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Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. This study identified a total of 58,652 genes and 150 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild-type (WT) Moso bamboo (Phyllostachys edulis) and a thick wall (TW) variant (P. edulis “Pachyloen”) at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 14,029 (65.17%) differentially expressed genes and 68 (45.33%) differentially expressed miRNAs were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations, each between two successive stages (WTS2/TWS2_versus_WTS1/TWS1, WTS3/TWS3_versus_WTS2/TWS2, WTS4/TWS4_versus_WTS3/TWS3, and WTS5/TWS5_versus_WTS4/TWS4), and the WTTW group was composed of five combinations, each between two relative stages (TWS1–5_versus_WTS1–5). Additionally, among the phytohormones, zeatin showed more remarkable changes in concentrations than indole-3-acetic acid, gibberellic acid, and abscisic acid throughout the five stages in the WT and the TW groups. Moreover, 125 cleavage sites were identified for 387 miRNA–mRNA pairs via degradome sequencing (P

Petals of the monocot Phalaenopsis aphrodite (Orchidaceae) possess conical epidermal cells on their adaxial surfaces, and a large amount of cuticular wax is deposited on them to serve as a primary barrier against biotic and abiotic stresses. It has been widely reported that subgroup 9A members of the R2R3-MYB gene family, MIXTA and MIXTA-like in eudicots, act to regulate the differentiation of conical epidermal cells. However, the molecular pathways underlying conical epidermal cell development and cuticular wax biosynthesis in monocot petals remain unclear. Here, we characterized two subgroup 9A R2R3-MYB genes, PaMYB9A1 and PaMYB9A2 (PaMYB9A1/2), from P. aphrodite through the transient overexpression of their coding sequences and corresponding chimeric repressors in developing petals. We showed that PaMYB9A1/2 function to coordinate conical epidermal cell development and cuticular wax biosynthesis. In addition, we identified putative targets of PaMYB9A1/2 through comparative transcriptome analyses, revealing that PaMYB9A1/2 acts to regulate the expression of cell wall-associated and wax biosynthetic genes. Furthermore, a chemical composition analysis of cuticular wax showed that even-chain n-alkanes and odd-chain primary alcohols are the main chemical constituents of cuticular wax deposited on petals, which is inconsistent with the well-known biosynthetic pathways of cuticular wax, implying a distinct biosynthetic pathway occurring in P. aphrodite flowers. These results reveal that the function of subgroup 9A R2R3-MYB family genes in regulating the differentiation of epidermal cells is largely conserved in monocots and dicots. Furthermore, both PaMYB9A1/2 have evolved additional functions controlling the biosynthesis of cuticular wax., Two subgroup 9A R2R3-MYB genes act to regulate the development of conical epidermal cells and the biosynthesis of cuticular wax in Phalaenopsis petals.

The rhizosheath is a belowground area that acts as a communication hub at the root–soil interface to promote water and nutrient acquisition. Certain crops, such as white lupin (Lupinus albus), acquire large amounts of phosphorus (P), owing partially to exudation of acid phosphatases (APases). Plant growth-promoting rhizobacteria also increase soil P availability. However, potential synergistic effects of root APases and rhizosheath-associated microbiota on P acquisition require further research. In this study, we investigated the roles of root purple APases (PAPs) and plant growth-promoting rhizobacteria in rhizosheath formation and P acquisition under conditions of soil drying (SD) and P treatment (+P: soil with P fertilizer; –P: soil without fertilizer). We expressed purple acid phosphatase12 (LaPAP12) in white lupin and rice (Oryza sativa) plants and analyzed the rhizosheath-associated microbiome. Increased or heterologous LaPAP12 expression promoted APase activity and rhizosheath formation, resulting in increased P acquisition mainly under SD–P conditions. It also increased the abundance of members of the genus Bacillus in the rhizosheath-associated microbial communities of white lupin and rice. We isolated a phosphate-solubilizing, auxin-producing Bacillus megaterium strain from the rhizosheath of white lupin and used this to inoculate white lupin and rice plants. Inoculation promoted rhizosheath formation and P acquisition, especially in plants with increased LaPAP12 expression and under SD–P conditions, suggesting a functional role of the bacteria in alleviating P deficit stress via rhizosheath formation. Together, our results suggest a synergistic enhancing effect of LaPAP12 and plant growth-promoting rhizobacteria on rhizosheath formation and P acquisition under SD–P conditions.

Mobilization of seed storage compounds, such as starch and oil, is required to provide energy and metabolic building blocks during seedling development. Over 50% of fatty acids in Arabidopsis (Arabidopsis thaliana) seed oil have a cis-double bond on an even-numbered carbon. Degradation of these substrates requires peroxisomal fatty acid β-oxidation plus additional enzyme activities. Such auxiliary enzymes, including the enoyl-CoA hydratase ECH2, convert (R)-3-hydroxyacyl-CoA intermediates to the core β-oxidation substrate (S)-3-hydroxyacyl-CoA. ECH2 was suggested to function in the peroxisomal conversion of indole-3-butyric acid (IBA) to indole-3-acetic acid, because ech2 seedlings have altered IBA responses. The underlying mechanism connecting ECH2 activity and IBA metabolism is unclear. Here, we show that ech2 seedlings have reduced root length, smaller cotyledons, and arrested pavement cell expansion. At the cellular level, reduced oil body mobilization and enlarged peroxisomes suggest compromised β-oxidation. ech2 seedlings accumulate 3-hydroxyoctenoate (C8:1-OH) and 3-hydroxyoctanoate (C8:0-OH), putative hydrolysis products of catabolic intermediates for α-linolenic acid and linoleic acid, respectively. Wild-type seedlings treated with 3-hydroxyoctanoate have ech2-like growth defects and altered IBA responses. ech2 phenotypes are not rescued by Suc or auxin application. However, ech2 phenotypes are suppressed in combination with the core β-oxidation mutants mfp2 or ped1, and ech2 mfp2 seedlings accumulate less C8:1-OH and C8:0-OH than ech2 seedlings. These results indicate that ech2 phenotypes require efficient core β-oxidation. Our findings suggest that low ECH2 activity causes metabolic alterations through a toxic effect of the accumulating intermediates. These effects manifest in altered lipid metabolism and IBA responses leading to disrupted seedling development.

Plant roots respond to soil moisture gradients and remodel their growth orientation toward water through hydrotropism, a process vital for acclimation to a changing soil environment. Mechanisms underlying the root hydrotropic response, however, remain poorly understood. Here, we examined hydrotropism in 31 Arabidopsis (Arabidopsis thaliana) ecotypes collected from different parts of the world and grown along moisture gradients in a specially designed soil-simulation system. Comparative transcriptome profiling and physiological analyses were carried out on three selected ecotypes, Wassilewskija (Ws), Columbia (Col-0) (strongly hydrotropic), Col-0 (moderately hydrotropic), and C24 (weakly hydrotropic), and in mutant lines with altered root hydrotropic responses. We show that H+ efflux, Ca2+ influx, redox homeostasis, epigenetic regulation, and phytohormone signaling may contribute to root hydrotropism. Among phytohormones, the role of brassinosteroids (BRs) was examined further. In the presence of an inhibitor of BR biosynthesis, the strong hydrotropic response observed in Ws was reduced. The root H+ efflux and primary root elongation also were inhibited when compared with C24, an ecotype that showed a weak hydrotropic response. The BR-insensitive mutant bri1-5 displayed higher rates of root growth inhibition and root curvature on moisture gradients in vertical or oblique orientation when compared with wild-type Ws. We also demonstrate that BRI1 (a BR receptor) interacts with AHA2 (a plasma membrane H+-ATPase) and that their expression patterns are highly coordinated. This synergistic action may contribute to the strong hydrotropism observed in Ws. Our results suggest that BR-associated H+ efflux is critical in the hydrotropic response of Arabidopsis roots.

The mitochondrial ATP-binding cassette transporter ATM3 has been studied in Arabidopsis. Its function, however, is poorly understood in other model plant species. This study reports that the ATM3 is required for cytosolic iron-sulfur cluster assembly and is essential for meristem maintenance in rice (Oryza sativa). The loss of function of OsATM3 is lethal in rice at the four-leaf stage. In the osatm3 T-DNA insertion mutant, the fourth leaf fails to develop and the lateral roots are short. Cytosolic iron-sulfur protein activities were significantly reduced in both osatm3 and RNA interference transgenic lines. The expression profiles of many iron metabolism genes were altered in the osatm3 and RNA interference lines. Glutathione metabolism was impaired and reactive oxygen species, particularly superoxide, accumulated in osatm3. Promoter-β-glucuronidase staining of the transgenic line indicated that OsATM3 is highly expressed in lateral root primordia, root tip meristem zones, and shoot apical meristem regions. The average cell size was significantly greater in osatm3 than in the wild type. Massive cell death occurred in the osatm3 root tip meristem zone. Quantitative RT-PCR revealed transcriptional reprogramming of the genes in the osatm3 and RNAi lines involved in DNA repair and cell cycle arrest. Our results suggest that the mitochondrial ATM3 is essential for iron homeostasis in rice.

The dicotyledon seedling undergoes organ-specific photomorphogenic development when exposed to light. The cotyledons open and expand, the apical hook opens, and the hypocotyl ceases to elongate. Using the large and easily dissected seedlings of soybean (Glycine max ‘Williams 82’), we show that genes involved in photosynthesis and its regulation dominate transcripts specific to the cotyledon, even in etiolated seedlings. Genes for cell wall biosynthesis and metabolism are expressed at higher levels in the hypocotyl, while examination of genes expressed at higher levels in the hook region (including the shoot apical meristem) reveals genes involved in cell division and protein turnover. The early transcriptional events in these three organs in response to a 1-h treatment of far-red light are highly distinctive. Not only are different regulatory genes rapidly regulated by light in each organ, but the early-responsive genes in each organ contain a distinctive subset of known light-responsive cis-regulatory elements. We detected specific light-induced gene expression for the root phototropism gene RPT2 in the apical hook and also phenotypes in Arabidopsis (Arabidopsis thaliana) rpt2 mutants demonstrating that the gene is necessary for normal photomorphogenesis in the seedling apex. Significantly, expression of the RPT2 promoter fused to a β-glucuronidase reporter gene shows differential expression across the hook region. We conclude that organ-specific, light-responsive transcriptional networks are active early in photomorphogenesis in the aerial parts of dicotyledon seedlings.

Rice (Oryza sativa) is the most aluminum (Al)-resistant crop species among the small-grain cereals, but the mechanisms responsible for this trait are still unclear. Using two rice cultivars differing in Al resistance, rice sp. japonica ‘Nipponbare’ (an Al-resistant cultivar) and rice sp. indica ‘Zhefu802’ (an Al-sensitive cultivar), it was found that Al content in the root apex (0–10 mm) was significantly lower in Al-resistant ‘Nipponbare’ than in sensitive ‘Zhefu802’, with more of the Al localized to cell walls in ‘Zhefu802’, indicating that an Al exclusion mechanism is operating in ‘Nipponbare’. However, neither organic acid efflux nor changes in rhizosphere pH appear to be responsible for the Al exclusion. Interestingly, cell wall polysaccharides (pectin, hemicellulose 1, and hemicellulose 2) in the root apex were found to be significantly higher in ‘Zhefu802’ than in ‘Nipponbare’ in the absence of Al, and Al exposure increased root apex hemicellulose content more significantly in ‘Zhefu802’. Root tip cell wall pectin methylesterase (PME) activity was constitutively higher in ‘Zhefu802’ than in ‘Nipponbare’, although Al treatment resulted in increased PME activity in both cultivars. Immunolocalization of pectins showed a higher proportion of demethylated pectins in ‘Zhefu802’, indicating a higher proportion of free pectic acid residues in the cell walls of ‘Zhefu802’ root tips. Al adsorption and desorption kinetics of root tip cell walls also indicated that more Al was adsorbed and bound Al was retained more tightly in ‘Zhefu802’, which was consistent with Al content, PME activity, and pectin demethylesterification results. These responses were specific to Al compared with other metals (CdCl2, LaCl3, and CuCl2), and the ability of the cell wall to adsorb these metals was also not related to levels of cell wall pectins. All of these results suggest that cell wall polysaccharides may play an important role in excluding Al specifically from the rice root apex.

Phytoplasmas have the smallest genome among bacteria and lack many essential genes required for biosynthetic and metabolic functions, making them unculturable, phloem-limited plant pathogens. In this study, we observed that transgenic Arabidopsis (Arabidopsis thaliana) expressing the secreted Aster Yellows phytoplasma strain Witches’ Broom protein11 shows an altered root architecture, similarly to the disease symptoms of phytoplasma-infected plants, by forming hairy roots. This morphological change is paralleled by an accumulation of cellular phosphate (Pi) and an increase in the expression levels of Pi starvation-induced genes and microRNAs. In addition to the Pi starvation responses, we found that secreted Aster Yellows phytoplasma strain Witches’ Broom protein11 suppresses salicylic acid-mediated defense responses and enhances the growth of a bacterial pathogen. These results contribute to an improved understanding of the role of phytoplasma effector SAP11 and provide new insights for understanding the molecular basis of plant-pathogen interactions.

To investigate sepal/petal/lip formation in Oncidium Gower Ramsey, three paleoAPETALA3 genes, O. Gower Ramsey MADS box gene5 (OMADS5; clade 1), OMADS3 (clade 2), and OMADS9 (clade 3), and one PISTILLATA gene, OMADS8, were characterized. The OMADS8 and OMADS3 mRNAs were expressed in all four floral organs as well as in vegetative leaves. The OMADS9 mRNA was only strongly detected in petals and lips. The mRNA for OMADS5 was only strongly detected in sepals and petals and was significantly down-regulated in lip-like petals and lip-like sepals of peloric mutant flowers. This result revealed a possible negative role for OMADS5 in regulating lip formation. Yeast two-hybrid analysis indicated that OMADS5 formed homodimers and heterodimers with OMADS3 and OMADS9. OMADS8 only formed heterodimers with OMADS3, whereas OMADS3 and OMADS9 formed homodimers and heterodimers with each other. We proposed that sepal/petal/lip formation needs the presence of OMADS3/8 and/or OMADS9. The determination of the final organ identity for the sepal/petal/lip likely depended on the presence or absence of OMADS5. The presence of OMADS5 caused short sepal/petal formation. When OMADS5 was absent, cells could proliferate, resulting in the possible formation of large lips and the conversion of the sepal/petal into lips in peloric mutants. Further analysis indicated that only ectopic expression of OMADS8 but not OMADS5/9 caused the conversion of the sepal into an expanded petal-like structure in transgenic Arabidopsis (Arabidopsis thaliana) plants.