showed a discontinuous structure with large granules of varying size. Chemical analysis revealed reduction in most of the cutin monomers in np1-4 anthers, and less cuticular wax. Map-based cloning suggested that NP1 encodes a putative glucose-methanol-choline oxidoreductase; and expression analyses found NP1 preferentially expressed in the tapetal layer from stage 8 to stage 10 of anther development. Additionally, the expression of several genes involved in biosynthesis and in the transport of lipid monomers of sporopollenin and cutin was decreased in np1-4 mutant anthers. Taken together, these observations suggest that NP1 is required for anther cuticle formation, and for patterning of Ubisch bodies and the exine. We propose that products of NP1 are likely important metabolites in the development of Ubisch bodies and pollen exine, necessary for polymerization, assembly, or both.

Cuticle ultrastructure, cuticular lipid composition, and gene expression in hypoxia-stressed Arabidopsis stems and leaves

An increased permeability of the cuticle is closely associated with downregulation of genes involved in cuticular lipid synthesis in hypoxia-stressed Arabidopsis and may allow plants to cope with oxygen deficiency. The hydrophobic cuticle layer consisting of cutin polyester and cuticular wax is the first barrier to protect the aerial parts of land plants from environmental stresses. In the present study, we investigated the role of cuticle membrane in Arabidopsis responses to oxygen deficiency. TEM analysis showed that the epidermal cells of hypoxia-treated Arabidopsis stems and leaves possessed a thinner electron-translucent cuticle proper and a more electron-dense cuticular layer. A reduction in epicuticular wax crystal deposition was observed in SEM images of hypoxia-treated Arabidopsis stem compared with normoxic control. Cuticular transpiration was more rapid in hypoxia-stressed leaves than in normoxic control. Total wax and cutin loads decreased by approximately 6-12 and 12-22%, respectively, and the levels of C29 alkanes, secondary alcohols, and ketones, C16:0 ω-hydroxy fatty acids, and C18:2 dicarboxylic acids were also prominently reduced in hypoxia-stressed Arabidopsis leaves and/or stems relative to normoxic control. Genome-wide transcriptome and quantitative RT-PCR analyses revealed that the expression of several genes involved in the biosynthesis and transport of cuticular waxes and cutin monomers were downregulated more than fourfold, but no significant alterations were detected in the transcript levels of fatty acid biosynthetic genes, BCCP2, PDH-E1α, and ENR1 in hypoxia-treated Arabidopsis stems and leaves compared with normoxic control. Taken together, an increased permeability of the cuticle is closely associated with downregulation of genes involved in cuticular lipid synthesis in hypoxia-stressed Arabidopsis. The present study elucidates one of the cuticle-related adaptive responses that may allow plants to cope with low oxygen levels.

Transcriptomics Analysis of Apple Leaves in Response to Alternaria alternata Apple Pathotype Infection

Alternaria blotch disease of apple (Malus × domestica Borkh.), caused by the apple pathotype of Alternaria alternata, is one of the most serious fungal diseases to affect apples. To develop an understanding of how apples respond to A. alternata apple pathotype (AAAP) infection, we examined the host transcript accumulation over the period between 0 and 72 h post AAAP inoculation. Large-scale gene expression analysis was conducted of the compatible interaction between "Starking Delicious" apple cultivar and AAAP using RNA-Seq and digital gene expression (DGE) profiling methods. Our results show that a total of 9080 differentially expressed genes (DEGs) were detected (>two-fold and FDR < 0.001) by RNA-Seq. During the early phase of infection, 12 h post inoculation (HPI), AAAP exhibited limited fungal development and little change in the transcript accumulation status (950 DEGs). During the intermediate phase of infection, the period between 18 and 36 HPI, increased fungal development, active infection, and increased transcript accumulation were detected (4111 and 3838 DEGs detected at each time point, respectively). The majority of DEGs were detected by 72 HPI, suggesting that this is an important time point in the response of apples' AAAP infection. Subsequent gene ontology (GO) and pathway enrichment analyses showed that DEGs are predominately involved in biological processes and metabolic pathways; results showed that almost gene associated with photosynthesis, oxidation-reduction were down-regulated, while transcription factors (i.e., WRKY, MYB, NAC, and Hsf) and DEGs involved in cell wall modification, defense signaling, the synthesis of defense-related metabolites, including pathogenesis-related (PRs) genes and phenylpropanoid/cyanoamino acid /flavonoid biosynthesis, were activated during this process. Our study also suggested that the cell wall defensive vulnerability and the down-regulation of most PRs and HSP70s in "Starking Delicious" following AAAP infection might interpret its susceptible to AAAP.

Construction of a male sterility system for hybrid rice breeding and seed production using a nuclear male sterility gene

The breeding and large-scale adoption of hybrid seeds is an important achievement in agriculture. Rice hybrid seed production uses cytoplasmic male sterile lines or photoperiod/thermo-sensitive genic male sterile lines (PTGMS) as female parent. Cytoplasmic male sterile lines are propagated via cross-pollination by corresponding maintainer lines, whereas PTGMS lines are propagated via self-pollination under environmental conditions restoring male fertility. Despite huge successes, both systems have their intrinsic drawbacks. Here, we constructed a rice male sterility system using a nuclear gene named Oryza sativa No Pollen 1 (OsNP1). OsNP1 encodes a putative glucose-methanol-choline oxidoreductase regulating tapetum degeneration and pollen exine formation; it is specifically expressed in the tapetum and miscrospores. The osnp1 mutant plant displays normal vegetative growth but complete male sterility insensitive to environmental conditions. OsNP1 was coupled with an α-amylase gene to devitalize transgenic pollen and the red fluorescence protein (DsRed) gene to mark transgenic seed and transformed into the osnp1 mutant. Self-pollination of the transgenic plant carrying a single hemizygous transgene produced nontransgenic male sterile and transgenic fertile seeds in 1:1 ratio that can be sorted out based on the red fluorescence coded by DsRed Cross-pollination of the fertile transgenic plants to the nontransgenic male sterile plants propagated the male sterile seeds of high purity. The male sterile line was crossed with ∼1,200 individual rice germplasms available. Approximately 85% of the F1s outperformed their parents in per plant yield, and 10% out-yielded the best local cultivars, indicating that the technology is promising in hybrid rice breeding and production.

Molecular characterization and targeted quantitative profiling of the sphingolipidome in rice

Recent advances in comprehensive metabolite profiling techniques, the foundation of metabolomics, is facilitating our understanding of the functions, regulation and complex networks of various metabolites in organisms. Here, we report a quantitative metabolomics technique for complex plant sphingolipids, composed of various polar head groups as well as structural isomers of hydrophobic ceramide moieties. Rice (Oryza sativa L.) was used as an experimental model of monocotyledonous plants and has been demonstrated to possess a highly complex sphingolipidome including hundreds of molecular species with a wide range of abundance. We established a high-throughput scheme for lipid preparation and mass spectrometry-based characterization of complex sphingolipid structures, which provided basic information to create a comprehensive theoretical library for targeted quantitative profiling of complex sphingolipids in rice. The established sphingolipidomic approach combined with multivariate analyses of the large dataset obtained clearly showed that different classes of rice sphingolipids, particularly including subclasses of glycosylinositol phosphoceramide with various sugar-chain head groups, are distributed with distinct quantitative profiles in various rice tissues, indicating tissue-dependent metabolism and biological functions of the lipid classes and subclasses. The sphingolipidomic analysis also highlighted that disruption of a lipid-associated gene causes a typical sphingolipidomic change in a gene-dependent manner. These results clearly support the utility of the sphingolipidomic approach in application to wide screening of sphingolipid-metabolic phenotypes as well as deeper investigation of metabolism and biological functions of complex sphingolipid species in plants.

Fine structure of the Arabidopsis stem cuticle: effects of fixation and changes over development

The Arabidopsis cuticle, as observed by electron microscopy, consists primarily of the cutin/cutan matrix. The cuticle possesses a complex substructure, which is correlated with the presence of intracuticular waxes. The plant cuticle is composed of an insoluble polyester, cutin, and organic solvent soluble cuticular waxes, which are embedded within and coat the surface of the cutin matrix. How these components are arranged in the cuticle is not well understood. The Arabidopsis cuticle is commonly understood as 'amorphous,' lacking in ultrastructural features, and is often observed as a thin (~80-100 nm) electron-dense layer on the surface of the cell wall. To examine this cuticle in more detail, we examined cuticles from both rapidly elongating and mature sections of the stem and compared the preservation of the cuticles using conventional chemical fixation methods and high-pressure freezing/freeze-substitution (HPF/FS). We found that HPF/FS preparation revealed a complex cuticle substructure, which was more evident in older stems. We also found that the cuticle increases in thickness with development, indicating an accretion of polymeric material, likely in the form of the non-hydrolyzable polymer, cutan. When wax was extracted by chloroform immersion prior to sample preparation, the contribution of waxes to cuticle morphology was revealed. Overall, the electron-dense cuticle layer was still visible but there was loss of the cuticle substructure. Furthermore, the cuticle of cer6, a wax-deficient mutant, also lacked this substructure, suggesting that these fine striations were dependent on the presence of cuticular waxes. Our findings show that HPF/FS preparation can better preserve plant cuticles, but also provide new insights into the fine structure of the Arabidopsis cuticle.

Solanum pennellii backcross inbred lines (BILs) link small genomic bins with tomato traits

We present a resource for fine mapping of traits derived from the wild tomato species Solanum pennellii (LA0716). The population of backcross inbred lines (BILs) is composed of 446 lines derived after a few generations of backcrosses of the wild species with cultivated tomato (cultivar M82; LA3475), followed by more than seven generations of self-pollination. The BILs were genotyped using the 10K SOL-CAP single nucleotide polymorphism (SNP) -Chip, and 3700 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs carry, on average, 2.7 introgressions per line, with a mean introgression length of 11.7 Mbp. Whereas the classic 76 introgression lines (ILs) partitioned the genome into 106 mapping bins, the BILs generated 633 bins, thereby enhancing the mapping resolution of traits derived from the wild species. We demonstrate the power of the BILs for rapid fine mapping of simple and complex traits derived from the wild tomato species.