MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins

The Cutinase Bdo_10846 Play an Important Role in the Virulence of Botryosphaeria dothidea and in Inducing the Wart Symptom on Apple Plant

Botryosphaeria dothidea is a pathogen with worldwide distribution, infecting hundreds of species of economically important woody plants. It infects and causes various symptoms on apple plants, including wart and canker on branches, twigs, and stems. However, the mechanism of warts formation is unclear. In this study, we investigated the mechanism of wart formation by observing the transection ultrastructure of the inoculated cortical tissues at various time points of the infection process and detecting the expression of genes related to the pathogen pathogenicity and plant defense response. Results revealed that wart induced by B. dothidea consisted of proliferous of phelloderm cells, the newly formed secondary phellem, and the suberized phelloderm cells surrounding the invading mycelia. The qRT-PCR analysis revealed the significant upregulation of apple pathogenesis-related and suberification-related genes and a pathogen cutinase gene Bdo_10846. The Bdo_10846 knockout transformants showed reduced cutinase activity and decreased virulence. Transient expression of Bdo_10846 in Nicotiana benthamiana induced ROS burst, callose formation, the resistance of N. benthamiana to Botrytis cinerea, and significant upregulation of the plant pathogenesis-related and suberification-related genes. Additionally, the enzyme activity is essential for the induction. Virus-induced gene silencing demonstrated that the NbBAK1 and NbSOBIR1 expression were required for the Bdo_10846 induced defense response in N. benthamiana. These results revealed the mechanism of wart formation induced by B. dothidea invasion and the important roles of the cutinase Bdo_10846 in pathogen virulence and in inducing plant immunity.

Russeting in Apple is Initiated after Exposure to Moisture Ends: Molecular and Biochemical Evidence

Exposure of the fruit surface to moisture during early development is causal in russeting of apple (Malus × domestica Borkh.). Moisture exposure results in formation of microcracks and decreased cuticle thickness. Periderm differentiation begins in the hypodermis, but only after discontinuation of moisture exposure. Expressions of selected genes involved in cutin, wax and suberin synthesis were quantified, as were the wax, cutin and suberin compositions. Experiments were conducted in two phases. In Phase I (31 days after full bloom) the fruit surface was exposed to moisture for 6 or 12 d. Phase II was after moisture exposure had been discontinued. Unexposed areas on the same fruit served as unexposed controls. During Phase I, cutin and wax synthesis genes were down-regulated only in the moisture-exposed patches. During Phase II, suberin synthesis genes were up-regulated only in the moisture-exposed patches. The expressions of cutin and wax genes in the moisture-exposed patches increased slightly during Phase II, but the levels of expression were much lower than in the control patches. Amounts and compositions of cutin, wax and suberin were consistent with the gene expressions. Thus, moisture-induced russet is a two-step process: moisture exposure reduces cutin and wax synthesis, moisture removal triggers suberin synthesis.

A review of current knowledge about the formation of native peridermal exocarp in fruit

The outer skin layer in any plant is essential in offering a protective barrier against water loss and pathogen attack. Within fleshy fruit, the skin supports internal cell layers and can provide the initial cues in attracting seed-dispersing animals. The skin of a fruit, termed the exocarp, is a key element of consumer preference and a target for many breeding programs. Across fruiting species there is a huge diversity of exocarp types and these range from a simple single living cell layer (epidermis) often covered with a waxy layer, to complex multicellular suberised and dead cell layers (periderm), with various intermediate russet forms in between. Each exocarp can be interspersed with other structures such as hairs or spines. The epidermis has been well characterised and remains pluripotent with the help of the cells immediately under the epidermis. The periderm, in contrast, is the result of secondary meristematic activity, which replaces the epidermal layers, and is not well characterised in fruits. In this review we explore the structure, composition and mechanisms that control the development of a periderm type fruit exocarp. We draw upon literature from non-fleshy fruit species that form periderm tissue, from which a considerable amount of research has been undertaken.

Drought activates MYB41 orthologs and induces suberization of grapevine fine roots

The permeability of roots to water and nutrients is controlled through a variety of mechanisms and one of the most conspicuous is the presence of the Casparian strips and suberin lamellae. Roots actively regulate the creation of these structures developmentally, along the length of the root, and in response to the environment, including drought. In the current study, we characterized the suberin composition along the length of grapevine fine roots during development and in response to water deficit, and in the same root systems we quantified changes in expression of suberin biosynthesis- and deposition-related gene families (via RNAseq) allowing the identification of drought-responsive suberin-related genes. Grapevine suberin composition did not differ between primary and lateral roots, and was similar to that of other species. Under water deficit there was a global upregulation of suberin biosynthesis which resulted in an increase of suberin specific monomers, but without changes in their relative abundances, and this upregulation took place across all the developmental stages of fine roots. These changes corresponded to the upregulation of numerous suberin biosynthesis- and export-related genes which included orthologs of the previously characterized AtMYB41 transcriptional factor. Functional validation of two grapevine MYB41 orthologs, VriMYB41 and VriMYB41-like, confirmed their ability to globally upregulate suberin biosynthesis, export, and deposition. This study provides a detailed characterization of the developmental and water deficit induced suberization of grapevine fine roots and identifies important orthologs responsible for suberin biosynthesis, export, and its regulation in grape.

The sugarcane ShMYB78 transcription factor activates suberin biosynthesis in Nicotiana benthamiana

KEY MESSAGE

A sugarcane MYB present in the culm induces suberin biosynthesis and is involved both with fatty acid and phenolics metabolism. Few transcription factors have been described as regulators of cell wall polymers deposition in C4 grasses. Particularly, regulation of suberin biosynthesis in this group of plants remains poorly understood. Here, we showed that the sugarcane MYB transcription factor ShMYB78 is an activator of suberin biosynthesis and deposition. ShMYB78 was identified upon screening genes whose expression was upregulated in sugarcane internodes undergoing suberization during culm development or triggered by wounding. Agrobacterium-mediated transient expression of ShMYB78 in Nicotiana benthamiana leaves induced the ectopic deposition of suberin and its aliphatic and aromatic monomers. Further, the expression of suberin-related genes was induced by ShMYB78 heterologous expression in Nicotiana benthamiana leaves. ShMYB78 was shown to be a nuclear protein based on its presence in sugarcane internode nuclear protein extracts, and protoplast transactivation assays demonstrated that ShMYB78 activates the promoters of the sugarcane suberin biosynthetic genes β-ketoacyl-CoA synthase (ShKCS20) and caffeic acid-O-methyltransferase (ShCOMT). Our results suggest that ShMYB78 may be involved in the transcriptional regulation of suberin deposition, from fatty acid metabolism to phenylpropanoid biosynthesis, in sugarcane internodes.

Developmental programs interact with abscisic acid to coordinate root suberization in Arabidopsis

Suberin lamellae, which provide a hydrophobic protective barrier against biotic and abiotic stresses, are widely deposited in various cell types during plant development and in response to stress. However, it remains unclear how developmental programs interact with stress responses to direct the precise spatiotemporal pattern of suberin deposition. In this study, we found that SHORT-ROOT (SHR), together with its downstream factor MYB36, guided suberization specifically in the root endodermis. Despite a partial dependence on abscisic acid (ABA), the suberization mediated by SHR and MYB36 appeared to derive from a slow readout of developmental programs, which was in contrast to the rapid but transient suberization induced by ABA. Furthermore, we found the MYB39 transcription factor functioned as a common downstream hub of the SHR/MYB36 pathway and the ABA-triggered response. MYB39 could directly bind to the FAR5 (alcohol-forming fatty acyl-coenzyme A reductase) promoter to activate its expression. In addition, overexpression of MYB39 dramatically increased the amount of suberization in Arabidopsis roots. Our results provide important insights into the interaction between developmental programs and environmental stimuli in root suberization in Arabidopsis.

AtMYB92 enhances fatty acid synthesis and suberin deposition in leaves of Nicotiana benthamiana

Acyl lipids are important constituents of the plant cell. Depending on the cell type, requirements in acyl lipids vary greatly, implying a tight regulation of fatty acid and lipid metabolism. The discovery of the WRINKLED1 (WRI1) transcription factors, members of the AP2-EREBP (APETALA2-ethylene-responsive element binding protein) family, has emphasized the importance of transcriptional regulation for adapting the rate of acyl chain production to cell requirements. Here, we describe the identification of another activator of the fatty acid biosynthetic pathway, the Arabidopsis MYB92 transcription factor. This MYB and all the members of the subgroups S10 and S24 of MYB transcription factors can directly activate the promoter of BCCP2 that encodes a component of the fatty acid biosynthetic pathway. Two adjacent MYB cis-regulatory elements are essential for the binding and activation of the BCCP2 promoter by MYB92. Overexpression of MYB92 or WRI1 in Nicotiana benthamiana induces the expression of fatty acid biosynthetic genes but results in the accumulation of different types of acyl lipids. In the presence of WRI1, triacylglycerol biosynthetic enzymes coded by constitutively expressed genes efficiently channel the excess fatty acids toward reserve lipid accumulation. By contrast, MYB92 activates both fatty acid and suberin biosynthetic genes; hence, the remarkable increase in suberin monomers measured in leaves expressing MYB92. These results provide additional insight into the molecular mechanisms that control the biosynthesis of an important cell wall-associated acylglycerol polymer playing critical roles in plants.

SUBERMAN regulates developmental suberization of the Arabidopsis root endodermis

Root endodermis, the innermost cortical layer surrounding the root vasculature, serves as the foremost barrier to water, solutes, and nutrients taken up from soil. Endodermis barrier functionality is achieved via its hydrophobic coating of lignified Casparian strips and the suberin lamellae; nonetheless the regulatory mechanisms underlying endodermis suberization are still elusive. Here, we discovered that the Arabidopsis SUBERMAN (SUB) transcription factor controls the establishment of the root suberin lamellae. Transient expression of SUB in Nicotiana benthamiana leaves resulted in the induction of heterologous suberin genes, the accumulation of suberin-type monomers, and consequent deposition of suberin-like lamellae. We demonstrate that SUB exerts its regulatory roles by transactivating promoters of suberin genes. In Arabidopsis, SUB is expressed in patchy and continuous suberization root endodermal cells, and thus roots with higher or lower expression of SUB display altered suberin polymer deposition patterns and modified composition. While these changes did not interfere with Casparian strip formation they had a substantial effect on root uptake capacity, resulting in varied root and leaf ionomic phenotypes. Gene expression profiling revealed that SUB function impacts transcriptional networks associated with suberin, phenylpropanoids, lignin, and cuticular lipid biosynthesis, as well as root transport activities, hormone signalling, and cell wall modification. Our findings highlight SUB as a regulator of root endodermis suberization during normal development, and its characterization is thus a key step towards dissecting the molecular mechanisms partaking in root endodermal barrier functionalities.

The developmental dynamics of the sweet sorghum root transcriptome elucidate the differentiation of apoplastic barriers

Apoplastic barriers in the endodermis, such as Casparian strips and suberin lamellae, control the passage of water and minerals into the stele. Apoplastic barriers are thus thought to contribute to salt exclusion in salt-excluding plants such as sweet sorghum (Sorghum bicolor). However, little is known about the genes involved in the development of the apoplastic barrier. Here, we identified candidate genes involved in Casparian strip and suberin lamella development in the roots of a sweet sorghum line (M-81E). Three distinct developmental regions (no differentiation, developing, and mature) were identified based on Casparian strip and suberin lamella staining in root cross sections. Sequencing of RNA extracted from these distinct sections identified key genes participating in the differentiation of the apoplastic barrier. The different sections were structurally distinct, presumably due to differences in gene expression. Genes controlling the phenylpropanoid pathway, fatty acid elongation, and fatty acid ω-hydroxylation appeared to be directly responsible for the formation of the apoplastic barrier. Our dataset elucidates the molecular processes underpinning apoplastic barrier development and provides a basis for future research on molecular mechanisms of apoplastic barrier formation and salt exclusion.Abbreviations: SHR, SHORTROOT; MYB, MYB DOMAIN PROTEIN; CIFs, Casparian strip integrity factors; CASP, Casparian strip domain proteins; PER, peroxidase; ESB1, ENHANCED SUBERIN1; CS, Casparian strip; RPKM, reads per kilobase per million reads; DEGs, differentially expressed genes; FDR, false discovery rate; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; RNA-seq, RNA sequencing; PAL, phenylalanine ammonia-lyase; CYP, cytochrome P450 monooxygenases; 4CL, 4-coumarate-CoA ligase; AAE5, ACYL-ACTIVATING ENZYME5; CCR, cinnamoyl CoA reductase; TKPR, TETRAKETIDE ALPHA-PYRONE REDUCTASE1; CAD, cinnamyl alcohol dehydrogenase; HST, shikimate O-hydroxycinnamoyltransferase; PMAT2, PHENOLIC GLUCOSIDE MALONYLTRANSFERASE2; CCOAOMT, caffeoyl-CoA O-methyltransferase; KCS, β-ketoacyl-CoA synthase; CUT1, CUTICULAR PROTEIN1; DET2, 5-alpha-reductase; TAX, 3'-N-debenzoyl-2'-deoxytaxol N-benzoyltransferase; CER1, ECERIFERUM1; FAR, fatty acyl reductase; AF-CoA, alcohol-forming fatty acyl-CoA reductase; ABCG, ATP-binding cassette, subfamily G; ERF, ethylene-responsive transcription factor; HSF, heat stress transcription factor; NTF, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-5; GPAT, glycerol 3-phosphate acyltransferase.

Effects of palmitic acid (16:0), hexacosanoic acid (26:0), ethephon and methyl jasmonate on the cuticular wax composition, structure and expression of key gene in the fruits of three pear cultivars

The chemical composition, crystal morphology and expression levels of associated genes involved in the cuticular wax of three pear cultivars 'Housui', 'Cuiguan' and 'Yuluxiang' after treatment with palmitic acid (PA), hexacosanoic acid (HA), ethephon and methyl jasmonate (Meja) were determined. A total of 59 cuticular wax compounds were detected across all samples. The wax coverage of 'Housui' fruits increased by 71.74, 93.48 and 89.13% after treatment with PA, ethephon and Meja, respectively, and treatment with PA, HA and Meja also increased the wax coverage in 'Cuiguan' (65.33, 20.00 and 21.33% respectively) and in 'Yuluxiang' (38.60, 63.16 and 42.11% respectively) fruits. Heatmap clustering analysis and partial least-squares-discriminate analysis (PLS-DA) also revealed that the different treatments exerted various influences on cuticular wax among the different cultivars. In addition, the wax component coverage and wax crystal structures showed variations among the different cultivars as well as different treatments. Gene expression analysis revealed 11 genes likely to be involved in pear fruit wax synthesis, transport and regulation. Taken together, the results of this study demonstrate that the differences in the cuticular waxes of the fruits of different cultivars after treatment with PA, HA, ethephon or Meja might lead to a better understanding of the regulatory effect of a substrate or elicitor on the composition and deposition of cuticular waxes.

Silencing against the conserved NAC domain of the potato StNAC103 reveals new NAC candidates to repress the suberin associated waxes in phellem

Both suberin and its associated waxes contribute to the formation of apoplastic barriers that protect plants from the environment. Some transcription factors have emerged as regulators of the suberization process. The potato StNAC103 gene was reported as a repressor of suberin polyester and suberin-associated waxes deposition because its RNAi-mediated downregulation (StNAC103-RNAi) over-accumulated suberin and associated waxes in the tuber phellem concomitantly with the induction of representative biosynthetic genes. Here, to explore if other genes of the large NAC gene family participate to this repressive function, we extended the silencing to other NAC members by targeting the conserved NAC domain of StNAC103 (StNAC103-RNAi-c). Transcript profile of the StNAC103-RNAi-c phellem indicated that StNAC101 gene was an additional potential target. In comparison with StNAC103-RNAi, the silencing with StNAC103-RNAi-c construct resulted in a similar effect in suberin but yielded an increased load of associated waxes in tuber phellem, mainly alkanes and feruloyl esters. Globally, the chemical effects in both silenced lines are supported by the transcript accumulation profile of genes involved in the biosynthesis, transport and regulation of apoplastic lipids. In contrast, the genes of polyamine biosynthesis were downregulated. Altogether these results point out to StNAC101 as a candidate to repress the suberin-associated waxes.

Proteome and transcriptome profile analysis reveals regulatory and stress-responsive networks in the russet fruit skin of sand pear

The epidermal tissues of the cuticular membrane (CM) and periderm membrane (PM) confer first-line protection from environmental stresses in terrestrial plants. Although PM protection is essentially ubiquitous in plants, the protective mechanism, the function of many transcription factors and enzymes, and the genetic control of metabolic signaling pathways are poorly understood. Different microphenotypes and cellular components in russet (PM-covered) and green (CM-covered) fruit skins of pear were revealed by scanning and transmission electron microscopy. The two types of fruit skins showed distinct phytohormone accumulation, and different transcriptomic and proteomic profiles. The enriched pathways were detected by differentially expressed genes and proteins from the two omics analyses. A detailed analysis of the suberin biosynthesis pathways identified the regulatory signaling network, highlighting the general mechanisms required for periderm formation in russet fruit skin. The regulation of aquaporins at the protein level should play an important role in the specialized functions of russet fruit skin and PM-covered plant tissues.

ABF2 and MYB transcription factors regulate feruloyl transferase FHT involved in ABA-mediated wound suberization of kiwifruit

Suberin is a cell-wall biopolymer with aliphatic and aromatic domains that is synthesized in the wound tissues of plants in order to restrict water loss and pathogen infection. ω-hydroxyacid/fatty alcohol hydroxycinnamoyl transferase (FHT) is required for cross-linking of the aliphatic and aromatic domains. ABA is known to play a positive role in suberin biosynthesis but it is not known how it interacts with FHT. In this study, the kiwifruit (Actinidia chinensis) AchnFHT gene was isolated and was found to be localized in the cytosol. Transient overexpression of AchnFHT in leaves of Nicotiana benthamiana induced massive production of ferulate, ω-hydroxyacids, and primary alcohols, consistent with the in vitro ability of AchnFHT to catalyse acyl-transfer from feruloyl-CoA to ω-hydroxypalmitic acid and 1-tetradecanol. A regulatory function of four TFs (AchnABF2, AchnMYB4, AchnMYB41, and AchnMYB107) on AchnFHT was identified. These TFs localized in the nucleus and directly interacted with the AchnFHT promoter in yeast one-hybrid assays. Dual-luciferase analysis indicated that AchnABF2, AchnMYB41, and AchnMYB107 activated the AchnFHT promoter while AchnMYB4 repressed it. These findings were supported by the results of transient overexpression in N. benthamiana, in which AchnABF2, AchnMYB41, and AchnMYB107 induced expression of suberin biosynthesis genes (including FHT) and accumulation of suberin monomers, whilst AchnMYB4 had the opposite effect. Exogenous ABA induced the expression of AchnABF2, AchnMYB41, AchnMYB107, and AchnFHT and induced suberin monomer formation, but it inhibited AchnMYB4 expression. In addition, fluridone (an inhibitor of ABA biosynthesis) was found to counter the inductive effects of ABA. Activation of suberin monomer biosynthesis by AchnFHT was therefore controlled in a coordinated way by both repression of AchnMYB4 and promotion of AchnABF2, AchnMYB41, and AchnMYB107.

MYB41, MYB107, and MYC2 promote ABA-mediated primary fatty alcohol accumulation via activation of AchnFAR in wound suberization in kiwifruit

Wound damage triggers the accumulation of abscisic acid (ABA), which induces the expression of a large number of genes involved in wound suberization in plants. Fatty acyl-CoA reductase (FAR) catalyzes the generation of primary fatty alcohols by the reduction of fatty acids in suberin biosynthesis. However, the regulatory effects of transcription factors (TFs) on AchnFAR in response to ABA are unexplored. In this study, kiwifruit AchnFAR displayed a biological function analogous to that of FAR in transiently overexpressed tobacco (Nicotiana benthamiana) leaves. The positive role of TFs, including AchnMYB41, AchnMYB107, and AchnMYC2, in the regulation of AchnFAR was identified. The three TFs could individually bind to the AchnFAR promoter to activate gene transcription in yeast one-hybrid and dual-luciferase assays. Transient overexpression of TFs in tobacco leaves resulted in the upregulation of aliphatic synthesis genes (including FAR) and the increase in aliphatics, including primary alcohols, α,ω-diacids, ω-hydroxyacids, and fatty acids. Moreover, exogenous ABA treatment elevated TF-mediated AchnFAR expression and the accumulation of primary alcohols. Conversely, fluridone, an inhibitor of ABA biosynthesis, suppressed the expression of AchnFAR and TF genes and reduced the formation of primary alcohols. The results indicate that AchnMYB41, AchnMYB107, and AchnMYC2 activate AchnFAR transcription to promote ABA-mediated primary alcohol formation in wound suberization in kiwifruit.

An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging "Golden Delicious" Apple

Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

Three Transcription Activators of ABA Signaling Positively Regulate Suberin Monomer Synthesis by Activating Cytochrome P450 CYP86A1 in Kiwifruit

Wound attack stimulates accumulation of abscisic acid (ABA) that activates a number of genes associated with wound suberization of plants. Cytochrome P450 fatty acid ω-hydroxylase CYP86A1 catalyzes ω-hydroxylation of fatty acids to form the ω-functionalized monomers that play a pivotal role in suberin synthesis. However, the transcriptional regulation of ABA signaling on AchnCYP86A1 has not been characterized in kiwifruit. In this study, AchnCYP86A1, a kiwifruit homolog of Arabidopsis AtCYP86A1, was isolated. AchnCYP86A1-overexpressed N. benthamiana leaves displayed that the AchnCYP86A1 functioned as a fatty acid ω-hydroxylase associated with synthesis of suberin monomer. The regulatory function of three transcription factors (TFs, including AchnMYC2, AchnMYB41 and AchnMYB107) on AchnCYP86A1 was identified. All the three TFs were localized in nucleus and could individually interact with AchnCYP86A1 promoter to activate gene expression in yeast one-hybrid and dual-luciferase assays. The findings were further demonstrated in transient overexpressed N. benthamiana, in which all TFs notably elevated the expression of aliphatic synthesis genes including CYP86A1 and the accumulation of ω-hydroxyacids, α, ω-diacids, fatty acids and primary alcohols. Moreover, exogenous ABA induced the expression of AchnMYC2, AchnMYB41 and AchnMYB107 that promoted AchnCYP86A1 involving in suberin monomer formation. Contrary to the inductive effects of ABA, however, fluridone (an inhibitor of ABA biosynthesis) inhibited the three TFs expression and suberin monomer formation. These results indicate that AchnMYC2, AchnMYB41 and AchnMYB107 positively regulate suberin monomer synthesis by activating AchnCYP86A1 promoter in response to ABA.

The Casparian strip-one ring to bring cell biology to lignification?

Lignin research has long been motivated by the outstanding importance of wood for human societies. The annual, non-woody Arabidopsis thaliana, has nevertheless contributed greatly to our understanding of lignification, due to its unrivalled genetic resources. Arabidopsis is also great for cell and developmental biology, allowing precise imaging and tracking of cell types. Root endodermis differentiation involves the precise lignification of the Casparian Strip, as an apoplastic barrier; while barrier damage triggers a less localized, compensatory lignification. Transcriptional reprogramming and peptide-induced signalling emerge as promising tools for the study of endodermal lignification. We argue that endodermis lignification is an attractive model complementary to equally powerful, cellular xylem differentiation systems, as it might better represent the restricted - often localized - lignification seen in non-vascular cells.

Identification of reference genes for RT-qPCR data normalization in Gammarus fossarum (Crustacea Amphipoda)

Gene expression profiling via RT-qPCR is a robust technique increasingly used in ecotoxicology. Determination and validation of optimal reference genes is a requirement for initiating RT-qPCR experiments. To our best knowledge, this study is the first attempt of identifying a set of reference genes for the freshwater crustacean Gammarus fossarum. Six candidate genes (Actin, TUB, UB, SDH, Clathrin and GAPDH) were tested in order to determine the most stable ones in different stress conditions and to increase the robustness of RT-qPCR data. SDH and Clathrin appeared as the most stable ones. A validation was performed using G. fossarum samples exposed for 15 days to AgNO₃, silver nanoparticles (AgNPs) 40 nm and gold nanoparticles (AuNPs) 40 nm. Effects on HSP90 were evaluated and data normalized using Clathrin and SDH. A down-regulation of HSP90 was observed when G. fossarum were exposed to AuNPs 40 nm whereas no effects were observed when G. fossarum were exposed to AgNPs 40 nm. This study highlights the importance of the preliminary determination of suitable reference genes for RT-qPCR experiments. Additionally, this study allowed, for the first time, the determination of a set of valuable genes that can be used in other RT-qPCR studies using G. fossarum as model organism.

ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

BACKGROUND

Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy.

RESULTS

Results provide direct evidence that QsMY1B targets genes encoding for enzymes involved in the lignin and suberin pathways as well as gene encoding for ABCG transporters and LTPs implicated in the transport of monomeric suberin units across the cellular membrane. These results highlight the role of QsMYB1 as a regulator of lignin and suberin biosynthesis, transport and assembly.

CONCLUSION

To our knowledge, this work constitutes the first ChIP-Seq experiment performed in cork oak, a non-model plant species with a long-life cycle, and these results will contribute to deepen the knowledge about the molecular mechanisms of cork formation and differentiation.

MYBs Drive Novel Consumer Traits in Fruits and Vegetables

Eating plant-derived compounds can lead to a longer and healthier life and also benefits the environment. Innovation in the fresh food sector, as well as new cultivars, can improve consumption of fruit and vegetables, with MYB transcription factors being a target to drive this novelty. Plant MYB transcription factors are implicated in diverse roles including development, hormone signalling, and metabolite biosynthesis. The reds and blues of fruit and vegetables provided by anthocyanins, phlobaphenes, and betalains are controlled by specific R2R3 MYBs. New studies are now revealing that MYBs also control carotenoid biosynthesis and other quality traits, such as flavour and texture. Future breeding techniques may manipulate or create alleles of key MYB transcription factors.

Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues

The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood. We have studied suberin and wax composition in four developmental stages of hybrid poplar (Populus tremula x Populus alba) stem periderm. The amounts of extracellular ester-linked acyl lipids per unit area increased with tissue age, a trend not observed with waxes. We used RNA-Seq deep-sequencing technology to investigate the cork transcriptome at two developmental stages. The transcript analysis yielded 455 candidates for the biosynthesis and regulation of poplar suberin, including genes with proven functions in suberin metabolism, genes highlighted as candidates in other plant species and novel candidates. Among these, a gene encoding a putative lipase/acyltransferase of the GDSL-motif family emerged as a suberin polyester synthase candidate, and specific isoforms of peroxidase and laccase genes were preferentially expressed in cork, suggesting that their corresponding proteins may be involved in cross-linking aromatics to form lignin-like polyphenolics. Many transcriptional regulators with possible roles in meristem identity, cork differentiation and acyl-lipid metabolism were also identified. Our work provides the first large-scale transcriptomic dataset on the suberin-synthesizing tissue of poplar bark, contributing to our understanding of tree bark development at the molecular level. Based on these data, we have proposed a number of hypotheses that can be used in future research leading to novel biological insights into suberin biosynthesis and its physiological function.

Heat and Drought Stresses in Crops and Approaches for Their Mitigation

Drought and heat are major abiotic stresses that reduce crop productivity and weaken global food security, especially given the current and growing impacts of climate change and increases in the occurrence and severity of both stress factors. Plants have developed dynamic responses at the morphological, physiological and biochemical levels allowing them to escape and/or adapt to unfavorable environmental conditions. Nevertheless, even the mildest heat and drought stress negatively affects crop yield. Further, several independent studies have shown that increased temperature and drought can reduce crop yields by as much as 50%. Response to stress is complex and involves several factors including signaling, transcription factors, hormones, and secondary metabolites. The reproductive phase of development, leading to the grain production is shown to be more sensitive to heat stress in several crops. Advances coming from biotechnology including progress in genomics and information technology may mitigate the detrimental effects of heat and drought through the use of agronomic management practices and the development of crop varieties with increased productivity under stress. This review presents recent progress in key areas relevant to plant drought and heat tolerance. Furthermore, an overview and implications of physiological, biochemical and genetic aspects in the context of heat and drought are presented. Potential strategies to improve crop productivity are discussed.

Heat and Drought Stresses in Crops and Approaches for Their Mitigation

Drought and heat are major abiotic stresses that reduce crop productivity and weaken global food security, especially given the current and growing impacts of climate change and increases in the occurrence and severity of both stress factors. Plants have developed dynamic responses at the morphological, physiological and biochemical levels allowing them to escape and/or adapt to unfavorable environmental conditions. Nevertheless, even the mildest heat and drought stress negatively affects crop yield. Further, several independent studies have shown that increased temperature and drought can reduce crop yields by as much as 50%. Response to stress is complex and involves several factors including signaling, transcription factors, hormones, and secondary metabolites. The reproductive phase of development, leading to the grain production is shown to be more sensitive to heat stress in several crops. Advances coming from biotechnology including progress in genomics and information technology may mitigate the detrimental effects of heat and drought through the use of agronomic management practices and the development of crop varieties with increased productivity under stress. This review presents recent progress in key areas relevant to plant drought and heat tolerance. Furthermore, an overview and implications of physiological, biochemical and genetic aspects in the context of heat and drought are presented. Potential strategies to improve crop productivity are discussed.

A comparative transcriptomic approach to understanding the formation of cork

The transcriptome comparison of two oak species reveals possible candidates accounting for the exceptionally thick and pure cork oak phellem, such as those involved in secondary metabolism and phellogen activity. Cork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer bark contains sequential periderms interspersed with dead secondary phloem (rhytidome), the cork oak outer bark only contains thick layers of phellem (cork rings) that accumulate until reaching a thickness that allows industrial uses. Here we compare the cork oak outer bark transcriptome with that of holm oak. Both transcriptomes present similitudes in their complexity, but whereas cork oak external bark is enriched with upregulated genes related to suberin, which is the main polymer responsible for the protective function of periderm, the upregulated categories of holm oak are enriched in abiotic stress and chromatin assembly. Concomitantly with the upregulation of suberin-related genes, there is also induction of regulatory and meristematic genes, whose predicted activities agree with the increased number of phellem layers found in the cork oak sample. Further transcript profiling among different cork oak tissues and conditions suggests that cork and wood share many regulatory mechanisms, probably reflecting similar ontogeny. Moreover, the analysis of transcripts accumulation during the cork growth season showed that most regulatory genes are upregulated early in the season when the cork cambium becomes active. Altogether our work provides the first transcriptome comparison between cork oak and holm oak outer bark, which unveils new regulatory candidate genes of phellem development.

Breeding for cuticle-associated traits in crop species: traits, targets, and strategies

Improving crop productivity and quality while promoting sustainable agriculture have become major goals in plant breeding. The cuticle is a natural film covering the aerial organs of plants and consists of lipid polyesters covered and embedded with wax. The cuticle protects plants against water loss and pathogens and affects traits with strong impacts on crop quality such as, for horticultural crops, fruit brightness, cracking, russeting, netting, and shelf life. Here we provide an overview of the most important cuticle-associated traits that can be targeted for crop improvement. To date, most studies on cuticle-associated traits aimed at crop breeding have been done on fleshy fruits. Less information is available for staple crops such as rice, wheat or maize. Here we present new insights into cuticle formation and properties resulting from the study of genetic resources available for the various crop species. Our review also covers the current strategies and tools aimed at exploiting available natural and artificially induced genetic diversity and the technologies used to transfer the beneficial alleles affecting cuticle-associated traits to commercial varieties.

Poaceae vs. Abiotic Stress: Focus on Drought and Salt Stress, Recent Insights and Perspectives

Poaceae represent the most important group of crops susceptible to abiotic stress. This large family of monocotyledonous plants, commonly known as grasses, counts several important cultivated species, namely wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays), and barley (Hordeum vulgare). These crops, notably, show different behaviors under abiotic stress conditions: wheat and rice are considered sensitive, showing serious yield reduction upon water scarcity and soil salinity, while barley presents a natural drought and salt tolerance. During the green revolution (1940-1960), cereal breeding was very successful in developing high-yield crops varieties; however, these cultivars were maximized for highest yield under optimal conditions, and did not present suitable traits for tolerance under unfavorable conditions. The improvement of crop abiotic stress tolerance requires a deep knowledge of the phenomena underlying tolerance, to devise novel approaches and decipher the key components of agricultural production systems. Approaches to improve food production combining both enhanced water use efficiency (WUE) and acceptable yields are critical to create a sustainable agriculture in the future. This paper analyzes the latest results on abiotic stress tolerance in Poaceae. In particular, the focus will be directed toward various aspects of water deprivation and salinity response efficiency in Poaceae. Aspects related to cell wall metabolism will be covered, given the importance of the plant cell wall in sensing environmental constraints and in mediating a response; the role of silicon (Si), an important element for monocots' normal growth and development, will also be discussed, since it activates a broad-spectrum response to different exogenous stresses. Perspectives valorizing studies on landraces conclude the survey, as they help identify key traits for breeding purposes.

Identification of genes related to skin development in potato

Newly identified genes that are preferentially expressed in potato skin include genes that are associated with the secondary cell wall and stress-related activities and contribute to the skin's protective function. Microarrays were used to compare the skin and tuber-flesh transcriptomes of potato, to identify genes that contribute to the unique characteristics of the skin as a protective tissue. Functional gene analysis indicated that genes involved in developmental processes such as cell division, cell differentiation, morphogenesis and secondary cell wall formation (lignification and suberization), and stress-related activities, are more highly expressed in the skin than in the tuber flesh. Several genes that were differentially expressed in the skin (as verified by qPCR) and had not been previously identified in potato were selected for further analysis. These included the StKCS20-like, StFAR3, StCYP86A22 and StPOD72-like genes, whose sequences suggest that they may be closely related to known suberin-related genes; the StHAP3 transcription factor that directs meristem-specific expression; and the StCASP1B2-like and StCASP1-like genes, which are two orthologs of a protein family that mediates the formation of Casparian strips in the suberized endodermis of Arabidopsis roots. An examination of microtubers induced from transgenic plants carrying GUS reporter constructs of these genes indicated that these genes were expressed in the skin, with little to no expression in the tuber flesh. Some of the reporter constructs were preferentially expressed in the inner layers of the skin, the root endodermis, the vascular cambium and the epidermis of the stem. Cis-regulatory elements within the respective promoter sequences support this gene-expression pattern.

Occurrence and Biosynthesis of Alkyl Hydroxycinnamates in Plant Lipid Barriers

The plant lipid barriers cuticle and suberin represent one of the largest biological interfaces on the planet. They are comprised of an insoluble polymeric domain with associated organic solvent-soluble waxes. Suberin-associated and plant cuticular waxes contain mixtures of aliphatic components that may include alkyl hydroxycinnamates (AHCs). The canonical alkyl hydroxycinnamates are comprised of phenylpropanoids, typically coumaric, ferulic, or caffeic acids, esterified with long chain to very long chain fatty alcohols. However, many related structures are also present in the plant kingdom. Although their functions remain elusive, much progress has been made on understanding the distribution, biosynthesis, and deposition of AHCs. Herein a summary of the current state of knowledge on plant AHCs is provided.

Differential Lipid Composition and Gene Expression in the Semi-Russeted "Cox Orange Pippin" Apple Variety

Russeting is characterized by a particular rough and brown phenotype, which is mainly due to the accumulation of suberin in the inner part of the epidermal cell walls. In our previous bulk transcriptomic analysis, comparing fully russeted, and waxy apple varieties, showed, in apple fruit skin, a massive decreased expression of cutin, wax and some pentacyclic triterpene biosynthesis genes in the russeted varieties, with an expected concomitant enhanced expression of the suberin biosynthetic genes. In the present work, we performed a deep investigation of the aliphatic composition of the cutin, suberin, waxes, and triterpenes in the waxy and russeted patches of the semi-russeted apple variety "Cox Orange Pippin." A targeted gene expression profiling was performed to validate candidate genes which were identified in our previous work and might be involved in the respective metabolic pathways. Our results showed that a decrease of cuticular waxes, ursolic acid and oleanolic acid, accompanied by an accumulation of alkyl-hydroxycinamates and betulinic acid, occurs in the russeted patches. The suberin monomer composition is characterized by specific occurrence of 20, 22, and 24 carbon aliphatic chains, whereas cutin is mainly represented by common C16 and C18 aliphatic chains. This work depicts, for the first time in apple, the complex composition of suberin, cutin, waxes and triterpenes, and confirms the strong interplay between these epidermal polymers in apple fruit skin.

Mutant Transcriptome Sequencing Provides Insights into Pod Development in Peanut (Arachis hypogaea L.)

Pod size is the major yield component and a key target trait that is selected for in peanut breeding. However, although numerous quantitative trait loci (QTLs) for peanut pod size have been described, the molecular mechanisms underlying the development of this characteristic remain elusive. A peanut mutant with a narrower pod was developed in this study using ethyl methanesulfonate (EMS) mutagenesis and designated as the "pod width" mutant line (pw). The fresh pod weight of pw was only about 40% of that seen in the wild-type (WT) Zhonghua16, while the hull and seed filling of the mutant both also developed at earlier stages. Pods from both pw and WT lines were sampled 20, 40, and 60 days after flowering (DAF) and used for RNA-Seq analysis; the results revealed highly differentially expressed lignin metabolic pathway genes at all three stages, but especially at DAF 20 and DAF 40. At the same time, expression of genes related to auxin signal transduction was found to be significantly repressed during the pw early pod developmental stage. A genome-wide comparative analysis of expression profiles revealed 260 differentially expressed genes (DEGs) across all three stages, and two candidate genes, c26901_g1 (CAD) and c37339_g1 (ACS), responsible for pod width were identified by integrating expression patterns and function annotation of the common DEGs within the three stages. Taken together, the information provided in this study illuminates the processes underlying peanut pod development, and will facilitate further identification of causal genes and the development of improved peanut varieties with higher yields.