Cell Wall-related Genes Research Articles

Indole-3-acetic acid treatment promotes postharvest kiwifruit softening by regulating starch and cell wall metabolism

The softening process of postharvest kiwifruit is a critical aspect of fruit quality that has been extensively studied. However, the impact of indole-3-acetic acid (IAA) treatment on this process remains largely unexplored. In this study, we examined the effect of IAA treatment on the softening of postharvest kiwifruit. The results depicted that kiwifruit treated with IAA exhibited decreased firmness and increased ethylene production. Treatment with IAA upregulated the expression of starch decomposition genes, including AcSEX and AcBAM, resulting in a reduction in starch content. Additionally, IAA treatment induced cell wall breakdown, attributed to the enhanced transcript levels of cell wall-related degradation genes such as AcPE, AcPG, AcPL, and AcCX compared to the control. Consequently, IAA-treated kiwifruit displayed lower levels of cellulose and protopectin but higher levels of water-soluble pectin. In summary, our findings indicate that exogenous IAA promoted postharvest starch and cell wall biodegradation in kiwifruit, which reduced fruit firmness and accelerated fruit softening.

In Vitro vs. In Vivo Transcriptomic Approach Revealed Core Pathways of Nitrogen Deficiency Response in Tea Plant (Camellia sinensis (L.) Kuntze).

For the first time, we used an in vitro vs. in vivo experimental design to reveal core pathways under nitrogen deficiency (ND) in an evergreen tree crop. These pathways were related to lignin biosynthesis, cell redox homeostasis, the defense response to fungus, the response to Karrikin, amino acid transmembrane transport, the extracellular region, the cellular protein catabolic process, and aspartic-type endopeptidase activity. In addition, the mitogen-activated protein kinase pathway and ATP synthase (ATP)-binding cassette transporters were significantly upregulated under nitrogen deficiency in vitro and in vivo. Most of the MAPK downstream genes were related to calcium signaling (818 genes) rather than hormone signaling (157 genes). Moreover, the hormone signaling pathway predominantly contained auxin- and abscisic acid-related genes, indicating the crucial role of these hormones in ND response. Overall, 45 transcription factors were upregulated in both experiments, 5 WRKYs, 3 NACs, 2 MYBs, 2 ERFs, HD-Zip, RLP12, bHLH25, RADIALIS-like, and others, suggesting their ND regulation is independent from the presence of a root system. Gene network reconstruction displayed that these transcription factors participate in response to fungus/chitin, suggesting that nitrogen response and pathogen response have common regulation. The upregulation of lignin biosynthesis genes, cytochrome genes, and strigalactone response genes was much more pronounced under in vitro ND as compared to in vivo ND. Several cell wall-related genes were closely associated with cytochromes, indicating their important role in flavanols biosynthesis in tea plant. These results clarify the signaling mechanisms and regulation of the response to nitrogen deficiency in evergreen tree crops.

Identification of Candidate Genes Associated with Flesh Firmness by Combining QTL Mapping and Transcriptome Profiling in Pyrus pyrifolia.

Flesh firmness is an important quality of pear fruits. Breeding cultivars with suitably low flesh firmness is one of the popular pear breeding goals. At present, SNP markers related to pear flesh firmness and genes affecting flesh firmness are still uncertain. In this study, a QTL analysis was performed, and the result showed that the position of 139.857 cM in lineage group 14 (LG14) had the highest average logarithm of odds (3.41) over two years. This newly discovered locus was identified as a flesh firmness-related QTL (qFirmness-LG14). The 'C/T' SNP was found in corresponding Marker1512129. The 'C' genotype is the high-firmness genotype, which is a dominant trait. The average firmness of fruits with genotype C is 21.4% higher than genotype without the C genotype. Transcriptome profiling was obtained between 'Zaoshengxinshui' and 'Qiushui' at five time points. Three candidate genes in the interval of qFirmness-LG14 might affect firmness. A gene of xyloglucan endotransglucosylase 1 (PpXTH1) was upregulated in 'Qiushui' at all five time points. Two transcription factors (PpHY5 and PpERF113) were upregulated in 'Zaoshengxinshui', which might be negative regulatory genes for high flesh firmness. The transcriptome results also isolated a large number of cell wall-related genes (e.g., Pectate lyase, Pectin acetylesterase, Pectin methylesterase, and 4-coumarate-CoA ligase) and transcription factors (e.g., ERF, WRKY). These genes are all potential upstream and downstream genes related to flesh firmness. In conclusion, this study provides valuable insights into the QTLs and molecular mechanisms associated with fruit firmness in Pyrus pyrifolia.

The MaNAP1-MaMADS1 transcription factor module mediates ethylene-regulated peel softening and ripening in banana.

The banana (Musa spp.) peel undergoes rapid softening during ripening, leading to finger drop and a shortened shelf life. The regulatory mechanism behind this process remains to be elucidated. In this study, we confirmed the role of peel softening in banana finger drop and uncovered the underlying transcriptional regulatory network. Cell wall-related (CWR) genes were substantially upregulated in both the peel and finger drop zone during ethylene-induced ripening. Transcriptome analysis and genome-wide profiling of chromatin accessibility and transcription factor (TF) binding revealed that two key regulators of fruit ripening, Musa acuminata NAC-like, Activated by apetala3/Pistillata1 (MaNAP1) and MaMADS1, regulate CWR genes by directly binding to their promoters or by targeting other ripening-related TFs to form a hierarchical regulatory network. Notably, MaNAP1 and MaMADS1 were directly targeted by ETHYLENE INSENSITIVE3 (MaEIN3), and MaNAP1 and MaMADS1 associated with tissue-specific histone modifications, enabling them to integrate MaEIN3-mediated ethylene signaling and undergo epigenetic regulation. Overexpression of MaNAP1, MaMADS1 or other identified regulatory TFs upregulated CWR genes and promoted peel softening. Our findings unveil a MaNAP1-MaMADS1-centered regulatory cascade governing banana peel softening and finger drop, offering potential targets for enhancing banana texture and shelf life.

Maize stigmas react differently to self- and cross-pollination and fungal invasion.

During sexual reproduction in flowering plants, tip-growing pollen tubes travel from the stigma inside the maternal tissues of the pistil towards ovules. In maize (Zea mays L.), the stigma is highly elongated, forming thread-like strands known as silks. Only compatible pollen tubes successfully penetrate and grow through the transmitting tract of the silk to reach the ovules. Like pollen, fungal spores germinate at the surface of silks and generate tube-like structures (hyphae) penetrating silk tissue. To elucidate commonalities and differences between silk responses to these distinctive invading cells, we compared growth behavior of the various invaders as well as the silk transcriptome after self-pollination, cross-pollination and infection using two different fungi. We report that self-pollination triggers mainly senescence genes, whereas incompatible pollen from Tripsacum dactyloides leads to downregulation of rehydration, microtubule, and cell wall-related genes, explaining the slower pollen tube growth and arrest. Invasion by the ascomycete Fusarium graminearum triggers numerous defense responses including the activation of monolignol biosynthesis and NAC as well as WRKY transcription factor genes, whereas responses to the basidiomycete Ustilago maydis are generally much weaker. We present evidence that incompatible pollination and fungal infection trigger transcriptional reprograming of maize silks cell wall. Pathogen invasion also activates the phytoalexin biosynthesis pathway.

Differences in transcriptomic responses upon Phytophthora palmivora infection among cultivars reveal potential underlying resistant mechanisms in durian

BackgroundPhytophthora palmivora is a devastating oomycete pathogen in durian, one of the most economically important crops in Southeast Asia. The use of fungicides in Phytophthora management may not be a long-term solution because of emerging chemical resistance issues. It is crucial to develop Phytophthora-resistant durian cultivars, and information regarding the underlying resistance mechanisms is valuable for smart breeding programs.ResultsIn this study, we conducted RNA sequencing (RNA-seq) to investigate early gene expression responses (at 8, 24, and 48 h) after the P. palmivora infection in three durian cultivars, which included one resistant cultivar (Puangmanee; PM) and two susceptible cultivars (Monthong; MT and Kradumthong; KD). We performed co-expression and differential gene expression analyses to capture gene expression patterns and identify the differentially expressed genes. The results showed that genes encoding heat shock proteins (HSPs) were upregulated in all infected durians. The expression levels of genes encoding HSPs, such as ERdj3B, were high only in infected PM. A higher level of P. palmivora resistance in PM appeared to be associated with higher expression levels of various genes encoding defense and chitin response proteins, such as lysM domain receptor-like kinases. MT had a lower resistance level than PM, although it possessed more upregulated genes during P. palmivora infection. Many photosynthetic and defense genes were upregulated in the infected MT, although their expression levels were lower than those in the infected PM. KD, the least resistant cultivar, showed downregulation of genes involved in cell wall organization or biogenesis during P. palmivora infection.ConclusionsOur results showed that the three durian cultivars exhibited significantly different gene expression patterns in response to P. palmivora infection. The upregulation of genes encoding HSPs was common in all studied durians. The high expression of genes encoding chitin response proteins likely contributed to P. palmivora resistance in durians. Durian susceptibility was associated with low basal expression of defense genes and downregulation of several cell wall-related genes. These findings enhance our understanding of durian resistance to Phytophthora infection and could be useful for the development of elite durian cultivars.

H3K4me3 changes occur in cell wall genes during the development of Fagopyrum tataricum morphogenic and non-morphogenic calli.

Epigenetic changes accompany the dynamic changes in the cell wall composition during the development of callus cells. H3K4me3 is responsible for active gene expression and reaction to environmental cues. Chromatin immunoprecipitation (ChIP) is a powerful technique for studying the interplay between epigenetic modifications and the DNA regions of interest. In combination with sequencing, it can provide the genome-wide enrichment of the specific epigenetic mark, providing vital information on its involvement in the plethora of cellular processes. Here, we describe the genome-wide distribution of H3K4me3 in morphogenic and non-morphogenic callus of Fagopyrum tataricum. Levels of H3K4me3 were higher around the transcription start site, in agreement with the role of this mark in transcriptional activation. The global levels of methylation were higher in the non-morphogenic callus, which indicated increased gene activation compared to the morphogenic callus. We also employed ChIP to analyse the changes in the enrichment of this epigenetic mark on the cell wall-related genes in both calli types during the course of the passage. Enrichment of H3K4me3 on cell wall genes was specific for callus type, suggesting that the role of this mark in cell-wall remodelling is complex and involved in many processes related to dedifferentiation and redifferentiation. This intricacy of the cell wall composition was supported by the immunohistochemical analysis of the cell wall epitopes' distribution of pectins and extensins. Together, these data give a novel insight into the involvement of H3K4me3 in the regeneration processes in F. tataricum in vitro callus tissue culture.

A fungal endophyte induces local cell wall-mediated resistance in wheat roots against take-all disease.

Take-all disease, caused by the Ascomycete fungus Gaeumannomyces tritici, is one of the most important root diseases of wheat worldwide. The fungus invades the roots and destroys the vascular tissue, hindering the uptake of water and nutrients. Closely related non-pathogenic species in the Magnaporthaceae family, such as Gaeumannomyces hyphopodioides, occur naturally in arable and grassland soils and have previously been reported to reduce take-all disease in field studies. However, the mechanism of take-all protection has remained unknown. Here, we demonstrate that take-all control is achieved via local but not systemic host changes in response to prior G. hyphopodioides root colonisation. A time-course wheat RNA sequencing analysis revealed extensive transcriptional reprogramming in G. hyphopodioides-colonised tissues, characterised by a striking downregulation of key cell wall-related genes, including genes encoding cellulose synthases (CESA), and xyloglucan endotransglucosylase/hydrolases (XTH). In addition, we characterise the root infection biologies of G. tritici and G. hyphopodioides in wheat. We investigate the ultrastructure of previously described "subepidermal vesicles" (SEVs), dark swollen fungal cells produced in wheat roots by non-pathogenic G. hyphopodioides, but not by pathogenic G. tritici. We show that G. hyphopodioides SEVs share key characteristics of fungal resting structures, containing a greater number of putative lipid bodies and a significantly thickened cell wall compared to infection hyphae. We hypothesise that SEVs are fungal resting structures formed due to halted hyphal growth in the root cortex, perhaps as a stress response to locally induced wheat defence responses. In the absence of take-all resistant wheat cultivars or non-virulent G. tritici strains, studying closely related non-pathogenic G. hyphopodioides provides a much needed avenue to elucidate take-all resistance mechanisms in wheat.

Determination and Analysis of Endogenous Hormones and Cell Wall Composition between the Straight and Twisted Trunk Types of Pinus yunnanensis Franch

Pinus yunnanensis Franch., one of the pioneer species of wild mountain afforestation in southwest China, plays an essential role in the economy, society and environment of Yunnan Province. Nonetheless, P. yunnanensis’ trunk twisting and bending phenomenon has become more common, which significantly restricts its use and economic benefits. In order to clarify the compositional differences between the straight and twisted trunk types of P. yunnanensis and to investigate the reasons for the formation of twisted stems, the present study was carried out to dissect the macroscopic and microscopic structure of the straight and twisted trunk types of P. yunnanensis, to determine the content of cell wall components (lignin, cellulose, hemicellulose), determine the content of endogenous hormones, and the expression validation of phytohormone-related differential genes (GA2OX, COI1, COI2) and cell wall-related genes (XTH16, TCH4). The results showed that the annual rings of twisted trunk types were unevenly distributed, eccentric growth, insignificant decomposition of early and late wood, rounding and widening of the tracheid cells, thickening of the cell wall, and reduction of the cavity diameter; the lignin and hemicellulose contents of twisted trunk types were higher; in twisted trunk types, the contents of gibberellin (GA) and jasmonic acid (JA) increased, and the content of auxin (IAA) was reduced; the GA2OX were significantly down-regulated in twisted trunk types, and the expressions of the genes associated with the cell wall, COI1, COI2, TCH4 and XTH16, were significantly up-regulated. In conclusion, the present study found that the uneven distribution of endogenous hormones may be an important factor leading to the formation of twisted trunk type of P. yunnanensis, which adds new discoveries to reveal the mechanism of the genesis of different trunk types in plants, and provides a theoretical basis for the genetic improvement of forest trees.

Comparative transcriptome analysis reveals defense responses against soft rot induced by Pectobacterium aroidearum and Pectobacterium carotovorum in Pinellia ternata

Pectobacterium carotovorum and Pectobacterium aroidearum represent the primary pathogens causing variable soft rot disease. However, the fundamental defense responses of Pinellia ternata to pathogens remain unclear. Our investigation demonstrated that the disease produced by P. carotovorum is more serious than P. aroidearum. RNA-seq analysis indicated that many cell wall-related genes, receptor-like kinase genes, and resistance-related genes were induced by P. aroidearum and P. carotovorum similarly. But many different regulatory pathways exert a crucial function in plant immunity against P. aroidearum and P. carotovorum, including hormone signaling, whereas more auxin-responsive genes were responsive to P. carotovorum, while more ethylene and gibberellin-responsive genes were responsive to P. aroidearum. 12 GDSL esterase/lipase genes and 3 fasciclin-like arabinogalactan protein genes were specifically upregulated by P. carotovorum, whereas 11 receptor-like kinase genes and 8 disease resistance genes were up-regulated only by P. aroidearum. Among them, a lectin gene (part1transcript/39001) was induced by P. carotovorum and P. aroidearum simultaneously. Transient expression in N. benthamiana demonstrated that the lectin gene improves plant resistance to P. carotovorum. This study offers a comprehensive perspective on P. ternata immunity produced by different soft rot pathogens and reveals the importance of lectin in anti-soft rot of P. ternata for the first time.

Organ-specific transcriptional regulation by HFR1 and HY5 in response to shade in Arabidopsis.

Light is crucial for plants and serves as a signal for modulating their growth. Under shade, where red to far-red light ratio is low, plants exhibit shade avoidance responses (SAR). LONG HYPOCOTYL IN FAR-RED 1 (HFR1) and ELONGATED HYPOCOTYL 5 (HY5) are known to be negative regulators of SAR and physically interact with one another. However, transcriptional regulatory network underlying SAR by these two transcription factors has not been explored. Here, we performed organ-specific transcriptome analyses of Arabidopsis thaliana hfr1-5, hy5-215 and hfr1hy5 to identify genes that are co-regulated by HFR1 and HY5 in hypocotyls and cotyledons. Genes co-regulated by HFR1 and HY5 were enriched in various processes related to cell wall modification and chlorophyll biosynthesis in hypocotyls. Phytohormone (abscisic acid and jasmonic acid) and light responses were significantly regulated by HFR1 and HY5 in both organs, though it is more prominent under shade in cotyledons. HFR1 and HY5 also differentially regulate the expression of the cell wall-related genes for xyloglucan endotransglucosylase/hydrolase, expansin, arabinogalactan protein and class III peroxidase depending on the organs. Furthermore, HFR1 and HY5 cooperatively regulated hypocotyl responsiveness to shade through auxin metabolism. Together, our study illustrates the importance of the HFR1-HY5 module in regulating organ-specific shade responses in Arabidopsis.

Exploring the diversity of galls on Artemisia indica induced by Rhopalomyia species through morphological and transcriptome analyses.

Plant galls generated by insects have highly organized structures, providing nutrients and shelter to the insects living within them. Most research on the physiological and molecular mechanisms of gall development has focused on single galls. To understand the diversity of gall development, we examined five galls with different morphologies generated by distinct species of Rhopalomyia (gall midge; Diptera: Cecidomyiidae) on a single host plant of Artemisia indica var. maximowiczii (Asteraceae). Vasculature developed de novo within the galls, indicating active transport of nutrients between galls and the host plant. Each gall had a different pattern of vasculature and lignification, probably due to differences in the site of gall generation and the gall midge species. Transcriptome analysis indicated that photosynthetic and cell wall-related genes were down-regulated in leaf and stem galls, respectively, compared with control leaf and stem tissues, whereas genes involved in floral organ development were up-regulated in all types of galls, indicating that transformation from source to sink organs occurs during gall development. Our results help to understand the diversity of galls on a single herbaceous host plant.

The β-galactosidase gene AtrBGAL2 regulates Akebia trifoliata fruit cracking

Cracking of Akebia trifoliata fruit at maturity is problematic for the cultivation of the horticultural crop, shortening shelf-life quality and compromising commercial value. However, the molecular mechanisms underlying this feature of A. trifoliata are not known. Genes involved in cell wall metabolism were identified by genome and transcriptome sequencing, which may play important roles in fruit cracking. One of the galactose metabolism related genes, β-galactosidase (AtrBGAL2), was identified in A. trifoliata, and overexpression (OE) of AtrBGAL2 resulted in early fruit cracking, higher water-soluble pectin contents, and lower acid-soluble pectin, cellulose, and hemicellulose content compared to the wild type. Whereas silencing of AtrBGAL2 in trifoliata by virus induced gene silencing showed opposite trends. The levels of AtrBGAL2 transcripts were 24.6 and 66.0-fold higher in OE A. trifoliata and tomato fruits, respectively, and the cell wall-related genes were also gradually greater than in control plants during fruit ripening. Whereas the expression levels of AtrBGAL2 was significantly down-regulated by 54.1 % and 73.7 % in gene silenced A. trifoliata and CRISPR/Cas9 tomato mutant plants, respectively, and cell wall-related genes were also significantly reduced. These results demonstrate that AtrBGAL2 plays important roles in regulating fruit cracking during fruit ripening.

Fighting Emerging Caspofungin-Resistant Candida Species: Mitigating Fks1-Mediated Resistance and Enhancing Caspofungin Efficacy by Chitosan.

Invasive candidiasis poses a worldwide threat because of the rising prevalence of antifungal resistance, resulting in higher rates of morbidity and mortality. Additionally, Candida species, which are opportunistic infections, have significant medical and economic consequences for immunocompromised individuals. This study explores the antifungal potential of chitosan to mitigate caspofungin resistance in caspofungin-resistant Candida albicans, C. krusei, and C. tropicalis isolates originating from human and animal sources using agar well diffusion, broth microdilution tests, and transmission electron microscope (TEM) analysis of treated Candida cells. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) was performed to assess the expression of SAGA complex genes (GCN5 and ADA2) and the caspofungin resistance gene (FKS) in Candida species isolates after chitosan treatment. The highest resistance rate was observed to ketoconazole (80%) followed by clotrimazole (62.7%), fluconazole (60%), terbinafine (58%), itraconazole (57%), miconazole (54.2%), amphotericin B (51.4%), voriconazole (34.28%), and caspofungin (25.7%). Nine unique FKS mutations were detected, including S645P (n = 3 isolates), S645F, L644F, S645Y, L688M, E663G, and F641S (one isolate in each). The caspofungin minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) values before chitosan treatment ranged from 2 to 8 µg/mL and 4 to 16 µg/mL, respectively. However, the MIC and MFC values were decreased after chitosan treatment (0.0625-1 µg/mL) and (0.125-2 µg/mL), respectively. Caspofungin MIC was significantly decreased (p = 0.0007) threefold following chitosan treatment compared with the MIC values before treatment. TEM analysis revealed that 0.5% chitosan disrupted the integrity of the cell surface, causing irregular morphologies and obvious aberrant changes in cell wall thickness in caspofungin-resistant and sensitive Candida isolates. The cell wall thickness of untreated isolates was 0.145 μm in caspofungin-resistant isolate and 0.125 μm in sensitive isolate, while it was significantly lower in chitosan-treated isolates, ranging from 0.05 to 0.08 μm when compared with the cell wall thickness of sensitive isolate (0.03 to 0.06 μm). Moreover, RT-qPCR demonstrated a significant (p < 0.05) decrease in the expression levels of histone acetyltransferase genes (GCN5 and ADA2) and FKS gene of caspofungin-resistant Candida species isolates treated with 0.5% chitosan when compared with before treatment (fold change values ranged from 0.001 to 0.0473 for GCN5, 1.028 to 4.856 for ADA2, and 2.713 to 12.38 for FKS gene). A comparison of the expression levels of cell wall-related genes (ADA2 and GCN5) between caspofungin-resistant and -sensitive isolates demonstrated a significant decrease following chitosan treatment (p < 0.001). The antifungal potential of chitosan enhances the efficacy of caspofungin against various caspofungin-resistant Candida species isolates and prevents the development of further antifungal resistance. The results of this study contribute to the progress in repurposing caspofungin and inform a development strategy to enhance its efficacy, appropriate antifungal activity against Candida species, and mitigate resistance. Consequently, chitosan could be used in combination with caspofungin for the treatment of candidiasis.

Impact of activated charcoal on the progression of somatic embryogenesis in grape cells: Histological and transcriptomic perspectives

Somatic embryogenesis is a crucial genetic transformation method in plants. Despite numerous studies being conducted for acquiring embryogenic competence in plant cells, somatic embryo (SE) induction from embryogenic cells (ECs) has attracted relatively limited research attention. In grapes, somatic cell induction is impeded by unidentified inhibitors, which hinders the progression of globular embryo (GE) formation and subsequently embryo development. We found that addition of activated charcoal (AC) to the grape SE induction medium augmented the speed, consistency, and synchronization of embryogenesis. Cell samples cultured in the induction medium with and without AC were thoroughly evaluated through histological anatomy analysis, subcellular structure observation, and comparative transcriptomic analysis. The histological observation revealed the specific timeline of SE formation. An intermediate developmental state, referred to as the globular embryo precursor (PGE), was observed during the induction of GE formation from EC. Members of transcription factor families such as WRKY, MYB, MADS, AP2/ERF, HB-KNOX, HB-HD-ZIP, HB-WOX, NAC, and GRF were identified in the early and middle stages of GE formation. Additionally, we explored the key roles of reactive oxygen species (ROS)-, starch-, cell wall-, and hormone-related genes. The cell wall-related genes were highly enriched in differentially expressed gene sets. Several amyloplasts in EC disappeared, potentially because of hydrolysis, and numerous mitochondria were observed. In AC-added samples, starch was consumed more, and cellulose hydrolysis-related genes were downregulated, whereas cellulose synthesis-related genes had higher expression than AC-free samples. ROS response-related genes were induced when GE induction was initiated. When applied, an optimal concentration of external H2O2 promoted SE initiation in grapes, whereas a high concentration caused delayed GE formation. This study suggests that, by absorbing and releasing substances, the added AC can create a stable buffer environment for cell survival, protect against excessive ROS- or inhibitor-induced cell damage, and support uninterrupted progress of somatic embryogenesis.

Analysis of Microstructure, Cell Wall Polysaccharides, and Candidate Cell Wall-related Genes in Clingstone-type and Freestone-type Stony Hard Peaches during Ripening

Stony hard (SH) peach (Prunus persica) fruits produce no ethylene and clingstone-type SH peaches have a crispy flesh texture; however, freestone-type SH peach fruits ripen to a soft, mealy state. During this study, we compared and analyzed changes in the microstructure, cell wall polysaccharides, and candidate cell wall-related genes of freestone-type SH ‘Zhongtao 14’ (‘CP14’), ‘Zhongtao White Jade 2’ (‘CPWJ2’), clingstone-type SH ‘Zhongtao 13’ (‘CP13’), and ‘Zhongtao 9’ (‘CP9’) during fruit ripening. The parenchyma cells of mealy freestone-type SH peaches became detached, were single, dried, and irregularly arranged, and remained intact in comparison with the nonmealy clingstone-type SH peaches. Methyl-esterified homogalacturonan was strongly immunolabeled in the cell wall of clingstone SH peaches; however, nonmethylated homogalacturonan was weakly immunolabeled in freestone SH peaches. A transcriptome analysis was performed to investigate the molecular mechanism of the mealiness process. A principal component analysis indicated that ‘CP14’ S4 III (mealy) could be distinguished from the samples of ‘CP13’ (S4 I, S4 II, S4 III) and ‘CP14’ (S4 I, S4 II). The highly coexpressed gene modules linked with firmness were found using a weighted gene coexpression network analysis; 189 upregulated genes and 817 downregulated genes were identified. Six upregulated cell wall-related genes (PpPG1, PpPG2, PpAGP1, PpAGP2, PpEXT1, and PpEXP1) and one downregulated cell wall-related gene (PpXET2) were involved in the mealiness process during freestone-type SH fruit ripening. These findings will improve our understanding of the relationship between clingstone, freestone, and stony hard fruits and lay the foundation for further exploration of the mechanisms underlying the softening of peach fruits.

Irreversibility of the cell wall modification acts as a limiting factor in desiccation tolerance of Oryza sativa ssp. Indica cv MR303

Desiccation tolerance has emerged as a potential strategy for crop improvement. However, the application of desiccation tolerance in crops, particularly rice, has been challenging and limited. Studies in angiosperms suggest that desiccation in vegetative tissues shares a common set of genes, developed convergently by modifying shared pathways associated with seed desiccation. The drought-tolerant Oryza sativa ssp. indica cv MR303 has demonstrated the capability to withstand desiccation state for a short period of time. Using this variety, we aim to investigate the factors that limit rice plants from achieving desiccation tolerance. The irreversibility of the cell wall emerges as a primary factor hindering rice plants from acquiring desiccation tolerance. Analysis of cell wall composition and transcriptomic data reveals an accumulation of secondary cell wall components and the expression of cell wall-related genes involved in secondary wall formation and modification, suggesting that these factors could be underlying causes for the irreversibility of the cell wall. Such factors contribute to the rigidity and stiffness of the cell wall, leading to its irreversibility during the rehydration process. This, in turn, impedes the recovery of rice after dehydration.

Jasmonate mimic modulates cell elongation by regulating antagonistic bHLH transcription factors via brassinosteroid signaling.

Lodging restricts growth, development, and yield formation in maize (Zea mays L.). Shorter internode length is beneficial for lodging tolerance. However, although brassinosteroids (BRs) and jasmonic acid (JA) are known to antagonistically regulate internode growth, the underlying molecular mechanism is still unclear. In this study, application of the JA mimic coronatine (COR) inhibited basal internode elongation at the jointing stage and repressed expression of the cell wall-related gene XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 1 (ZmXTH1), whose overexpression in maize plants promoted internode elongation. We demonstrated that the basic helix-loop-helix (bHLH) transcription factor ZmbHLH154 directly binds to the ZmXTH1 promoter and induces its expression, whereas the bHLH transcription factor ILI1 BINDING BHLH 1 (ZmIBH1) inhibits this transcriptional activation by forming a heterodimer with ZmbHLH154. Overexpressing ZmbHLH154 led to longer internodes, whereas zmbhlh154 mutants had shorter internodes than the wild type. The core JA-dependent transcription factors ZmMYC2-4 and ZmMYC2-6 interacted with BRASSINAZOLE RESISTANT 1 (ZmBZR1), a key factor in BR signaling, and these interactions eliminated the inhibitory effect of ZmBZR1 on its downstream gene ZmIBH1. Collectively, these results reveal a signaling module in which JA regulates a bHLH network by attenuating BR signaling to inhibit ZmXTH1 expression, thereby regulating cell elongation in maize.

The heat shock factor 20-HSF4-cellulose synthase A2 module regulates heat stress tolerance in maize.

Temperature shapes the geographical distribution and behavior of plants. Understanding the regulatory mechanisms underlying the plant heat stress response is important for developing climate-resilient crops, including maize (Zea mays). To identify transcription factors (TFs) that may contribute to the maize heat stress response, we generated a dataset of short- and long-term transcriptome changes following a heat treatment time course in the inbred line B73. Co-expression network analysis highlighted several TFs, including the class B2a heat shock factor (HSF) ZmHSF20. Zmhsf20 mutant seedlings exhibited enhanced tolerance to heat stress. Furthermore, DNA affinity purification sequencing and Cleavage Under Targets and Tagmentation assays demonstrated that ZmHSF20 binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three class A Hsf genes, including ZmHsf4, repressing their transcription. We showed that ZmCesA2 and ZmHSF4 promote the heat stress response, with ZmHSF4 directly activating ZmCesA2 transcription. In agreement with the transcriptome analysis, ZmHSF20 inhibited cellulose accumulation and repressed the expression of cell wall-related genes. Importantly, the Zmhsf20 Zmhsf4 double mutant exhibited decreased thermotolerance, placing ZmHsf4 downstream of ZmHsf20. We proposed an expanded model of the heat stress response in maize, whereby ZmHSF20 lowers seedling heat tolerance by repressing ZmHsf4 and ZmCesA2, thus balancing seedling growth and defense.

Comparative transcriptomic profile of two mandarin varieties during maturation reveals pectinase regulating peelability

Peelability is an important fruit quality trait of citrus. Pectinase is a group of heterozygous enzymes that function in pectin degradation, which is implicated in fruit ripening and softening. Previously we established a method to quantify citrus peelability through two mechanical indexes (peel-pulp adherence and peel resistance of penetration), and exhibited the genetic diversity of peelability in mandarins (Citrus reticulata Blanco). With this method, the present study first confirmed that Clementine is an easy-peeling mandarin in comparison with Fremont, and both showed increasingly easy peeling as the fruits matured. A range of measurements for the two mandarins at three maturation stages demonstrated that peelability had negative correlation with pectin contents but positive with pectinase activity. Subsequently, RNA sequencing was performed for comparative transcriptomic profiling of the two varieties at three maturation stages. We identified 12322 differentially expressed genes (DEGs) in total. Through comparative time-course analysis, the gene expression patterns were displayed with 12 clusters each in albedo and flavedo. Some cell wall-related gene ontology terms were over-represented in albedo and flavedo Cluster6. We mined 153 genes encoding pectinase (pectin methylesterase, polygalacturonase, pectin lyase (PL), beta-galactanase, pectin acetylesterase and alpha-arabinofuranosidase) in silica from Clementine genome, and 78 of them were significantly expressed in the peel of Clementine or Fremont, whereas 62/60 belonged to the DEGs in albedo/flavedo. In weighted correlation network analysis, six/five out of eight/nine modules in albedo/flavedo had eigengene values that were significantly correlated with the two mechanical indexes, pectin contents and pectinase activity, and six/eight pectinase genes were present in the co-expression networks. Based on the results of multi-approach bioinformatics analysis, three PL genes (Ciclev10004783m.g, Ciclev10020423m.g and Ciclev10031429m.g) were highlighted as potential regulators for peelability. This study provides clues for understanding the molecular basis of the regulation of citrus peelability, and proposes pectinase as a target for peelability-oriented breeding of citrus.