Stamen abscission zone transcriptome profiling reveals new candidates for abscission control: enhanced retention of floral organs in transgenic plants overexpressing Arabidopsis ZINC FINGER PROTEIN2

Dissection of the IDA promoter identifies WRKY transcription factors as abscission regulators in Arabidopsis

Plants shed organs such as leaves, petals, or fruits through the process of abscission. Monitoring cues such as age, resource availability, and biotic and abiotic stresses allow plants to abscise organs in a timely manner. How these signals are integrated into the molecular pathways that drive abscission is largely unknown. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) gene is one of the main drivers of floral organ abscission in Arabidopsis and is known to transcriptionally respond to most abscission-regulating cues. By interrogating the IDA promoter in silico and in vitro, we identified transcription factors that could potentially modulate IDA expression. We probed the importance of ERF- and WRKY-binding sites for IDA expression during floral organ abscission, with WRKYs being of special relevance to mediate IDA up-regulation in response to biotic stress in tissues destined for separation. We further characterized WRKY57 as a positive regulator of IDA and IDA-like gene expression in abscission zones. Our findings highlight the promise of promoter element-targeted approaches to modulate the responsiveness of the IDA signaling pathway to harness controlled abscission timing for improved crop productivity.

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L

The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.

Phytohormones and candidate genes synergistically regulate fruitlet abscission in Areca catechu L

BACKGROUND

The fruit population of most plants is under the control of a process named "physiological drop" to selectively abort some developing fruitlets. However, frequent fruitlet abscission severely restricts the yield of Areca catechu. To reveal the physiological and molecular variations in this process, we detected the variation of phytohormone levels in abscised and non-abscised fruitlets in A. catechu.

RESULTS

The levels of gibberellin acid, jasmonic acid, salicylic acid, abscisic acid and zeatin were elevated, while the indole-3-acetic acid and indole-3-carboxaldehyde levels were declined in the "about-to-abscise" part (AB) of abscission zone (AZ) compared to the "non-abscised" part (CK). Then the differentially expressed genes (DEGs) between AB and CK were screened based on transcriptome data. DEGs involved in phytohormone synthesis, response and transportation were identified as key genes. Genes related to cell wall biosynthesis, degradation, loosening and modification, and critical processes during fruit abscission were identified as role players. In addition, genes encoding transcription factors, such as NAC, ERF, WRKY, MADS and Zinc Finger proteins, showed differentially expressed patterns between AB and CK, were also identified as candidates.

CONCLUSIONS

These results unraveled a phytohormone signaling cross talk and key genes involved in the fruitlet abscission process in A. catechu. This study not only provides a theoretical basis for fruitlet abscission in A. catechu, but also identified many candidate genes or potential molecular markers for further breeding of fruit trees.

Brt9SIDA/IDALs as peptide signals mediate diverse biological pathways in plants

As signal molecules, plant peptides play key roles in intercellular communication during growth and development, as well as stress responses. The 14-amino-acid (aa) INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide was originally identified to play an essential role in the floral organ abscission of Arabidopsis. It is synthesized from its precursor, a small protein containing 77-aa residues with an N-terminal signal peptide sequence. Recently, the IDA/IDA-like (IDLs) genes are isolated in several angiosperms and are highly conserved in land plants. In addition, IDA/IDLs are not only involved in organ abscission but also function in multiple biological processes, including biotic and abiotic stress responses. Here, we summarize the post-translational modification and proteolytic processing, the evolutionary conservation, and the potential regulatory function of IDA/IDLs, and also present future perspectives to investigate the IDA/IDLs signaling pathway. We anticipate that this detailed knowledge will help to improve the understanding of the molecular mechanism of plant peptide signaling.

Integrative analysis of transcriptome, proteome, and ubiquitome changes during rose petal abscission

Plant organ abscission is regulated by multiple physiological and biochemical processes. However, the transcriptional, translational, and post-translational modifications occurring during organ abscission have not been systematically investigated. In this study, we report transcriptome, proteome, and ubiquitome data for the abscission zone (AZ) of rose petals collected during petal shedding. We quantified 40,506 genes, 6,595 proteins, and 2,720 ubiquitinated proteins in rose petal AZ. Our results showed that during petal abscission, 1,496 genes were upregulated and 2,199 were downregulated; 271 proteins were upregulated and 444 were downregulated; and 139 ubiquitination sites in 100 proteins were upregulated and 55 ubiquitination sites in 48 proteins were downregulated. Extracellular levels of cell component proteins were significantly increased, while levels within protoplasts were significantly decreased. During petal abscission, transcript levels of genes involved in defense response, transport, and metabolism changed significantly. Levels of proteins involved in the starch and sucrose metabolism and phenylpropanoid biosynthesis pathways were significantly altered at both the transcript and protein levels. The transcriptional and translational upregulation of peroxidase (POD), in the phenylpropanoid biosynthesis, pathway may be associated with deposition of lignin, which forms a protective layer during petal abscission. Overall, our data provide a comprehensive assessment of the translational and post-translational changes that occur during rose petal abscission.

Genome-Wide Identification of the DOF Gene Family Involved in Fruitlet Abscission in Areca catechu L

Fruitlet abscission frequently occurs in Areca catechu L. and causes considerable production loss. However, the inducement mechanism of fruitlet abscission remains mysterious. In this study, we observed that the cell architecture in the abscission zone (AZ) was distinct with surrounding tissues, and varied obviously before and after abscission. Transcriptome analysis of the “about-to-abscise” and “non-abscised” AZs were performed in A. catechu, and the genes encoding the plant-specific DOF (DNA-binding with one finger) transcription factors showed a uniform up-regulation in AZ, suggesting a role of the DOF transcription in A. catechu fruitlet abscission. In total, 36 members of the DOF gene family distributed in 13 chromosomes were identified from the A. catechu genome. The 36 AcDOF genes were classified into nine subgroups based on phylogenic analysis. Six of them showed an AZ-specific expression pattern, and their expression levels varied according to the abscission process. In total, nine types of phytohormone response cis-elements and five types of abiotic stress related cis-elements were identified in the promoter regions of the AcDOF genes. In addition, histochemical staining showed that lignin accumulation of vascular bundles in AZ was significantly lower than that in pedicel and mesocarp, indicating the specific characteristics of the cell architecture in AZ. Our data suggests that the DOF transcription factors might play a role in fruitlet abscission regulation in A. catechu.

Transcriptomics Using the Enriched Arabidopsis Shoot Apex Reveals Developmental Priming Genes Involved in Plastic Plant Growth under Salt Stress Conditions

In the shoot apical meristem (SAM), the homeostasis of the stem cell population supplying new cells for organ formation is likely a key mechanism of multicellular plant growth and development. As plants are sessile organisms and constantly encounter environmental abiotic stresses, postembryonic development from the shoot stem cell population must be considered with surrounding abiotic stresses for plant adaptation. However, the underlying molecular mechanisms for plant adaptation remain unclear. Previous studies found that the stem-cell-related mutant clv3-2 has the property of salt tolerance without the differential response of typical stress-responsive genes compared to those in WT Ler. Based on these facts, we hypothesized that shoot meristems contain developmental priming genes having comprehensively converged functions involved in abiotic stress response and development. To better understand the biological process of developmental priming genes in the SAM, we performed RNA sequencing (RNA-seq) and transcriptome analysis through comparing genome-wide gene expression profiles between enriched shoot apex and leaf tissues. As a result, 121 putative developmental priming genes differentially expressed in the shoot apex compared to the leaf were identified under normal and salt stress conditions. RNA-seq experiments also revealed the shoot apex-specific responsive genes for salt stress conditions. Based on combinatorial comparisons, 19 developmental priming genes were finally identified, including developmental genes related to cell division and abiotic/biotic-stress-responsive genes. Moreover, some priming genes showed CLV3-dependent responses under salt stress conditions in the clv3-2. These results presumably provide insight into how shoot meristem tissues have relatively high viability against stressful environmental conditions for the developmental plasticity of plants.

MSD2-mediated ROS metabolism fine-tunes the timing of floral organ abscission in Arabidopsis

The timely removal of end-of-purpose flowering organs is as essential for reproduction and plant survival as timely flowering. Despite much progress in understanding the molecular mechanisms of floral organ abscission, little is known about how various environmental factors are integrated into developmental programmes that determine the timing of abscission. Here, we investigated whether reactive oxygen species (ROS), mediators of various stress-related signalling pathways, are involved in determining the timing of abscission and, if so, how they are integrated with the developmental pathway in Arabidopsis thaliana. MSD2, encoding a secretory manganese superoxide dismutase, was preferentially expressed in the abscission zone of flowers, and floral organ abscission was accelerated by the accumulation of ROS in msd2 mutants. The expression of the genes encoding the receptor-like kinase HAESA (HAE) and its cognate peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), the key signalling components of abscission, was accelerated in msd2 mutants, suggesting that MSD2 acts upstream of IDA-HAE. Further transcriptome and pharmacological analyses revealed that abscisic acid and nitric oxide facilitate abscission by regulating the expression of IDA and HAE during MSD2-mediated signalling. These results suggest that MSD2-dependent ROS metabolism is an important regulatory point integrating environmental stimuli into the developmental programme leading to abscission.

Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

BACKGROUND

Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system.

RESULTS

We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFULL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs.

CONCLUSIONS

Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as candidate genes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.

Thidiazuron Promotes Leaf Abscission by Regulating the Crosstalk Complexities between Ethylene, Auxin, and Cytokinin in Cotton

Thidiazuron (TDZ) is widely used as a defoliant to induce leaf abscission in cotton. However, the underlying molecular mechanism is still unclear. In this study, RNA-seq and enzyme-linked immunosorbent assays (ELISA) were performed to reveal the dynamic transcriptome profiling and the change of endogenous phytohormones upon TDZ treatment in leaf, petiole, and abscission zone (AZ). We found that TDZ induced the gene expression of ethylene biosynthesis and signal, and promoted ethylene accumulation earlier in leaf than that in AZ. While TDZ down-regulated indole-3-acetic acid (IAA) biosynthesis genes mainly in leaf and IAA signal and transport genes. Furthermore, the IAA content reduced more sharply in the leaf than that in AZ to change the auxin gradient for abscission. TDZ suppressed CTK biosynthesis genes and induced CTK metabolic genes to reduce the IPA accumulation for the reduction of ethylene sensitivity. Furthermore, TDZ regulated the gene expression of abscisic acid (ABA) biosynthesis and signal and induced ABA accumulation between 12-48 h, which could up-regulate ABA response factor genes and inhibit IAA transporter genes. Our data suggest that TDZ orchestrates metabolism and signal of ethylene, auxin, and cytokinin, and also the transport of auxin in leaf, petiole, and AZ, to control leaf abscission.

The HB40-JUB1 transcriptional regulatory network controls gibberellin homeostasis in Arabidopsis

The gibberellins (GAs) are phytohormones that play fundamental roles in almost every aspect of plant growth and development. Although GA biosynthetic and signaling pathways are well understood, the mechanisms that control GA homeostasis remain largely unclear in plants. Here, we demonstrate that the homeobox transcription factor (TF) HB40 of the HD-Zip family regulates GA content at two additive control levels in Arabidopsis thaliana. We show that HB40 expression is induced by GA and in turn reduces the levels of endogenous bioactive GAs by simultaneously reducing GA biosynthesis and increasing GA deactivation. Consistently, HB40 overexpression leads to typical GA-deficiency traits, such as small rosettes, reduced plant height, delayed flowering, and male sterility. By contrast, a loss-of-function hb40 mutation enhances GA-controlled growth. Genome-wide RNA sequencing combined with molecular-genetic analyses revealed that HB40 directly activates the transcription of JUNGBRUNNEN1 (JUB1), a key TF that represses growth by suppressing GA biosynthesis and signaling. HB40 also activates genes encoding GA 2-oxidases (GA2oxs), which are major GA-catabolic enzymes. The effect of HB40 on plant growth is ultimately mediated through the induction of nuclear growth-repressing DELLA proteins. Collectively, our results reveal the important role of the HB40-JUB1 regulatory network in controlling GA homeostasis during plant growth.

Functional Characterization of an Amaranth Natterin-4-Like-1 Gene in Arabidopsis thaliana

The functional characterization of an Amaranthus hypochondriacus Natterin-4-Like-1 gene (AhN4L-1) coding for an unknown function protein characterized by the presence of an aerolysin-like pore-forming domain in addition to two amaranthin-like agglutinin domains is herewith described. Natterin and nattering-like proteins have been amply described in the animal kingdom. However, the role of nattering-like proteins in plants is practically unknown. The results described in this study, obtained from gene expression data in grain amaranth and from AhN4L-1-overexpressing Arabidopsis thaliana plants indicated that this gene was strongly induced by several biotic and abiotic conditions in grain amaranth, whereas data obtained from the overexpressing Arabidopsis plants further supported the defensive function of this gene, mostly against bacterial and fungal plant pathogens. GUS and GFP AhN4L-1 localization in roots tips, leaf stomata, stamens and pistils also suggested a defensive function in these organs, although its participation in flowering processes, such as self-incompatibility and abscission, is also possible. However, contrary to expectations, the overexpression of this gene negatively affected the vegetative and reproductive growth of the transgenic plants, which also showed no increased tolerance to salinity and water-deficit stress. The latter despite the maintenance of significantly higher chlorophyll levels and photosynthetic parameters under intense salinity stress. These results are discussed in the context of the physiological roles known to be played by related lectins and AB proteins in plants.

Characterising the mechanics of cell-cell adhesion in plants

Cell-cell adhesion is a fundamental feature of multicellular organisms. To ensure multicellular integrity, adhesion needs to be tightly controlled and maintained. In plants, cell-cell adhesion remains poorly understood. Here, we argue that to be able to understand how cell-cell adhesion works in plants, we need to understand and quantitatively measure the mechanics behind it. We first introduce cell-cell adhesion in the context of multicellularity, briefly explain the notions of adhesion strength, work and energy and present the current knowledge concerning the mechanisms of cell-cell adhesion in plants. Because still relatively little is known in plants, we then turn to animals, but also algae, bacteria, yeast and fungi, and examine how adhesion works and how it can be quantitatively measured in these systems. From this, we explore how the mechanics of cell adhesion could be quantitatively characterised in plants, opening future perspectives for understanding plant multicellularity.

Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development

Chia (Salvia hispanica L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information available in the public domain for this crop are scanty, which hinders an understanding of its growth and development and genetic improvement. We report an RNA-sequencing (RNA-Seq)-based comprehensive transcriptome atlas of Chia sampled from 13 tissue types covering vegetative and reproductive growth stages. We used ~355 million high-quality reads of total ~394 million raw reads from transcriptome sequencing to generate de novo reference transcriptome assembly and the tissue-specific transcript assemblies. After the quality assessment of the merged assemblies and implementing redundancy reduction methods, 82,663 reference transcripts were identified. About 65,587 of 82,663 transcripts were translated into 99,307 peptides, and we were successful in assigning InterPro annotations to 45,209 peptides and gene ontology (GO) terms to 32,638 peptides. The assembled transcriptome is estimated to have the complete sequence information for ~86% of the genes found in the Chia genome. Furthermore, the analysis of 53,200 differentially expressed transcripts (DETs) revealed their distinct expression patterns in Chia's vegetative and reproductive tissues; tissue-specific networks and developmental stage-specific networks of transcription factors (TFs); and the regulation of the expression of enzyme-coding genes associated with important metabolic pathways. In addition, we identified 2,411 simple sequence repeats (SSRs) as potential genetic markers from the transcripts. Overall, this study provides a comprehensive transcriptome atlas, and SSRs, contributing to building essential genomic resources to support basic research, genome annotation, functional genomics, and molecular breeding of Chia.

SlERF52 regulates SlTIP1;1 expression to accelerate tomato pedicel abscission

Abscission of plant organs is induced by developmental signals and diverse environmental stimuli and involves multiple regulatory networks, including biotic or abiotic stress-impaired auxin flux in the abscission zone (AZ). Depletion of auxin activates AZ ethylene (ETH) production and triggers acceleration of abscission, a process that requires hydrogen peroxide (H2O2). However, the interaction between these networks and the underlying mechanisms that control abscission are poorly understood. Here, we found that expression of tonoplast intrinsic proteins, which belong to the aquaporin (AQP) family in the AZ was important for tomato (Solanum lycopersicum) pedicel abscission. Liquid chromatography-tandem mass spectrometry and in situ hybridization revealed that SlTIP1;1 was most abundant and specifically present in the tomato pedicel AZ. SlTIP1;1 localized in the plasma membrane and tonoplast. Knockout of SlTIP1;1 resulted in delayed abscission, whereas overexpression of SlTIP1;1 accelerated abscission. Further analysis indicated that SlTIP1;1 mediated abscission via gating of cytoplasmic H2O2 concentrations and osmotic water permeability (Pf). Elevated cytoplasmic levels of H2O2 caused a suppressed auxin signal in the early abscission stage and enhanced ETH production during abscission. Furthermore, we found that increasing Pf was required to enhance the turgor pressure to supply the break force for AZ cell separation. Moreover, we observed that SlERF52 bound directly to the SlTIP1;1 promoter to regulate its expression, demonstrating a positive loop in which cytoplasmic H2O2 activates ETH production, which activates SlERF52. This, in turn, induces SlTIP1;1, which leads to elevated cytoplasmic H2O2 and water influx.

Non-specific phospholipases C2 and C6 redundantly function in pollen tube growth via triacylglycerol production in Arabidopsis

Non-specific phospholipase Cs (NPCs) are responsible for membrane lipid remodeling that involves hydrolysis of the polar head group of membrane phospholipids. Arabidopsis NPC2 and NPC6 are essential in gametogenesis, but their underlying role in the lipid remodeling remains elusive. Here, we show that these NPCs are required for triacylglycerol (TAG) production in pollen tube growth. NPC2 and NPC6 are highly expressed in developing pollen tubes and are localized at the endoplasmic reticulum. Mutants of NPC2 and NPC6 showed reduced rate of pollen germination, length of pollen tube and amount of lipid droplets (LDs). Overexpression of NPC2 or NPC6 induced LD accumulation, which suggests that these NPCs are involved in LD production. Furthermore, mutants defective in the biosynthesis of TAG, a major component of LDs, showed defective pollen tube growth. These results suggest that NPC2 and NPC6 are essential in gametogenesis for a role in hydrolyzing phospholipids and producing TAG required for pollen tube growth. Thus, lipid remodeling from phospholipids to TAG during pollen tube growth represents an emerging role for the NPC family in plant developmental control.

A Plant Based Modified Biostimulant (Copper Chlorophyllin), Mediates Defense Response in Arabidopsis thaliana under Salinity Stress

To date, managing salinity stress in agriculture relies heavily on development of salt tolerant plant varieties, a time-consuming process particularly challenging for many crops. Plant based biostimulants (PBs) that enhance plant defenses under stress can potentially address this drawback, as they are not crop specific and are easy to apply in the field. Unfortunately, limited knowledge about their modes of action makes it harder to utilize them on a broader scale. Understanding how PBs enhance plant defenses at cellular and molecular levels, is a prerequisite for the development of sustainable management practices utilizing biostimulants to improve crop health. In this study we elucidated the protective mechanism of copper chlorophyllin (Cu-chl), a PB, under salinity stress. Our results indicate that Cu-chl exerts protective effects primarily by decreasing oxidative stress through modulating cellular H₂O₂ levels. Cu-chl treated plants increased tolerance to oxidative stress imposed by an herbicide, methyl viologen dichloride hydrate as well, suggesting a protective role against various sources of reactive oxygen species (ROS). RNA-Seq analysis of Cu-chl treated Arabidopsis thaliana seedlings subjected to salt stress identified genes involved in ROS detoxification, and cellular growth.

EPIP-Evoked Modifications of Redox, Lipid, and Pectin Homeostasis in the Abscission Zone of Lupine Flowers

Yellow lupine is a great model for abscission-related research given that excessive flower abortion reduces its yield. It has been previously shown that the EPIP peptide, a fragment of LlIDL (INFLORESCENCE DEFICIENT IN ABSCISSION) amino-acid sequence, is a sufficient molecule to induce flower abortion, however, the question remains: What are the exact changes evoked by this peptide locally in abscission zone (AZ) cells? Therefore, we used EPIP peptide to monitor specific modifications accompanied by early steps of flower abscission directly in the AZ. EPIP stimulates the downstream elements of the pathway-HAESA and MITOGEN-ACTIVATED PROTEIN KINASE6 and induces cellular symptoms indicating AZ activation. The EPIP treatment disrupts redox homeostasis, involving the accumulation of H2O2 and upregulation of the enzymatic antioxidant system including superoxide dismutase, catalase, and ascorbate peroxidase. A weakening of the cell wall structure in response to EPIP is reflected by pectin demethylation, while a changing pattern of fatty acids and acyl lipids composition suggests a modification of lipid metabolism. Notably, the formation of a signaling molecule-phosphatidic acid is induced locally in EPIP-treated AZ. Collectively, all these changes indicate the switching of several metabolic and signaling pathways directly in the AZ in response to EPIP, which inevitably leads to flower abscission.

MPK14-mediated auxin signaling controls lateral root development via ERF13-regulated very-long-chain fatty acid biosynthesis

Auxin plays a critical role in lateral root (LR) formation. The signaling module composed of auxin-response factors (ARFs) and lateral organ boundaries domain transcription factors mediates auxin signaling to control almost every stage of LR development. Here, we show that auxin-induced degradation of the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor ERF13, dependent on MITOGEN-ACTIVATED PROTEIN KINASE MPK14-mediated phosphorylation, plays an essential role in LR development. Overexpression of ERF13 results in restricted passage of the LR primordia through the endodermal layer, greatly reducing LR emergence, whereas the erf13 mutants showed an increase in emerged LR. ERF13 inhibits the expression of 3-ketoacyl-CoA synthase16 (KCS16), which encodes a fatty acid elongase involved in very-long-chain fatty acid (VLCFA) biosynthesis. Overexpression of KCS16 or exogenous VLCFA treatment rescues the LR emergence defects in ERF13 overexpression lines, indicating a role downstream of the auxin-MPK14-ERF13 signaling module. Collectively, our study uncovers a novel molecular mechanism by which MPK14-mediated auxin signaling modulates LR development via ERF13-regulated VLCFA biosynthesis.

Histone Demethylases ELF6 and JMJ13 Antagonistically Regulate Self-Fertility in Arabidopsis

The chromatin modification H3K27me3 is involved in almost every developmental stage in Arabidopsis. Much remains unknown about the dynamic regulation of this histone modification in flower development and control of self-fertility. Here we demonstrate that the H3K27me3-specific demethylases ELF6 and JMJ13 antagonistically regulate carpel and stamen growth and thus modulate self-fertility. Transcriptome and epigenome data are used to identify potential targets of ELF6 and JMJ13 responsible for these physiological functions. We find that ELF6 relieves expansin genes of epigenetic silencing to promote cell elongation in the carpel, enhancing carpel growth and therefore encouraging out-crossing. On the other hand, JMJ13 activates genes of the jasmonic acid regulatory network alongside the auxin responsive SAUR26, to inhibit carpel growth, enhance stamen growth, and overall promote self-pollination. Our evidence provides novel mechanisms of self-fertility regulation in A. thaliana demonstrating how chromatin modifying enzymes govern the equilibrium between flower self-pollination and out-crossing.

Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome

Flowers of fragrant roses such as Rosa bourboniana are ethylene-sensitive and undergo rapid petal abscission while hybrid roses show reduced ethylene sensitivity and delayed abscission. To understand the molecular mechanism underlying these differences, a comparative transcriptome of petal abscission zones (AZ) of 0 h and 8 h ethylene-treated flowers from R. bourboniana was performed. Differential regulation of 3700 genes (1518 up, 2182 down) representing 8.5% of the AZ transcriptome was observed between 0 and 8 h ethylene-treated R. bourboniana petal AZ. Abscission was associated with large scale up-regulation of the ethylene pathway but prominent suppression of the JA, auxin and light-regulated pathways. Regulatory genes encoding kinases/phosphatases/F-box proteins and transcription factors formed the major group undergoing differential regulation besides genes for transporters, wall modification, defense and phenylpropanoid pathways. Further comparisons with ethylene-treated petals of R. bourboniana and 8 h ethylene-treated AZ (R. hybrida) identified a core set of 255 genes uniquely regulated by ethylene in R. bourboniana AZ. Almost 23% of these encoded regulatory proteins largely conserved with Arabidopsis AZ components. Most of these were up-regulated while an entire set of photosystem genes was prominently down-regulated. The studies provide important information on regulation of petal abscission in roses.

Spatio-temporal immunolocalization of extensin protein and hemicellulose polysaccharides during olive fruit abscission

Immunocytochemical and molecular analyses reveal that the disassembly of the cell wall may be mediated by changes in the level and subcellular location of extensin protein and hemicelluloses during olive-fruit abscission. Although cell-wall modification is believed to underlie the changes in organ abscission, information concerning the changes in cell-wall proteins and hemicellulose polysaccharides is still limited. The aim of this work was to analyze the spatio-temporal patterns of the distribution of different extensin proteins and hemicelluloses in the abscission zone (AZ) during natural ripe-fruit abscission in olive (Olea europaea L.). In this study, we employed immunogold labeling in the ripe-fruit AZ during olive AZ cell separation, using an expanded set of monoclonal antibodies that recognize different types of hemicelluloses (LM11, LM15, and LM21), callose (anti-(1,3)-β-D-glucan) and extensin (JIM19) epitopes, and transmission electron microscopy imaging. Our data demonstrate that AZ cell separation was accompanied by a loss of the JIM19 extensin epitopes and a reduction in the detection of the LM15 xyloglucan epitopes in AZ cell walls, whereas AZ cells were found to be enriched with respect to the xylan and callose levels of the cell wall during olive ripe-fruit abscission. By contrast, AZ cell-wall polysaccharide remodeling did not involve mannans. Moreover, in ripe-fruit AZ, quantitative RT-PCR analysis revealed that OeEXT1, OeEXT2, OeXTH9, and OeXTH13 genes were downregulated during abscission, whereas the expression of OeXTH1, OeXTH5, and OeXTH14 genes increased during abscission. Taken together, the results indicate that AZ cell-wall dynamics during olive ripe-fruit abscission involves extensin protein and hemicellulose modifications, as well as related expressed genes. This is the first study available demonstrating temporal degradation of extensin protein and hemicelluloses in the AZ at the subcellular level.

Two receptor-like protein kinases, MUSTACHES and MUSTACHES-LIKE, regulate lateral root development in Arabidopsis thaliana

Receptor-like protein kinases (RLKs) play key roles in regulating plant growth, development and stress adaptations. There are at least 610 RLKs (including receptor-like cytoplasmic kinases) in Arabidopsis. The functions of the majority of RLKs have not yet been determined. We previously generated promoter::GUS transgenic plants for all leucine-rich repeat (LRR)-RLKs in Arabidopsis and analyzed their expression patterns during various developmental stages. We found the expression of two LRR-RLKs, MUSTACHES (MUS) and MUSTACHES-LIKE (MUL), are overlapped in lateral root primordia. Independent mutants, mus-3 mul-1 and mus-4 mul-2, show a significantly decreased emerged lateral root phenotype. Our analyses indicate that the defects of the double mutant occur mainly at stage I of lateral root development. Exogenous application of auxin can dramatically enhance the transcription of MUS, which is largely dependent on AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19. MUS and MUL are inactive kinases in vitro but are phosphorylated in planta, possibly by an unknown kinase. The kinase activity of MUS is dispensable for its function in lateral root development. Many cell wall related genes are down regulated in mus-3 mul-1. In conclusion, we identified MUS and MUL, two kinase-inactive RLKs, in controlling the early development of lateral root primordia likely via regulating cell wall synthesis and remodeling.

Transcription factor CDF4 promotes leaf senescence and floral organ abscission by regulating abscisic acid and reactive oxygen species pathways in Arabidopsis

Leaf senescence is a highly complex developmental process that is tightly controlled by multiple layers of regulation. Abscisic acid (ABA) and reactive oxygen species (ROS) are two well-known factors that promote leaf senescence. We show here that the transcription factor CDF4 positively regulates leaf senescence. Constitutive and inducible overexpression of CDF4 accelerates leaf senescence, while knockdown of CDF4 delays it. CDF4 increases endogenous ABA levels by upregulating the transcription of the ABA biosynthesis genes 9-cis-epoxycarotenoid dioxygenase 2, 3 (NCED2, 3) and suppresses H₂ O₂ scavenging by repressing expression of the catalase2 (CAT2) gene. NCED2, 3 knockout and CAT2 overexpression partially rescue premature leaf senescence caused by CDF4 overexpression. We also show that CDF4 promotes floral organ abscission by activating the polygalacturonase PGAZAT gene. Based on these results, we propose that the levels of CDF4, ABA, and ROS undergo a gradual increase driven by their interlinking positive feedback loops during the leaf senescence and floral organ abscission processes.

Mechanism and Regulation of Silique Dehiscence, Which Affects Oil Seed Production

Silique dehiscence is an important physiological process during natural growth that enables mature seeds to be released from plants, which then undergo reproduction and ensure the survival of future generations. In agricultural production, the time and degree of silique dehiscence affect the harvest time and processing of crops. Premature silique dehiscence leads to seeds being shed before harvest, resulting in substantial reductions to yields. Conversely, late silique dehiscence is not conducive to harvesting, and grain weight and oil content will be reduced due to the respiratory needs of seeds. In this paper, the mechanisms and regulation of silique dehiscence, and its application in agricultural production is reviewed.

Hydrogen sulfide inhibits ethylene-induced petiole abscission in tomato (Solanum lycopersicum L.)

Abscission is a dynamic physiological process that is ubiquitous in plants and can also be an essential agronomic trait in crops, thus attracting attention from plant growers and breeders. In general, the process of plant organ abscission can be divided into four steps, among which the step to obtain the competence to respond to abscission signals (step 2) is the most complex; however, the molecular mechanism underlying this process remains unclear. In this study, we found that hydrogen sulfide (H2S) inhibited the abscission of the tomato petiole in a dose-dependent manner, and the abscission of the petiole was accelerated when an H2S scavenger was applied. Further enzymatic activity and gene expression analyses showed that H2S suppressed the activity of enzymes capable of modifying the cell wall by inhibiting the usual upregulation of the transcription of the corresponding genes during the abscission process but not by affecting the activities of these enzymes by direct posttranslational modification. H2S treatment upregulated the expression levels of SlIAA3 and SlIAA4 but downregulated the transcription of ILR-L3 and ILR-L4 in the earlier stages of the abscission process, indicating that H2S probably functioned in the second step of the abscission process by preventing the abscission zone cells from obtaining the competence to respond to abscission signals by modulating the content of the bioactive-free auxin in these cells. Moreover, similar H2S inhibitory effects were also demonstrated in the process of floral organ abscission and anther dehiscence in other plant species, suggesting a ubiquitous role for H2S in cell separation processes.

Early transcriptional responses to soybean cyst nematode HG Type 0 show genetic differences among resistant and susceptible soybeans

KEY MESSAGE

Root transcriptome profiling of three soybean cultivars and a wild relative infected with soybean cyst nematode at migratory phase revealed differential resistance pathway responses between resistant and susceptible genotypes. The soybean cyst nematode (SCN), Heterodera glycines, is the most serious pathogen of soybean production throughout the world. Using resistant cultivars is the primary management strategy against SCN infestation. To gain insight into the still obscure mechanisms of genetic resistance to nematodes in different soybean genotypes, RNA-Seq profiling of the roots of Glycine max cv. Peking, Fayette, Williams 82, and a wild relative (Glycine soja PI 468916) was performed during SCN infection at the migratory phase. The analysis showed statistically significant changes of expression beginning at eight hours after inoculation in genes associated with defense mechanisms and pathways, such as the phenylpropanoid biosynthesis pathway, plant innate immunity and hormone signaling. Our results indicate the importance of the early plant response to migratory phase nematodes in pathogenicity determination. The transcriptome changes occurring during early SCN infection included a number of genes and pathways specific to the different resistant genotypes. We observed the most extensive resistant transcriptome reaction in PI 468916, where the resistant response was qualitatively different from that of commonly used G. max varieties.

The Roles of Arabidopsis C1-2i Subclass of C2H2-type Zinc-Finger Transcription Factors

The Cys2His2 (C2H2)-type zinc-finger protein (ZFP) family, which includes 176 members in Arabidopsis thaliana, is one of the largest families of putative transcription factors in plants. Of the Arabidopsis ZFP members, only 33 members are conserved in other eukaryotes, with 143 considered to be plant specific. C2H2-type ZFPs have been extensively studied and have been shown to play important roles in plant development and environmental stress responses by transcriptional regulation. The ethylene-responsive element binding-factor-associated amphiphilic repression (EAR) domain (GCC box) has been found to have a critical role in the tolerance response to abiotic stress. Many of the plant ZFPs containing the EAR domain, such as AZF1/2/3, ZAT7, ZAT10, and ZAT12, have been shown to function as transcriptional repressors. In this review, we mainly focus on the C1-2i subclass of C2H2 ZFPs and summarize the latest research into their roles in various stress responses. The role of C2H2-type ZFPs in response to the abiotic and biotic stress signaling network is not well explained, and amongst them, C1-2i is one of the better-characterized classifications in response to environmental stresses. These studies of the C1-2i subclass ought to furnish the basis for future studies to discover the pathways and receptors concerned in stress defense. Research has implied possible protein-protein interactions between members of C1-2i under various stresses, for which we have proposed a hypothetical model.

Control of Organ Abscission and Other Cell Separation Processes by Evolutionary Conserved Peptide Signaling

Plants both generate and shed organs throughout their lifetime. Cell separation is in function during opening of anthers to release pollen; floral organs are detached after pollination when they have served their purpose; unfertilized flowers are shed; fruits and seeds are abscised from the mother plant to secure the propagation of new generations. Organ abscission takes place in specialized abscission zone (AZ) cells where the middle lamella between adjacent cell files is broken down. The plant hormone ethylene has a well-documented promoting effect on abscission, but mutation in ethylene receptor genes in Arabidopsis thaliana only delays the abscission process. Microarray and RNA sequencing have identified a large number of genes differentially expressed in the AZs, especially genes encoding enzymes involved in cell wall remodelling and disassembly. Mutations in such genes rarely give a phenotype, most likely due to functional redundancy. In contrast, mutation in the INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) blocks floral organ abscission in Arabidopsis. IDA encodes a small peptide that signals through the leucine-rich repeat receptor-like kinases HAESA (HAE) and HAE-LIKE2 (HSL2) to control floral organ abscission and facilitate lateral root emergence. Untimely abscission is a severe problem in many crops, and in a more applied perspective, it is of interest to investigate whether IDA-HAE/HSL2 is involved in other cell separation processes and other species. Genes encoding IDA and HSL2 orthologues have been identified in all orders of flowering plants. Angiosperms have had enormous success, with species adapted to all kinds of environments, adaptations which include variation with respect to which organs they shed. Here we review, from an evolutionary perspective, the properties of the IDA-HAE/HSL2 signaling module and the evidence for its hypothesized involvement in various cell separation processes in angiosperms.

Transcriptional Regulation of Abscission Zones

Precise and timely regulation of organ separation from the parent plant (abscission) is consequential to improvement of crop productivity as it influences both the timing of harvest and fruit quality. Abscission is tightly associated with plant fitness as unwanted organs (petals, sepals, filaments) are shed after fertilization while seeds, fruits, and leaves are cast off as means of reproductive success or in response to abiotic/biotic stresses. Floral organ abscission in Arabidopsis has been a useful model to elucidate the molecular mechanisms that underlie the separation processes, and multiple abscission signals associated with the activation and downstream pathways have been uncovered. Concomitantly, large-scale analyses of omics studies in diverse abscission systems of various plants have added valuable insights into the abscission process. The results suggest that there are common molecular events linked to the biosynthesis of a new extracellular matrix as well as cell wall disassembly. Comparative analysis between Arabidopsis and soybean abscission systems has revealed shared and yet disparate regulatory modules that affect the separation processes. In this review, we discuss our current understanding of the transcriptional regulation of abscission in several different plants that has improved on the previously proposed four-phased model of organ separation.

A MAPK cascade downstream of IDA-HAE/HSL2 ligand-receptor pair in lateral root emergence

Lateral root (LR) emergence is a highly coordinated process involving precise cell-cell communication. Here, we show that MITOGEN-ACTIVATED PROTEIN KINASE3 (MPK3) and MPK6, and their upstream MAP-kinase kinases (MAPKKs), MKK4 and MKK5, function downstream of HAESA (HAE)/HAESA-LIKE2 (HSL2) and their ligand INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) during LR emergence. Loss of function of MKK4/MKK5 or MPK3/MPK6 results in restricted passage of the growing lateral root primordia (LRP) through the overlaying endodermal, cortical and epidermal cell layers, leading to reduced LR density. The MKK4/MKK5-MPK3/MPK6 module regulates the expression of cell wall remodelling genes in cells overlaying LRP and therefore controls pectin degradation in the middle lamella. Expression of constitutively active MKK4 or MKK5 driven by the HAE or HSL2 promoter fully rescues the LR emergence defect in the ida and hae hsl2 mutants. In addition, the MKK4/MKK5-MPK3/MPK6 module is indispensable in auxin-facilitated LR emergence. Our study provides insights into the auxin-governed and IDA-HAE/HLS2 ligand-receptor pair-mediated LR emergence process.

Crosstalk between cytokinin and ethylene signaling pathways regulates leaf abscission in cotton in response to chemical defoliants

Abscission is a process that allows plants to shed tissues or organs via cell separation, and occurs throughout the life cycle. Removal of leaves through the use of chemical defoliants is very important for mechanical harvesting of cotton (Gossypium hirsutum). However, our knowledge of the molecular mechanisms of the defoliation response involved is limited. In this study, RNA-seq was conducted in order to profile the differentially expressed genes (DEGs) between cultivars X50 (sensitive to chemical defoliants) and X33 (relatively insensitive) at different time points after treatment with thidiazuron and ethephon (TE). A total of 2434 DEGs were identified between the two cultivars across the different time-points. Functional categories according to GO and KEGG analyses revealed that plant hormone signal transduction and zeatin biosynthesis were involved in the response to TE. Cytokinin oxidase/dehydrogenase (CKX) genes and ethylene-related genes were up-regulated following TE treatment, and were associated with increased level of ethylene, especially in cultivar X50. Down-regulation of GhCKX3 resulted in delayed defoliation and a reduced ethylene response. The results show that crosstalk between cytokinin and ethylene regulates cotton defoliation, and provide new insights into the molecular mechanisms underlying the mode of action of defoliants in cotton.

Re-evaluation of the ethylene-dependent and -independent pathways in the regulation of floral and organ abscission

Abscission is a developmental process with important implications for agricultural practices. Ethylene has long been considered as a key regulator of the abscission process. The existence of an ethylene-independent abscission pathway, controlled by the complex of INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide and the HAESA (HAE) and HAESA-like2 (HSL2) kinases, has been proposed, based mainly on observations that organ abscission in ethylene-insensitive mutants was delayed but not inhibited. A recent review on plant organ abscission signaling highlighted the IDA-HAE-HSL2 components as the regulators of organ abscission, while the role of auxin and ethylene in this process was hardly addressed. After a careful analysis of the relevant abscission literature, we propose that the IDA-HAE-HSL2 pathway is essential for the final stages of organ abscission, while ethylene plays a major role in its initiation and progression. We discuss the view that the IDA-HAE-HSL2 pathway is ethylene independent, and present recent evidence showing that ethylene activates the IDA-HAE-HSL2 complex. We conclude that the ability of an organ to abscise is tightly linked to cell turgidity in the abscission zone, and suggest that lack of cell turgidity might contribute to the failure of floral organ abscission in the ida mutants.

GmIDL2a and GmIDL4a, Encoding the Inflorescence Deficient in Abscission-Like Protein, Are Involved in Soybean Cell Wall Degradation during Lateral Root Emergence

The number of lateral roots (LRs) of a plant determines the efficiency of water and nutrient uptake. Soybean is a typical taproot crop which is deficient in LRs. The number of LRs is therefore an important agronomic trait in soybean breeding. It is reported that the inflorescence deficient in abscission (IDA) protein plays an important role in the emergence of Arabidopsis LRs. Previously, the genes which encode IDA-like (IDL) proteins have been identified in the soybean genome. However, the functions of these genes in LR development are unknown. Therefore, it is of great value to investigate the function of IDL genes in soybean. In the present study, the functions of two root-specific expressed IDL genes, GmIDL2a and GmIDL4a, are investigated. The expressions of GmIDL2a and GmIDL4a, induced by auxin, are located in the overlaying tissue, where LRs are initiated. Overexpression of GmIDL2a and GmIDL4a increases the LR densities of the primary roots, but not in the elder root. Abnormal cell layer separation has also been observed in GmIDL2a- and GmIDL4a-overexpressing roots. These results suggest that the overlaying tissues of GmIDL2a- and GmIDL4a-overexpressing roots are looser and are suitable for the emergence of the LR primordium. Further investigation shows that the expression of some of the cell wall remodeling (CWR) genes, such as xyloglucan endotransglucosylase/hydrolases, expansins, and polygalacturonases, are increased when GmIDL2a and GmIDL4a are overexpressed in hairy roots. Here, we conclude that GmIDL2a and GmIDL4a function in LR emergence through regulating soybean CWR gene expression.

Transcriptome Analysis of Litsea cubeba Floral Buds Reveals the Role of Hormones and Transcription Factors in the Differentiation Process

BACKGROUND

Litsea cubeba (Lour.) Pers. is an important economic plant that is rich in valuable essential oil. The essential oil is often used as a raw material for perfumes, food additives, insecticides and bacteriostats. Most of the essential oil is contained in the fruit, and the quantity and quality of fruit are dependent on the flowers. To explore the molecular mechanism of floral bud differentiation, high-throughput RNA sequencing was used to detect differences in the gene expression of L. cubeba female and male floral buds at three differentiation stages.

RESULTS

This study obtained 160.88 Gbp of clean data that were assembled into 100,072 unigenes, and a total of 38,658 unigenes were annotated. A total of 27,521 simple sequence repeats (SSRs) were identified after scanning the assembled transcriptome, and the mono-nucleotide repeats were predominant, followed by di-nucleotide and tri-nucleotide repeats. A total of 12,559 differentially expressed genes (DEGs) were detected from the female (F) and male (M) floral bud comparisons. The gene ontology (GO) databases revealed that these DEGs were primarily contained in "metabolic processes", "cellular processes", and "single-organism processes". The Kyoto Encyclopedia of Genes and Genomes (KEGG) databases suggested that the DEGs belonged to "plant hormone signal transduction" and accounted for a relatively large portion in all of these comparisons. We analyzed the expression level of plant hormone-related genes and detected the contents of several relevant plant hormones in different stages. The results revealed that the dynamic changes in each hormone content were almost consistent with the expression levels of relevant genes. The transcription factors selected from the DEGs were analyzed. Most DEGs of MADS-box were upregulated and most DEGs of bZIP were downregulated. The expression trends of the DEGs were nearly identical in female and male floral buds, and qRT-PCR analysis revealed consistency with the transcriptome data.

CONCLUSIONS

We sequenced and assembled a high-quality L. cubeba floral bud transcriptome, and the data appeared to be well replicated (n = 3) over three developmental time points during flower development. Our study explored the changes in the contents of several plant hormones during floral bud differentiation using biochemical and molecular biology techniques, and the changes in expression levels of several flower development related transcription factors. These results revealed the role of these factors (i.e., hormones and transcription factors) and may advance our understanding of their functions in flower development in L. cubeba.

Advances in abscission signaling

Abscission is a process in plants for shedding unwanted organs such as leaves, flowers, fruits, or floral organs. Shedding of leaves in the fall is the most visually obvious display of abscission in nature. The very shape plants take is forged by the processes of growth and abscission. Mankind manipulates abscission in modern agriculture to do things such as prevent pre-harvest fruit drop prior to mechanical harvesting in orchards. Abscission occurs specifically at abscission zones that are laid down as the organ that will one day abscise is developed. A sophisticated signaling network initiates abscission when it is time to shed the unwanted organ. In this article, we review recent advances in understanding the signaling mechanisms that activate abscission. Physiological advances and roles for hormones in abscission are also addressed. Finally, we discuss current avenues for basic abscission research and potentially lucrative future directions for its application to modern agriculture.

The Tomato Hybrid Proline-rich Protein regulates the abscission zone competence to respond to ethylene signals

The Tomato Hybrid Proline-rich Protein (THyPRP) gene was specifically expressed in the tomato (Solanum lycopersicum) flower abscission zone (FAZ), and its stable antisense silencing under the control of an abscission zone (AZ)-specific promoter, Tomato Abscission Polygalacturonase4, significantly inhibited tomato pedicel abscission following flower removal. For understanding the THyPRP role in regulating pedicel abscission, a transcriptomic analysis of the FAZ of THyPRP-silenced plants was performed, using a newly developed AZ-specific tomato microarray chip. Decreased expression of THyPRP in the silenced plants was already observed before abscission induction, resulting in FAZ-specific altered gene expression of transcription factors, epigenetic modifiers, post-translational regulators, and transporters. Our data demonstrate that the effect of THyPRP silencing on pedicel abscission was not mediated by its effect on auxin balance, but by decreased ethylene biosynthesis and response. Additionally, THyPRP silencing revealed new players, which were demonstrated for the first time to be involved in regulating pedicel abscission processes. These include: gibberellin perception, Ca²⁺-Calmodulin signaling, Serpins and Small Ubiquitin-related Modifier proteins involved in post-translational modifications, Synthaxin and SNARE-like proteins, which participate in exocytosis, a process necessary for cell separation. These changes, occurring in the silenced plants early after flower removal, inhibited and/or delayed the acquisition of the competence of the FAZ cells to respond to ethylene signaling. Our results suggest that THyPRP acts as a master regulator of flower abscission in tomato, predominantly by playing a role in the regulation of the FAZ cell competence to respond to ethylene signals.

Leaf shedding as an anti-bacterial defense in Arabidopsis cauline leaves

Plants utilize an innate immune system to protect themselves from disease. While many molecular components of plant innate immunity resemble the innate immunity of animals, plants also have evolved a number of truly unique defense mechanisms, particularly at the physiological level. Plant's flexible developmental program allows them the unique ability to simply produce new organs as needed, affording them the ability to replace damaged organs. Here we develop a system to study pathogen-triggered leaf abscission in Arabidopsis. Cauline leaves infected with the bacterial pathogen Pseudomonas syringae abscise as part of the defense mechanism. Pseudomonas syringae lacking a functional type III secretion system fail to elicit an abscission response, suggesting that the abscission response is a novel form of immunity triggered by effectors. HAESA/HAESA-like 2, INFLORESCENCE DEFICIENT IN ABSCISSION, and NEVERSHED are all required for pathogen-triggered abscission to occur. Additionally phytoalexin deficient 4, enhanced disease susceptibility 1, salicylic acid induction-deficient 2, and senescence-associated gene 101 plants with mutations in genes necessary for bacterial defense and salicylic acid signaling, and NahG transgenic plants with low levels of salicylic acid fail to abscise cauline leaves normally. Bacteria that physically contact abscission zones trigger a strong abscission response; however, long-distance signals are also sent from distal infected tissue to the abscission zone, alerting the abscission zone of looming danger. We propose a threshold model regulating cauline leaf defense where minor infections are handled by limiting bacterial growth, but when an infection is deemed out of control, cauline leaves are shed. Together with previous results, our findings suggest that salicylic acid may regulate both pathogen- and drought-triggered leaf abscission.

Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat

Many important genes in agriculture correspond to transcription factors (TFs) that regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. In this study, we identified 5776 TFs in hexaploid wheat (Triticum aestivum) and classified them into gene families. We further investigated the NAC family exploring the phylogeny, C-terminal domain (CTD) conservation, and expression profiles across 308 RNA-seq samples. Phylogenetic trees of NAC domains indicated that wheat NACs divided into eight groups similar to rice (Oryza sativa) and barley (Hordeum vulgare). CTD motifs were frequently conserved between wheat, rice, and barley within phylogenetic groups; however, this conservation was not maintained across phylogenetic groups. Three homeologous copies were present for 58% of NACs, whereas evidence of single homeolog gene loss was found for 33% of NACs. We explored gene expression patterns across a wide range of developmental stages, tissues, and abiotic stresses. We found that more phylogenetically related NACs shared more similar expression patterns compared to more distant NACs. However, within each phylogenetic group there were clades with diverse expression profiles. We carried out a coexpression analysis on all wheat genes and identified 37 modules of coexpressed genes of which 23 contained NACs. Using gene ontology (GO) term enrichment, we obtained putative functions for NACs within coexpressed modules including responses to heat and abiotic stress and responses to water: these NACs may represent targets for breeding or biotechnological applications. This study provides a framework and data for hypothesis generation for future studies on NAC TFs in wheat.

Ethephon induced oxidative stress in the olive leaf abscission zone enables development of a selective abscission compound

BACKGROUND

Table olives (Olea europaea L.), despite their widespread production, are still harvested manually. The low efficiency of manual harvesting and the rising costs of labor have reduced the profitability of this crop. A selective abscission treatment, inducing abscission of fruits but not leaves, is crucial for the adoption of mechanical harvesting of table olives. In the present work we studied the anatomical and molecular differences between the three abscission zones (AZs) of olive fruits and leaves.

RESULTS

The fruit abscission zone 3 (FAZ3), located between the fruit and the pedicel, was found to be the active AZ in mature fruits and is sensitive to ethephon, whereas FAZ2, between the pedicel and the rachis, is the flower active AZ as well as functioning as the most ethephon induced fruit AZ. We found anatomical differences between the leaf AZ (LAZ) and the two FAZs. Unlike the FAZs, the LAZ is characterized by small cells with less pectin compared to neighboring cells. In an attempt to differentiate between the fruit and leaf AZs, we examined the effect of treating olive-bearing trees with ethephon, an ethylene-releasing compound, with or without antioxidants, on the detachment force (DF) of fruits and leaves 5 days after the treatment. Ethephon treatment enhanced pectinase activity and reduced DF in all the three olive AZs. A transcriptomic analysis of the three olive AZs after ethephon treatment revealed induction of several genes encoding for hormones (ethylene, auxin and ABA), as well as for several cell wall degrading enzymes. However, up-regulation of cellulase genes was found only in the LAZ. Many genes involved in oxidative stress were induced by the ethephon treatment in the LAZ alone. In addition, we found that reactive oxygen species (ROS) mediated abscission in response to ethephon only in leaves. Thus, adding antioxidants such as ascorbic acid or butyric acid to the ethephon inhibited leaf abscission but enhanced fruit abscission.

CONCLUSION

Our findings suggest that treating olive-bearing trees with a combination of ethephon and antioxidants reduces the detachment force (DF) of fruit without weakening that of the leaves. Hence, this selective abscission treatment may be used in turn to promote mechanized harvest of olives.

Transcriptome profiling of Elymus sibiricus, an important forage grass in Qinghai-Tibet plateau, reveals novel insights into candidate genes that potentially connected to seed shattering

BACKGROUND

Elymus sibiricus is an important forage grass in semi-arid regions, but it is difficult to grow for commercial seed production due to high seed shattering. To better understand the underlying mechanism and explore the putative genes related to seed shattering, we conducted a combination of morphological, histological, physiochemical and transcriptome analysis on two E. sibiricus genotypes (XH09 and ZhN03) that have contrasting seed shattering.

RESULTS

The results show that seed shattering is generally caused by a degradation of the abscission layer. Early degradation of abscission layers was associated with the increased seed shattering in high seed shattering genotype XH09. Two cell wall degrading enzymes, cellulase (CE) and polygalacturonase (PG), had different activity in the abscission zone, indicating their roles in differentiation of abscission layer. cDNA libraries from abscission zone tissue of XH09 and ZhN03 at 7 days, 21 days and 28 days after heading were constructed and sequenced. A total of 86,634 unigenes were annotated and 7110 differentially expressed transcripts (DETs) were predicted from "XH09-7 vs ZhN03-7", "XH09-21 vs ZhN03-21" and "XH09-28 vs ZhN03-28", corresponding to 2058 up-regulated and 5052 down-regulated unigenes. The expression profiles of 10 candidate transcripts involved in cell wall-degrading enzymes, lignin biosynthesis and phytohormone activity were validated using quantitative real-time PCR (qRT-PCR), 8 of which were up-regulated in low seed shattering genotype ZhN03, suggesting these genes may be associated with reduction of seed shattering.

CONCLUSIONS

The expression data generated in this study provides an important resource for future molecular biological research in E. sibiricus.

Joint genome-wide association and transcriptome sequencing reveals a complex polygenic network underlying hypocotyl elongation in rapeseed (Brassica napus L.)

Hypocotyl elongation is considered an important typical seedling trait contributing directly to an increase in and stabilization of the yield in Brassica napus, but its molecular genetic mechanism is poorly understood. In the present study, hypocotyl lengths of 210 lines were measured in an illuminated culture room. A genome-wide association study (GWAS) was performed with 23,435 single nucleotide polymorphisms (SNPs) for hypocotyl length. Three lines with long hypocotyl length and three lines with short hypocotyl length from one doubled haploid line (DH) population were used for transcriptome sequencing. A GWAS followed by transcriptome analysis identified 29 differentially expressed genes associated with significant SNPs in B. napus. These genes regulate hypocotyl elongation by mediating flowering morphogenesis, circadian clock, hormone biosynthesis, or important metabolic signaling pathways. Among these genes, BnaC07g46770D negatively regulates hypocotyl elongation directly, as well as flowering time. Our results indicate that a joint GWAS and transcriptome analysis has significant potential for identifying the genes responsible for hypocotyl elongation; The extension of hypocotyl is a complex biological process regulated by a polygenic network.

The Arabidopsis Gene zinc finger protein 3(ZFP3) Is Involved in Salt Stress and Osmotic Stress Response

Plants are continuously challenged by various abiotic and biotic stresses. To tide over these adversities, plants evolved intricate regulatory networks to adapt these unfavorable environments. So far, many researchers have clarified the molecular and genetic pathways involved in regulation of stress responses. However, the mechanism through which these regulatory networks operate is largely unknown. In this study, we cloned a C₂H₂-type zinc finger protein gene ZFP3 from Arabidopsis thaliana and investigated its function in salt and osmotic stress response. Our results showed that the expression level of ZFP3 was highly suppressed by NaCl, mannitol and sucrose. Constitutive expression of ZFP3 enhanced tolerance of plants to salt and osmotic stress while the zfp3 mutant plants displays reduced tolerance in Arabidopsis. Gain- and Loss-of-function studies of ZFP3 showed that ZFP3 significantly changes proline accumulation and chlorophyll content. Furthermore, over-expression of ZFP3 induced the expressions of stress-related gene KIN1, RD22, RD29B and AtP5CS1. These results suggest that ZFP3 is involved in salt and osmotic stress response.

Gene coexpression network analysis of oil biosynthesis in an interspecific backcross of oil palm

Global demand for vegetable oils is increasing at a dramatic rate, while our understanding of the regulation of oil biosynthesis in plants remains limited. To gain insights into the mechanisms that govern oil synthesis and fatty acid (FA) composition in the oil palm fruit, we used a multilevel approach combining gene coexpression analysis, quantification of allele-specific expression and joint multivariate analysis of transcriptomic and lipid data, in an interspecific backcross population between the African oil palm, Elaeis guineensis, and the American oil palm, Elaeis oleifera, which display contrasting oil contents and FA compositions. The gene coexpression network produced revealed tight transcriptional coordination of fatty acid synthesis (FAS) in the plastid with sugar sensing, plastidial glycolysis, transient starch storage and carbon recapture pathways. It also revealed a concerted regulation, along with FAS, of both the transfer of nascent FA to the endoplasmic reticulum, where triacylglycerol assembly occurs, and of the production of glycerol-3-phosphate, which provides the backbone of triacylglycerols. Plastid biogenesis and auxin transport were the two other biological processes most tightly connected to FAS in the network. In addition to WRINKLED1, a transcription factor (TF) known to activate FAS genes, two novel TFs, termed NF-YB-1 and ZFP-1, were found at the core of the FAS module. The saturated FA content of palm oil appeared to vary above all in relation to the level of transcripts of the gene coding for β-ketoacyl-acyl carrier protein synthase II. Our findings should facilitate the development of breeding and engineering strategies in this and other oil crops.

Exposure to various abscission-promoting treatments suggests substantial ERF subfamily transcription factors involvement in the regulation of cassava leaf abscission

BACKGROUND

Cassava plants (Manihot esculenta Crantz) have obvious abscission zone (AZ) structures in their leaf pulvinus-petioles. Cassava leaf abscission can be triggered by either 17 days of water-deficit stress or 4 days of ethylene treatment. To date, little is known about cassava AP2/ERF factors, and less is known regarding their roles in regulating abscission zone development.

RESULTS

Here, the cassava and Arabidopsis AP2/ERF genes were compared, finding that the cassava genome contains approximately 1.54-fold more ERF subfamily than the Arabidopsis genome. Microarray analysis was used to identify the AP2/ERF genes that are expressed in cassava leaf pulvinus-petiole abscission zones by comparing the AP2/ERF gene expression profiles of ethylene- and water-deficit stress-induced leaf abscission. In total, 99 AP2/ERF genes were identified as expressed in AZs across six time points during both ethylene- and water-deficit stress-induced leaf abscission. Comparative expression profile analysis of similar SOTA (Self Organizing Tree Algorithm) clusters at six time points during ethylene- and water-deficit stress-induced leaf abscission demonstrated that 20 ERF subfamily genes had similar expression patterns in response to both treatments. GO (Gene Ontology) annotation confirmed that all 20 ERF subfamily genes participate in ethylene-mediated signalling. Analysis of the putative ERF promoter regions shown that the genes contained primarily ethylene- and stress-related cis-elements. Further analysis of ACC oxidase activity in AZs across six time points during abscission shown increased ethylene production in response to both ethylene and water-deficit stress; however, the difference was more dramatic for water-deficit stress. Finally, the expression ratios of 20 ERF subfamily genes were analysed in two cassava cultivars, 'KU50' and 'SC5', that exhibit different levels of leaf abscission when challenged with the same water-deficit stress. The analysis indicated that most of the ERF genes were expressed at higher levels in the precocious abscission 'KU50' cultivar than in the delayed abscission 'SC5' cultivar.

CONCLUSION

Ccomparative analysis of both ethylene- and water-deficit stress-induced leaf abscission shown that the ERF subfamily functions in the regulation of cassava abscission zone development.

Serine 231 and 257 of Agamous-like 15 are phosphorylated in floral receptacles

The large dynamic range of gene expression changes accompanying floral organ abscission can be explained by a molecular positive feedback loop that regulates the process. In short, a mitogen-activated protein kinase (MAPK) cascade, positioned genetically downstream from the abscission receptor HAESA (HAE), phosphorylates the transcription factor, AGAMOUS-like 15 (AGL15), allowing HAE to be expressed. However, it is unknown which residues of AGL15 are phosphorylated and precisely how phosphorylation alters AGL15 function. Here we report that serine 231 and 257 of AGL15 are phosphorylated in floral receptacles. Effects of phosphorylation on AGL15 are discussed.

De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.)

Background

Sugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. The growing demands for sugar and biofuel is asking for breeding a sugarcane variety that can shed their leaves during the maturity time due to the increasing cost on sugarcane harvest.

Results

To determine leaf abscission related genes in sugarcane, we generated 524,328,950 paired reads with RNA-Seq and profiled the transcriptome of new born leaves of leaf abscission sugarcane varieties (Q1 and T) and leaf packaging sugarcane varieties (Q2 and B). Initially, 275,018 transcripts were assembled with N50 of 1,177 bp. Next, the transcriptome was annotated by mapping them to NR, UniProtKB/Swiss-Prot, Gene Ontology and KEGG pathway databases. Further, we used TransDecoder and Trinotate to obtain the likely proteins and annotate them in terms of known proteins, protein domains, signal peptides, transmembrane regions and rRNA transcripts. Different expression analysis showed 1,202 transcripts were up regulated in leaf abscission sugarcane varieties, relatively to the leaf packaging sugarcane varieties. Functional analysis told us 62, 38 and 10 upregulated transcripts were involved in plant-pathogen interaction, response to stress and abscisic acid associated pathways, respectively. The upregulation of transcripts encoding 4 disease resistance proteins (RPM1, RPP13, RGA2, and RGA4), 6 ABC transporter G family members and 16 transcription factors including WRK33 and heat stress transcription factors indicate they may be used as candidate genes for sugarcane breeding. The expression levels of transcripts were validated by qRT-PCR. In addition, we characterized 3,722 SNPs between leaf abscission and leaf packaging sugarcane plants.

Conclusion

Our results showed leaf abscission associated genes in sugarcane during the maturity period. The output of this study provides a valuable resource for future genetic and genomic studies in sugarcane.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2552-2) contains supplementary material, which is available to authorized users.

Proteomic insights into floral biology

The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear

BACKGROUND

The objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (Pyrus brestschneideri Rehd). Flowers were collected at early bloom, full bloom, and late bloom. The RNA was extracted from the flowers and then combined according to calyx type. Transcriptome and digital gene expression (DGE) profiles of flowers, ovaries, and sepals with persistent calyx (SC_hua, SC_ep, and SC_zf, respectively) were compared with those of flowers, ovaries, and sepals with deciduous calyx (TL_hua, TL_ep, and TL_zf, respectively). Temporal changes in the expression of selected genes in floral organs with either persistent or deciduous calyx were compared using real-time quantitative PCR (qRT-PCR).

RESULTS

Comparison of the transcriptome sequences for SC_hua and TL_hua indicated 26 differentially expressed genes (DEGs) with known relationship to abscission and 10 DEGs with unknown function. We identified 98 MYB and 21 SPL genes from the assembled unigenes. From SC_zf vs TL_zf, we identified 21 DEGs with known relationship to abscission and 18 DEGs with unknown function. From SC_ep vs TL_ep, 12 DEGs with known relationship to abscission were identified along with 11 DEGs with unknown function. Ten DEGs were identified by both transcriptome sequencing and DGE sequencing.

CONCLUSIONS

More than 50 DEGs were observed that were related to calyx persistence in Korla fragrant pear. Some of the genes were related to cell wall degradation, plant hormone signal transduction, and stress response. Other DEGs were identified as zinc finger protein genes and lipid transfer protein genes. Further analysis showed that calyx persistence in Korla fragment pear was a metabolic process regulated by many genes related to cell wall degradation and plant hormones.