Distribution of XTH, expansin, and secondary-wall-related CesA in floral and fruit abscission zones during fruit development in tomato (Solanum lycopersicum)

EXPANSIN15 is involved in flower and fruit development in Arabidopsis

KEY MESSAGE

EXPANSIN15 is involved in petal cell morphology and size, the fusion of the medial tissues in the gynoecium and expansion of fruit valve cells. It genetically interacts with SPATULA and FRUITFULL. Cell expansion is fundamental for the formation of plant tissues and organs, contributing to their final shape and size during development. To better understand this process in flower and fruit development, we have studied the EXPANSIN15 (EXPA15) gene, which showed expression in petals and in the gynoecium. By analyzing expa15 mutant alleles, we found that EXPA15 is involved in petal shape and size determination, by affecting cell morphology and number. EXPA15 also has a function in fruit size, by affecting cell size and number. Furthermore, EXPA15 promotes fusion of the medial tissues in the gynoecium. In addition, we observed genetic interactions with the transcription factors SPATULA (SPT) and FRUITFULL (FUL) in gynoecium medial tissue fusion, style and stigma development and fruit development in Arabidopsis. These findings contribute to the importance of EXPANSINS in floral and fruit development in Arabidopsis.

WOX2 functions redundantly with WOX1 and WOX4 to positively regulate seed germination in Arabidopsis

MAIN CONCLUSION

WOX family gene WOX2 is highly expressed during seed development, which functions redundantly with WOX1 and WOX4 to positively regulate seed germination. WOX (WUSCHEL-related homeobox) is a family of transcription factors in plants. They play essential roles in the regulation of plant growth and development, but their function in seed germination is not well understood. In this report, we show that WOX1, WOX2, and WOX4 are close homologues in Arabidopsis. WOX2 has a redundant function with WOX1 and WOX4, respectively, in seed germination. WOX2 is highly expressed during seed development, from the globular embryonic stage to mature dry seeds, and its expression is decreased after germination. Loss of function single mutant wox2, and double mutants wox1 wox2 and wox2 wox4-1 show decreased germination speed. WOX2 and WOX4 are essential for hypocotyl-radicle zone elongation during germination, potentially by promoting the expression of cell wall-related genes. We also found that WOX2 and WOX4 regulate germination through the gibberellin (GA) pathway. These results suggest that WOX2 and WOX4 integrate the GA pathway and downstream cell wall-related genes during germination.

Ectopic Expression of MADS-Box Transcription Factor VvAGL12 from Grape Promotes Early Flowering, Plant Growth, and Production by Regulating Cell-Wall Architecture in Arabidopsis

The MADS-box family, a substantial group of plant transcription factors, crucially regulates plant growth and development. Although the functions of AGL12-like subgroups have been elucidated in Arabidopsis, rice, and walnut, their roles in grapes remain unexplored. In this study, we isolated VvAGL12, a member of the grape MADS-box group, and investigated its impact on plant growth and biomass production. VvAGL12 was found to localize in the nucleus and exhibit expression in both vegetative and reproductive organs. We introduced VvAGL12 into Arabidopsis thaliana ecotype Columbia-0 and an agl12 mutant. The resulting phenotypes in the agl12 mutant, complementary line, and overexpressed line underscored VvAGL12's ability to promote early flowering, augment plant growth, and enhance production. This was evident from the improved fresh weight, root length, plant height, and seed production, as well as the reduced flowering time. Subsequent transcriptome analysis revealed significant alterations in the expression of genes associated with cell-wall modification and flowering in the transgenic plants. In summary, the findings highlight VvAGL12's pivotal role in the regulation of flowering timing, overall plant growth, and development. This study offers valuable insights, serving as a reference for understanding the influence of the VvAGL12 gene in other plant species and addressing yield-related challenges.

Transcriptome analysis showed that tomato-rootstock enhanced salt tolerance of grafted seedlings was accompanied by multiple metabolic processes and gene differences

Introduction

Grafting is a commonly used cultural practice to counteract salt stress and is especially important for vegetable production. However, it is not clear which metabolic processes and genes are involved in the response of tomato rootstocks to salt stress.

Methods

To elucidate the regulatory mechanism through which grafting enhances salt tolerance, we first evaluated the salt damage index, electrolyte permeability and Na⁺ accumulation in tomato (Solanum lycopersicum L.) leaves of grafted seedlings (GSs) and nongrafted seedlings (NGSs) subjected to 175 mmol·L^{- 1} NaCl for 0-96 h, covering the front, middle and rear ranges.

Results

Compared with the NGS, the GSs were more salt tolerant, and the Na⁺ content in the leaves decreased significantly. Through transcriptome sequencing data analysis of 36 samples, we found that GSs exhibited more stable gene expression patterns, with a lower number of DEGs. WRKY and PosF21 transcription factors were significantly upregulated in the GSs compared to the NGSs. Moreover, the GSs presented more amino acids, a higher photosynthetic index and a higher content of growth-promoting hormones. The main differences between GSs and NGSs were in the expression levels of genes involved in the BR signaling pathway, with significant upregulation of XTHs. The above results show that the metabolic pathways of "photosynthetic antenna protein", "amino acid biosynthesis" and "plant hormone signal transduction" participate in the salt tolerance response of grafted seedlings at different stages of salt stress, maintaining the stability of the photosynthetic system and increasing the contents of amino acids and growth-promoting hormones (especially BRs). In this process, the transcription factors WRKYs, PosF21 and XTHs might play an important role at the molecular level.

Discussion

The results of this study demonstrates that grafting on salt tolerant rootstocks can bring different metabolic processes and transcription levels changes to scion leaves, thereby the scion leaves show stronger salt tolerance. This information provides new insight into the mechanism underlying tolerance to salt stress regulation and provides useful molecular biological basis for improving plant salt resistance.

Involvement of IDA-HAE Module in Natural Development of Tomato Flower Abscission

The unwanted detachment of organs such as flowers, leaves, and fruits from the main body of a plant (abscission) has significant effects on agricultural practice. Both timely and precise regulation of organ abscission from a plant is crucial as it influences the agricultural yield. The tomato (Solanum lycopersicum) has become a model system for research on organ abscission. Here, we characterized four tomato natural abscission variants named jointless (j), functionally impaired jointless (fij), functionally impaired jointless like (fij like), and normal joint (NJ), based on their cellular features within the flower abscission zones (AZ). Using eight INFLORESCENCE DEFICIENT IN ABSCISSION (SlIDA) genes and eight HAESA genes (SlHAE) identified in the genome sequence of tomato, we analyzed the pattern of gene expression during flower abscission. The AZ-specific expression for three tomato abscission polygalacturonases (SlTAPGs) in the development of flower AZ, and the progression of abscission validated our natural abscission system. Compared to that of j, fij, and fij like variants, the AZ-specific expression for SlIDA, SlIDL2, SlIDL3, SlIDL4, and SlIDL5 in the NJ largely corelated and increased with the process of abscission. Of eight SlHAE genes examined, the expression for SlHSL6 and SlHSL7 were found to be AZ-specific and increased as abscission progressed in the NJ variant. Unlike the result of gene expression obtained from natural abscission system, an in silico analysis of transcriptional binding sites uncovered that SlIDA genes (SlIDA, SlIDL6, and SlIDL7) are predominantly under the control of environmental stress, while most of the SlHSL genes are affiliated with the broader context in developmental processes and stress responses. Our result presents the potential bimodal transcriptional regulation of the tomato IDA-HAE module associated with flower abscission in tomatoes.

Xyloglucan endotransglucosylase/hydrolase genes LcXTH4/7/19 are involved in fruitlet abscission and are activated by LcEIL2/3 in litchi

Organ abscission in plants requires the hydrolysis of cell wall components, mainly including celluloses, pectins, and xyloglucans. However, how the genes that encode those hydrolytic enzymes are regulated and their function in abscission remains unclear. Previously we revealed that two cellulase genes LcCEL2/8 and two polygalacturonase genes LcPG1/2 were responsible for the degradation of celluloses and pectins, respectively, during fruitlet abscission in litchi. Here, we further identified three xyloglucan endotransglucosylase/hydrolase genes (LcXTH4, LcXTH7, LcXTH19) that are also involved in this process. Nineteen LcXTHs, named LcXTH1-19, were identified in the litchi genome. Transcriptome data and qRT-PCR confirmed that LcXTH4/7/19 were significantly induced at the abscission zone (AZ) during fruitlet abscission in litchi. The GUS reporter driven by each promoter of LcXTH4/7/19 was specifically expressed at the floral abscission zone of Arabidopsis, and importantly ectopic expression of LcXTH19 in Arabidopsis resulted in precocious floral organ abscission. Moreover, electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter analysis showed that the expression of LcXTH4/7/19 could be directly activated by two ETHYLENE INSENSITIVE 3-like (EIL) transcription factors LcEIL2/3. Collectively, we propose that LcXTH4/7/19 are involved in fruitlet abscission, and LcEIL2/3-mediated transcriptional regulation of diverse cell wall hydrolytic genes is responsible for this process in litchi.

Virtual issue: cell wall functions in plant growth and environmental responses

Plant cell walls have multiple functions, including determining cell shape and size, cell-cell adhesion, controlling cell differentiation and growth, and promoting abiotic and biotic stress tolerance. This virtual issue introduces the physiological functions of cell walls in growth and environmental responses. The articles detail research on (1) embryogenesis and seed development, (2) vegetative growth, (3) reproductive growth, and (4) environmental responses. These articles, published in the Journal of Plant Research, will provide valuable information for future research on the function and dynamics of cell walls at various growth stages, and in response to environmental factors.

Transcriptomics of Improved Fruit Retention by Hexanal in 'Honeycrisp' Reveals Hormonal Crosstalk and Reduced Cell Wall Degradation in the Fruit Abscission Zone

Apples (Malus domestica Borkh) are prone to preharvest fruit drop, which is more pronounced in 'Honeycrisp'. Hexanal is known to improve fruit retention in several economically important crops. The effects of hexanal on the fruit retention of 'Honeycrisp' apples were assessed using physiological, biochemical, and transcriptomic approaches. Fruit retention and fruit firmness were significantly improved by hexanal, while sugars and fresh weight did not show a significant change in response to hexanal treatment. At commercial maturity, abscisic acid and melatonin levels were significantly lower in the treated fruit abscission zone (FAZ) compared to control. At this stage, a total of 726 differentially expressed genes (DEGs) were identified between treated and control FAZ. Functional classification of the DEGs showed that hexanal downregulated ethylene biosynthesis genes, such as S-adenosylmethionine synthase (SAM2) and 1-aminocyclopropane-1-carboxylic acid oxidases (ACO3, ACO4, and ACO4-like), while it upregulated the receptor genes ETR2 and ERS1. Genes related to ABA biosynthesis (FDPS and CLE25) were also downregulated. On the contrary, key genes involved in gibberellic acid biosynthesis (GA20OX-like and KO) were upregulated. Further, hexanal downregulated the expression of genes related to cell wall degrading enzymes, such as polygalacturonase (PG1), glucanases (endo-β-1,4-glucanase), and expansins (EXPA1-like, EXPA6, EXPA8, EXPA10-like, EXPA16-like). Our findings reveal that hexanal reduced the sensitivity of FAZ cells to ethylene and ABA. Simultaneously, hexanal maintained the cell wall integrity of FAZ cells by regulating genes involved in cell wall modifications. Thus, delayed fruit abscission by hexanal is most likely achieved by minimizing ABA through an ethylene-dependent mechanism.

Building a Flower: The Influence of Cell Wall Composition on Flower Development and Reproduction

Floral patterning is a complex task. Various organs and tissues must be formed to fulfill reproductive functions. Flower development has been studied, mainly looking for master regulators. However, downstream changes such as the cell wall composition are relevant since they allow cells to divide, differentiate, and grow. In this review, we focus on the main components of the primary cell wall-cellulose, hemicellulose, and pectins-to describe how enzymes involved in the biosynthesis, modifications, and degradation of cell wall components are related to the formation of the floral organs. Additionally, internal and external stimuli participate in the genetic regulation that modulates the activity of cell wall remodeling proteins.

Cross-talk between transcriptome, phytohormone and HD-ZIP gene family analysis illuminates the molecular mechanism underlying fruitlet abscission in sweet cherry (Prunus avium L)

BACKGROUND

The shedding of premature sweet cherry (Prunus avium L) fruitlet has significantly impacted production, which in turn has a consequential effect on economic benefits.

RESULT

To better understand the molecular mechanism of sweet cherry fruitlet abscission, pollen viability and structure had been observed from the pollination trees. Subsequently, the morphological characters of the shedding fruitlet, the plant hormone titers of dropping carpopodium, the transcriptome of the abscising carpopodium, as well as the HD-ZIP gene family were investigated. These findings showed that the pollens giving rise to heavy fruitlet abscission were malformed in structure, and their viability was lower than the average level. The abscising fruitlet and carpopodium were characterized in red color, and embryos of abscising fruitlet were aborted, which was highly ascribed to the low pollen viability and malformation. Transcriptome analysis showed 6462 were significantly differentially expressed, of which 2456 genes were up-regulated and 4006 down-regulated in the abscising carpopodium. Among these genes, the auxin biosynthesis and signal transduction genes (α-Trp, AUX1), were down-regulated, while the 1-aminocyclopropane-1-carboxylate oxidase gene (ACO) affected in ethylene biosynthesis, was up-regulated in abscising carpopodium. About genes related to cell wall remodeling (CEL, PAL, PG EXP, XTH), were up-regulated in carpopodium abscission, which reflecting the key roles in regulating the abscission process. The results of transcriptome analysis considerably conformed with those of proteome analysis as documented previously. In comparison with those of the retention fruitlet, the auxin contents in abscising carpopodium were significantly low, which presumably increased the ethylene sensitivity of the abscission zone, conversely, the abscisic acid (ABA) accumulation was considerably higher in abscising carpopodium. Furthermore, the ratio of (TZ + IAA + GA3) / ABA also obviously lower in abscising carpopodium. Besides, the HD-ZIP gene family analysis showed that PavHB16 and PavHB18 were up-regulated in abscising organs.

CONCLUSION

Our findings combine morphology, cytology and transcriptional regulation to reveal the molecular mechanism of sweet cherry fruitlet abscission. It provides a new perspective for further study of plant organ shedding.

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.

A high maternal genome excess causes severe seed abortion leading to ovary abscission in Nicotiana interploidy-interspecific crosses

Seed abortion and ovary abscission, two types of postzygotic reproductive barriers, are often observed in interspecific and/or interploidy crosses in plants. However, the mechanisms underlying these reproductive barriers remain unclear. Here, we show that the distinct types of seed developmental abnormalities (type I and type II seed abortion) occur in a phased manner as maternal to paternal genome dosage increases and that type II seed abortion is followed by ovary abscission. We revealed that these two types of seed developmental abnormalities are observed during seed development in the interploidy-interspecific crosses of Nicotiana suaveolens and N. tabacum. Moreover, in the cross showing type II seed abortion, several events, such as changes in abscission-related gene expression and lignin deposition, occurred in the ovary abscission zone, eventually leading to ovary abscission. Notably, successive increases in maternal ploidy using ploidy manipulated lines resulted in successive type I and type II seed abortions, and the latter was accompanied by ovary abscission. Conversely, both types of seed abortion and ovary abscission could be overcome with a ploidy manipulation technique that balances parental ploidy levels. We thus concluded that a high maternal genome excess cross may cause severe seed developmental defects and ovary abscission. Based on our findings, we propose a model explaining the abortion phenomena, where an interaction between the promotive and inhibitive effects of the parental genomes determines the developmental destiny of seeds.

SIGNIFICANCE STATEMENT

We demonstrate that a stepwise increase in maternal ploidy results in a stepwise increase in seed abortion severity, leading to ovary abscission in plants. We propose a model explaining the abortion phenomena, where an interaction between the promotive and inhibitive effects of the parental genomes determines the developmental destiny of seeds.

Cell Wall Composition and Ultrastructural Immunolocalization of Pectin and Arabinogalactan Protein during Olea europaea L. Fruit Abscission

Cell wall modification is integral to many plant developmental processes where cells need to separate, such as abscission. However, changes in cell wall composition during natural fruit abscission are poorly understood. In olive (Olea europaea L.), some cultivars such as 'Picual' undergo massive natural fruit abscission after fruit ripening. This study investigates the differences in cell wall polysaccharide composition and the localization of pectins and arabinogalactan protein (AGP) in the abscission zone (AZ) during cell separation to understand fruit abscission control in 'Picual' olive. To this end, immunogold labeling employing a suite of monoclonal antibodies to cell wall components (JIM13, LM5, LM6, LM19 and LM20) was investigated in olive fruit AZ. Cell wall polysaccharide extraction revealed that the AZ cell separation is related to the de-esterification and degradation of pectic polysaccharides. Moreover, ultrastructural localization showed that both esterified and unesterified homogalacturonans (HGs) localize mainly in the AZ cell walls, including the middle lamella and tricellular junction zones. Our results indicate that unesterified HGs are likely to contribute to cell separation in the olive fruit AZ. Similarly, immunogold labeling demonstrated a decrease in both galactose-rich and arabinose-rich pectins in AZ cell walls during ripe fruit abscission. In addition, AGPs were localized in the cell wall, plasma membrane and cytoplasm of AZ cells with lower levels of AGPs during ripe fruit abscission. This detailed temporal profile of the cell wall polysaccharide composition, and the pectins and AGP immunolocalization in the olive fruit AZ, offers new insights into cell wall remodeling during ripe fruit abscission.

Comparative Proteomics Profiling Illuminates the Fruitlet Abscission Mechanism of Sweet Cherry as Induced by Embryo Abortion

Sweet cherry (Prunus avium L.) is a delicious nutrient-rich fruit widely cultivated in countries such as China, America, Chile, and Italy. However, the yield often drops severely due to the frequently-abnormal fruitlet abscission, and few studies on the metabolism during its ripening process at the proteomic level have been executed so far. To get a better understanding regarding the sweet cherry abscission mechanism, proteomic analysis between the abscising carpopodium and non-abscising carpopodium of sweet cherry was accomplished using a newly developed Liquid chromatography-mass spectrometry/mass spectrometry with Tandem Mass Tag (TMT-LC-MS/MS) methodology. The embryo viability experiments showed that the vigor of the abscission embryos was significantly lower than that of retention embryo. The activity of cell wall degrading enzymes in abscising carpopodium was significantly higher than that in non-abscising carpopodium. The anatomy results suggested that cells in the abscission zone were small and separated. In total, 6280 proteins were identified, among which 5681 were quantified. It has been observed that differentially accumulated proteins (DAPs) influenced several biological functions and various subcellular localizations. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that plenty of metabolic pathways were notably enriched, particularly those involved in phytohormone biosynthesis, cell wall metabolism, and cytoskeletal metabolism, including 1-aminocyclopropane-1-carboxylate oxidase proteins which promote ethylene synthesis, and proteins promoting cell wall degradation, such as endoglucanases, pectinase, and polygalacturonase. Differential expression of proteins concerning phytohormone biosynthesis might activate the shedding regulation signals. Up-regulation of several cell wall degradation-related proteins possibly regulated the shedding of plant organs. Variations of the phytohormone biosynthesis and cell wall degradation-related proteins were explored during the abscission process. Furthermore, changes in cytoskeleton-associated proteins might contribute to the abscission of carpopodium. The current work represented the first study using comparative proteomics between abscising carpopodium and non-abscising carpopodium. These results indicated that embryo abortion might lead to phytohormone synthesis disorder, which effected signal transduction pathways, and hereby controlled genes involved in cell wall degradation and then caused the abscission of fruitlet. Overall, our data may give an intrinsic explanation of the variations in metabolism during the abscission of carpopodium.

High-Resolution Linkage Map and QTL Analyses of Fruit Firmness in Autotetraploid Blueberry

Blueberry (Vaccinium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last 20 years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding the genetic architecture of traits related to machine harvestability through Quantitative Trait Loci (QTL) mapping is the first step toward implementation of molecular breeding for faster genetic gains. Despite recent advances in software development for autotetraploid genetic mapping, a high-resolution map is still not available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 5.78 markers/cM). This map was subsequently used to perform QTL analyses in 2-year field trials for a trait crucial to machine harvesting: fruit firmness. Preliminary insights were also sought for single evaluations of firmness retention after cold storage, and fruit detachment force traits. Significant QTL peaks were identified for all the traits and overlapping QTL intervals were detected for firmness across the years. We found low-to-moderate QTL effects explaining the phenotypic variance, which suggest a quantitative nature of these traits. The QTL intervals were further speculated for putative gene repertoire. Altogether, our findings provide the basis for future fine-mapping and molecular breeding efforts for machine harvesting in blueberry.

Fruit ripening: the role of hormones, cell wall modifications, and their relationship with pathogens

Fruits result from complex biological processes that begin soon after fertilization. Among these processes are cell division and expansion, accumulation of secondary metabolites, and an increase in carbohydrate biosynthesis. Later fruit ripening is accomplished by chlorophyll degradation and cell wall lysis. Fruit maturation is an essential step to optimize seed dispersal, and is controlled by a complex network of transcription factors and genetic regulators that are strongly influenced by phytohormones. Abscisic acid (ABA) and ethylene are the major regulators of ripening and senescence in both dry and fleshy fruits, as demonstrated by numerous ripening-defective mutants, effects of exogenous hormone application, and transcriptome analyses. While ethylene is the best characterized player in the final step of a fruit's life, ABA also has a key regulatory role, promoting ethylene production and acting as a stress-related hormone in response to drought and pathogen attack. In this review, we focus on the role of ABA and ethylene in relation to the interconnected biotic and abiotic phenomena that affect ripening and senescence. We integrate and discuss the most recent data available regarding these biological processes, which are crucial for post-harvest fruit conservation and for food safety.

Transcriptome-wide effects of expansin gene manipulation in etiolated Arabidopsis seedling

Expansin is a non-enzymatic protein which plays a pivotal role in cell wall loosening by inducing stress relaxation and extension in the plant cell wall. Previous studies on Arabidopsis, Petunia × hybrida, and tomato demonstrated that the suppression of expansin gene expression reduced plant growth but expansin overexpression does not necessarily promotes growth. In this study, both expansin gene suppression and overexpression in dark-grown transgenic Arabidopsis seedlings resulted in reduced hypocotyl length at late growth stages with a more pronounced effect for the overexpression. This defect in hypocotyl elongation raises questions about the molecular effect of expansin gene manipulation. RNA-seq analysis of the transcriptomic changes between day 3 and day 5 seedlings for both transgenic lines found numerous differentially expressed genes (DEGs) including transcription factors and hormone-related genes involved in different aspects of cell wall development. These DEGs imply that the observed hypocotyl growth retardation is a consequence of the concerted effect of regulatory factors and multiple cell-wall related genes, which are important for cell wall remodelling during rapid hypocotyl elongation. This is further supported by co-expression analysis through network-centric approach of differential network cluster analysis. This first transcriptome-wide study of expansin manipulation explains why the effect of expansin overexpression is greater than suppression and provides insights into the dynamic nature of molecular regulation during etiolation.

Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.)

Main conclusion 30 expansin genes were identified in the jujube genome. Phylogenetic analysis classified expansins into 17 subgroups. Closely related expansins share a conserved gene structure. ZjEXPs had different expression patterns in different tissues. Plant-specific expansins were first discovered as pH-dependent cell-wall-loosening proteins involved in diverse physiological processes. No comprehensive analysis of the expansin gene family has yet been carried out at the whole genome level in Chinese jujube (Ziziphus jujuba Mill.). In this study, 30 expansin genes were identified in the jujube genome. These genes, which were distributed with varying densities across 10 of the 12 jujube chromosomes, could be divided into four subfamilies: 19 ZjEXPAs, 3 ZjEXPBs, 1 ZjEXLA, and 7 ZjEXLBs. Phylogenetic analysis of expansin genes in Arabidopsis, rice, apple, grape, and jujube classified these genes into 17 subgroups. Members of the same subfamily and subgroup shared conserved gene structure and motif compositions. Homology analysis identified 20 homologous gene pairs between jujube and Arabidopsis. Further analysis of ZjEXP gene promoter regions uncovered various growth, development and stress-responsive cis-acting elements. Expression analysis and transcript profiling revealed that ZjEXPs had different expression patterns in different tissues at various developmental stages. ZjEXPA4 and ZjEXPA6 were highly expressed in young fruits, ZjEXPA3 and ZjEXPA5 were significantly expressed in flowers, and ZjEXPA7 was specifically expressed in young leaves. The results of this study, the first systematic analysis of the jujube expansin gene family, can serve as a strong foundation for further elucidation of the physiological functions and biological roles of jujube expansin genes.

Suppression of a Prolyl 4 Hydroxylase Results in Delayed Abscission of Overripe Tomato Fruits

The tomato pedicel abscission zone (AZ) is considered a model system for flower and fruit abscission development, activation, and progression. O-glycosylated proteins such as the Arabidopsis IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) peptide and Arabinogalactan proteins (AGPs) which undergo proline hydroxylation were demonstrated to participate in abscission regulation. Considering that the frequency of occurrence of proline hydroxylation might determine the structure as well the function of such proteins, the expression of a tomato prolyl 4 hydroxylase, SlP4H3 (Solanum lycopersicum Prolyl 4 Hydroxylase 3) was suppressed in order to investigate the physiological significance of this post-translational modification in tomato abscission. Silencing of SlP4H3 resulted in the delay of abscission progression in overripe tomato fruits 90 days after the breaker stage. The cause of this delay was attributed to the downregulation of the expression of cell wall hydrolases such as SlTAPGs (tomato abscission polygalacturonases) and cellulases as well as expansins. In addition, minor changes were observed in the mRNA levels of two SlAGPs and one extensin. Moreover, structural changes were observed in the silenced SlP4H3AZs. The fracture plane of the AZ was curved and not along a line as in wild type and there was a lack of lignin deposition in the AZs of overripe fruits 30 days after breaker. These results suggest that proline hydroxylation might play a role in the regulation of tomato pedicel abscission.

Spatiotemporal Changes in Xylan-1/Xyloglucan and Xyloglucan Xyloglucosyl Transferase (XTH-Xet5) as a Step-In of Ultrastructural Cell Wall Remodelling in Potato⁻Potato Virus Y (PVYNTN) Hypersensitive and Susceptible Reaction

One type of monitoring system in a plant cell is the cell wall, which intensively changes its structure during interaction with pathogen-stress factors. The wall plays a role as a dynamic and controlled structure, although it is not fully understood how relevant these modifications are to the molecular mechanisms during plant–virus interactions. In this work we localise the non-cellulosic polysaccharides such as xyloglucan, xylan (xylan-1) and xyloglucosyl transferase (XTH-Xet5), the enzyme that participates in the metabolism of xyloglucan. This provided us with information about the in situ distribution of the components of the hemicellulotic cell wall matrix in hypersensitive and susceptible potato–PVY^NTN interactions. The loosening of the cell wall was accompanied by an increase in xylan depositions during susceptible interactions, whereas, during the hypersensitive response, when the cell wall was reinforced, the xylan content decreased. Moreover, the PVY inoculation significantly redirected XTH-Xet5 depositions, regardless of types of interactions, compared to mock-inoculated tissues. Furthermore, the immunogold localisation clearly revealed the domination of Xet5 in the cell wall and in vesicles in the susceptible host. In contrast, in the resistant host increased levels of Xet5 were observed in cytoplasm, in the cell wall and in the trans-Golgi network. These findings show that the hypersensitive reaction activated XTH-Xet5 in the areas of xyloglucan endo-transglycosylase (XET) synthesis, which was then actively transported to cytoplasm, cell wall and to vacuoles. Our results provide novel insight into cell wall reorganisation during PVY^NTN infection as a response to biotic stress factors. These novel findings help us to understand the mechanisms of defence responses that are incorporated into the cell wall signalling network.

Waterlogging affects plant morphology and the expression of key genes in tef (Eragrostis tef)

Tef [Eragrostis tef (Zucc.) Trotter], an allotetraploid cereal that is a staple food to over 60 million people in the Horn of Africa, has a high nutritional content and is resistant to many biotic and abiotic stresses such as waterlogging and drought. Three tef genotypes, Alba, Tsedey, and Quncho, were subjected to waterlogging conditions and their growth, physiology, and change in transcript expression were measured with the goal of identifying targets for breeding cultivars with improved waterlogging tolerance. Root and shoot growth and dry weight were observed over 22 days. Stomatal conductance and chlorophyll and carotenoid contents were quantified. Microscopy was used to monitor changes in the stem cross sections. Illumina RNA sequencing was used to obtain the expression profiles of tef under flooding and control conditions and was verified using qPCR. Results indicated differences in growth between the three genotypes. Waterlogged Tsedey plants grew higher and had more root biomass than normally watered Tsedey plants. Quncho and Alba genotypes were more susceptible to the excess moisture stress. The effects of these changes were observed on the plant physiology. Among the three tested tef genotypes, Tsedey formed more aerenchyma than Alba and had accelerated growth under waterlogging. Tsedey and Quncho had constitutive aerenchyma. Genes affecting carbohydrate metabolism, cell growth, response to reactive oxygen species, transport, signaling, and stress responses were found to change under excess moisture stress. In general, these results show the presence of substantial anatomical and physiological differences among tef genotypes when waterlogged during the early growth stage.

De novo Transcriptome Profiling of Flowers, Flower Pedicels and Pods of Lupinus luteus (Yellow Lupine) Reveals Complex Expression Changes during Organ Abscission

Yellow lupine (Lupinus luteus L., Taper c.), a member of the legume family (Fabaceae L.), has an enormous practical importance. Its excessive flower and pod abscission represents an economic drawback, as proper flower and seed formation and development is crucial for the plant's productivity. Generative organ detachment takes place at the basis of the pedicels, within a specialized group of cells collectively known as the abscission zone (AZ). During plant growth these cells become competent to respond to specific signals that trigger separation and lead to the abolition of cell wall adhesion. Little is known about the molecular network controlling the yellow lupine organ abscission. The aim of our study was to establish the divergences and similarities in transcriptional networks in the pods, flowers and flower pedicels abscised or maintained on the plant, and to identify genes playing key roles in generative organ abscission in yellow lupine. Based on de novo transcriptome assembly, we identified 166,473 unigenes representing 219,514 assembled unique transcripts from flowers, flower pedicels and pods undergoing abscission and from control organs. Comparison of the cDNA libraries from dropped and control organs helped in identifying 1,343, 2,933 and 1,491 differentially expressed genes (DEGs) in the flowers, flower pedicels and pods, respectively. In DEG analyses, we focused on genes involved in phytohormonal regulation, cell wall functioning and metabolic pathways. Our results indicate that auxin, ethylene and gibberellins are some of the main factors engaged in generative organ abscission. Identified 28 DEGs common for all library comparisons are involved in cell wall functioning, protein metabolism, water homeostasis and stress response. Interestingly, among the common DEGs we also found an miR169 precursor, which is the first evidence of micro RNA engaged in abscission. A KEGG pathway enrichment analysis revealed that the identified DEGs were predominantly involved in carbohydrate and amino acid metabolism, but some other pathways were also targeted. This study represents the first comprehensive transcriptome-based characterization of organ abscission in L. luteus and provides a valuable data source not only for understanding the abscission signaling pathway in yellow lupine, but also for further research aimed at improving crop yields.

Conservation of the abscission signaling peptide IDA during Angiosperm evolution: withstanding genome duplications and gain and loss of the receptors HAE/HSL2

The peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), which signals through the leucine-rich repeat receptor-like kinases HAESA (HAE) and HAESA-LIKE2 (HSL2), controls different cell separation events in Arabidopsis thaliana. We hypothesize the involvement of this signaling module in abscission processes in other plant species even though they may shed other organs than A. thaliana. As the first step toward testing this hypothesis from an evolutionarily perspective we have identified genes encoding putative orthologs of IDA and its receptors by BLAST searches of publically available protein, nucleotide and genome databases for angiosperms. Genes encoding IDA or IDA-LIKE (IDL) peptides and HSL proteins were found in all investigated species, which were selected as to represent each angiosperm order with available genomic sequences. The 12 amino acids representing the bioactive peptide in A. thaliana have virtually been unchanged throughout the evolution of the angiosperms; however, the number of IDL and HSL genes varies between different orders and species. The phylogenetic analyses suggest that IDA, HSL2, and the related HSL1 gene, were present in the species that gave rise to the angiosperms. HAE has arisen from HSL1 after a genome duplication that took place after the monocot-eudicots split. HSL1 has also independently been duplicated in the monocots, while HSL2 has been lost in gingers (Zingiberales) and grasses (Poales). IDA has been duplicated in eudicots to give rise to functionally divergent IDL peptides. We postulate that the high number of IDL homologs present in the core eudicots is a result of multiple whole genome duplications (WGD). We substantiate the involvement of IDA and HAE/HSL2 homologs in abscission by providing gene expression data of different organ separation events from various species.

Genome-wide identification and expression analysis of the expansin gene family in tomato

Plant expansins are capable of inducing pH-dependent cell wall extension and stress relaxation. They may be useful as targets for crop improvement to enhance fruit development and stress resistance. Tomato is a major agricultural crop and a model plant for studying fruit development. Because only some tomato expansins have been studied, a genome-wide analysis of the tomato expansin family is necessary. In this study, we identified 25 SlEXPAs, eight SlEXPBs, one SlEXLA, four SlEXLBs, and five short homologs in the tomato genome. 25 of these genes were identified as being expressed. Bioinformatic analysis showed that although tomato expansins share similarities with those from other plants, they also exhibit specific features regarding genetic structure and amino acid sequences, which indicates a unique evolutionary process. Segmental and tandem duplication events have played important roles in expanding the tomato expansin family. Additionally, the 3-exon/2-intron structure may form the basic organization of expansin genes. We identified new expansin genes preferentially expressed in fruits (SlEXPA8, SlEXPB8, and SlEXLB1), roots (SlEXPA9, SlEXLB2, and SlEXLB4), and floral organs. Among the analyzed genes those that were inducible by hormone or stress treatments, including SlEXPA3, SlEXPA7, SlEXPB1-B2, SlEXPB8, SlEXLB1-LB2, and SlEXLB4. Our findings may further clarify the biological activities of tomato expansins, especially those related to fruit development and stress resistance, and contribute to the genetic modification of tomato plants to improve crop quality and yield.