Effects of boron deficiency on major metabolites, key enzymes and gas exchange in leaves and roots of Citrus sinensis seedlings

Boron-mediated amelioration of copper toxicity in Citrus sinensis seedlings involved reduced concentrations of copper in leaves and roots and their cell walls rather than increased copper fractions in their cell walls

Little information is available on how boron (B) supplementation affects plant cell wall (CW) remodeling under copper (Cu) excess. 'Xuegan' (Citrus sinensis) seedlings were submitted to 0.5 or 350 µM Cu × 2.5 or 25 µM B for 24 weeks. Thereafter, we determined the concentrations of CW materials (CWMs) and CW components (CWCs), the degree of pectin methylation (DPM), and the pectin methylesterase (PME) activities and PME gene expression levels in leaves and roots, as well as the Cu concentrations in leaves and roots and their CWMs (CWCs). Additionally, we analyzed the Fourier transform infrared (FTIR) and X-ray diffraction (XRD) spectra of leaf and root CWMs. Our findings suggested that adding B reduced the impairment of Cu excess to CWs by reducing the Cu concentrations in leaves and roots and their CWMs and maintaining the stability of CWs, thereby improving leaf and root growth. Cu excess increased the Cu fractions in leaf and root pectin by decreasing DPM due to increased PME activities, thereby contributing to citrus Cu tolerance. FTIR and XRD indicated that the functional groups of the CW pectin, hemicellulose, cellulose, and lignin could bind and immobilize Cu, thereby reducing Cu cytotoxicity in leaves and roots.

Regulation on copper-tolerance in Citrus sinensis seedlings by boron addition: Insights from root exudates, related metabolism, and gene expression

Boron (B) can alleviate Citrus copper (Cu)-toxicity. However, the underlying mechanism by which B mitigates Cu-toxicity is unclear. 'Xuegan' (Citrus sinensis) seedlings were exposed to 0.5 (control) or 350 (Cu-toxicity) µM Cu and 2.5 or 25 µM B for 24 weeks. Thereafter, we investigated the secretion of low molecular weight compounds [LMWCs; citrate, malate, total soluble sugars (TSS), total phenolics (TP), and total free amino acids (TFAA)] by excised roots and their concentrations in roots and leaves, as well as related enzyme gene expression and activities in roots and leaves. Cu-stress stimulated root release of malate and TFAA, which might contribute to citrus Cu-tolerance. However, B-mediated-mitigation of Cu-stress could not be explained in this way, since B addition failed to further stimulate malate and TFAA secretion. Indeed, B addition decreased Cu-stimulated-secretion of malate. Further analysis suggested that Cu-induced-exudation of malate and TFAA was not regulated by their levels in roots. By contrast, B addition increased malate, citrate, and TFAA concentrations in Cu-toxic roots. Cu-toxicity increased TP concentration in 25 μM B-treated leaves, but not in 2.5 μM B-treated leaves. Our findings suggested that the internal detoxification of Cu by LMWCs played a role in B-mediated-alleviation of Cu-toxicity.

A critical review of plant adaptation to environmental boron stress: Uptake, utilization, and interplay with other abiotic and biotic factors

Boron (B) is an indispensable mineral nutrient for plants and is primarily taken up by roots mainly in the form of boric acid (H3BO3). Recently, research shows that B has a significant impact on plant growth and productivity due to its narrow range between deficiency and toxicity. Fertilization and other procedures to address B stress (deficiency and toxicity) in soils are generally expensive and time-consuming. Over the past 20 years, substantial studies have been conducted to investigate the mechanisms underlying B acquisition and the molecular regulation of B stress in plants. In this review, we discuss the effects of B stress on plant growth, physiology, and biochemistry, and finding on enhancing plant tolerance from the perspective of plant B uptake, transport, and utilization. We also refer to recent results demonstrating the interactions among B and other biological and abiotic factors, including nitrogen, phosphorus, aluminum, and microorganisms. Finally, emerging trends in this field are discussed.

The regulation of plant lignin biosynthesis under boron deficiency conditions

Boron (B) is a required micronutrient that is crucial for the growth and development of vascular plants. A deficiency in B is generally regarded as a limiting factor affecting agricultural production in many parts of the world. Boron is involved in the metabolism of plant lignin and additionally, B deficiency can lead to the excessive accumulation of lignin in plant leaves/roots, resulting in corking symptoms and inhibited growth. However, the effect of B on lignin biosynthesis is not as well characterized as the specific function of B in the cell wall. In this article, recent studies on the regulation of lignin biosynthesis in plants under low-B stress conditions are reviewed. Moreover, the following possible mechanisms underlying the lignin synthesis promoted by B deficiency are discussed: (1) the accumulation of phenolic substances during B deficiency directly enhances lignin synthesis; (2) excess H₂ O₂ has a dual function to the enhancement of lignin under boron deficiency conditions, serving as a substrate and a signaling molecule; and (3) B deficiency regulates lignin synthesis through the expression of genes encoding transcription factors such as MYBs. Finally, future studies regarding physiology, molecules, and transcriptional regulation may reveal the mechanism(s) mediating the relationship between lignin synthesis and B deficiency. This review provides new insights and important references for future research and the enhancement of plant B nutrition.

Effects of Nitrogen Deficiency on the Metabolism of Organic Acids and Amino Acids in Oryza sativa

Organic acids metabolism and nitrogen (N) metabolism in rice seedlings and the relationship between them are not fully understood. In this study, rice (Oryza sativa L. ssp. Indica) variety "Huanghuazhan" was used as the experimental material, and three N levels (5 mM, 1 mM, and 0 mM NH₄NO₃) were set by the hydroponic method for different levels of N treatment. Our results showed that the increased content of malate in rice leaves caused by reducing N level was related to the increased synthesis of malate (the activity of leaf PEPC increased)and the decreased degradation of malate (the activity of leaf NADP-ME decreased), while the increased contents of citrate and isocitrate in rice leaves caused by reducing N level might not be caused by the increased biosynthesis, but due to the decrease in degradation of citrate and isocitrate (the activities of leaf CS, ACO, and NADP-IDH decreased). The increased content of malate in rice roots caused by reducing N level might be related to the increased biosynthesis and the decreased degradation of root malate (the activities of root NAD-MDH and PEPC increased, while the activity of NADP-ME decreased). Compared to the control (5 mM NH₄NO₃), the increased content of citrate in rice roots caused by reducing N level might be related to the increased biosynthesis rather than the decreased degradation of citrate, due to the higher activities of CS and ACO in rice roots under 0 mM N and 1mM N treatment when compared to that of the control ones. At the same time, the increased content of isocitrate in roots was related to the increased isomerization of isocitrate (the activity of root ACO increased) and the decreased degradation of isocitrate (the activity of root NADP-IDH decreased). With the reducing N level, the activities of N metabolism-related enzymes, such as nitrate reductase (NR), glutamine synthetase (GS), and glutamate synthase (GOGAT), decreased in rice leaves and roots, resulting in the decreased contents of total free amino acids (TFAAs) and soluble proteins in rice seedlings, and finally led to the growth inhibition. Our results showed that the dynamics of organic acids metabolism caused by reducing N level were different in rice leaves and roots. In conclusion, there was a close correlation between organic acids metabolism and N metabolism in rice leaves and roots under N-limited conditions; furthermore, such a correlation was more obvious in rice leaves than that of roots.

Adaptive responses of carbon and nitrogen metabolisms to nitrogen-deficiency in Citrus sinensis seedlings

BACKGROUND

In China, nitrogen (N)-deficiency often occurs in Citrus orchards, which is one of the main causes of yield loss and fruit quality decline. Little information is known about the adaptive responses of Citrus carbon (C) and N metabolisms to N-deficiency. Seedlings of 'Xuegan' (Citrus sinensis (L.) Osbeck) were supplied with nutrient solution at an N concentration of 0 (N-deficiency), 5, 10, 15 or 20 mM for 10 weeks. Thereafter, we examined the effects of N supply on the levels of C and N in roots, stems and leaves, and the levels of organic acids, nonstructural carbohydrates, NH₄⁺-N, NO₃^--N, total soluble proteins, free amino acids (FAAs) and derivatives (FAADs), and the activities of key enzymes related to N assimilation and organic acid metabolism in roots and leaves.

RESULTS

N-deficiency elevated sucrose export from leaves to roots, C and N distributions in roots and C/N ratio in roots, stems and leaves, thus enhancing root dry weight/shoot dry weight ratio and N use efficiency. N-deficient leaves displayed decreased accumulation of starch and total nonstructural carbohydrates (TNC) and increased sucrose/starch ratio as well as a partitioning trend of assimilated C toward to sucrose, but N-deficient roots displayed elevated accumulation of starch and TNC and reduced sucrose/starch ratio as well as a partitioning trend of assimilated C toward to starch. N-deficiency reduced the concentrations of most FAADs and the ratios of total FAADs (TFAADs)/N in leaves and roots. N-deficiency reduced the demand for C skeleton precursors for amino acid biosynthesis, thus lowering TFAADs/C ratio in leaves and roots. N-deficiency increased (decreased) the relative amounts of C-rich (N-rich) FAADs, thus increasing the molar ratio of C/N in TFAADs in leaves and roots.

CONCLUSIONS

Our findings corroborated our hypothesis that C and N metabolisms displayed adaptive responses to N-deficiency in C. sinensis seedlings, and that some differences existed between roots and leaves in N-deficiency-induced alterations of and C and N metabolisms.

Identification of Twelve Different Mineral Deficiencies in Hydroponically Grown Sunflower Plants on the Basis of Short Measurements of the Fluorescence and P700 Oxidation/Reduction Kinetics

The photosynthetic electron transport chain is mineral rich. Specific mineral deficiencies can modify the electron transport chain specifically. Here, it is shown that on the basis of 2 short Chl fluorescence and P700⁺ measurements (approx. 1 s each), it is possible to discriminate between 10 out of 12 different mineral deficiencies: B, Ca, Cu, Fe, K, Mg, Mn, Mo, N, P, S, and Zn. B- and Mo-deficient plants require somewhat longer measurements to detect the feedback inhibition they induce. Eight out of twelve deficiencies mainly affect PS I and NIR measurements are, therefore, very important for this analysis. In Cu- and P-deficient plants, electron flow from the plastoquinone pool to PS I, is affected. In the case of Cu-deficiency due to the loss of plastocyanin and in the case of P-deficiency probably due to a fast and strong generation of Photosynthetic Control. For several Ca-, K-, and Zn-deficient plant species, higher levels of reactive oxygen species have been measured in the literature. Here, it is shown that this not only leads to a loss of Pm (maximum P700 redox change) reflecting a lower PS I content, but also to much faster P700⁺ re-reduction kinetics during the I₂-P (~30-200 ms) fluorescence rise phase. The different mineral deficiencies affect the relation between the I₂-P and P700⁺ kinetics in different ways and this is used to discuss the nature of the relationship between these two parameters.

Increasing media pH contribute to the absorption of boron via roots to promote the growth of citrus

Low pH is an important limiting factor for plant development in the south of China due to problems of acid red soil and boron (B) deficiency. Whereas, there is very limited information on the relationship between media pH and B distribution in plant, the physiological process changed by the interaction of pH and B in citrus growth also unclear. This experiment was conducted on trifoliate rootstock by employing two different concentrations of B (0 or 10 μM B) under three pH levels: pH 4, pH 5, and pH 6. Our results illustrate that low pH inhibite plant growth and cause oxidative stress in the roots, resulting in cell membrane injury. The increase of pH and B addition reduce the accumulation of ROS (O₂^.- and H₂O₂) by regulating the activity of Class Ⅲ peroxidases (CIII Prxs). Moreover, increased pH improves the internal circulation of B in plants and decrease the content of lignin and cellulose in cell wall (CW). In summary, our investigation demonstrated that the increase of pH in nutrient solution can accelerate the re-distribution of B by roots to promote citrus growth. The accumulation of B in roots can protect plants from the damage of ROS by regulating the activity of CIII Prxs as well as decrease the content of lignin and cellulose are to promotes roots elongation.

Carbon-11 Radiotracing Reveals Physiological and Metabolic Responses of Maize Grown under Different Regimes of Boron Treatment

In agriculture, boron is known to play a critical role in healthy plant growth. To dissect the role of boron in maize metabolism, radioactive carbon-11 (t_½ 20.4 min) was used to examine the physiological and metabolic responses of 3-week-old B73 maize plants to different levels of boron spanning 0 mM, 0.05 mM, and 0.5 mM boric acid (BA) treatments. Growth behavior, of both shoots and roots, was recorded and correlated to plant physiological responses. ¹¹CO₂ fixation, leaf export of [¹¹C]-photosynthates, and their rate of transport increased systematically with increasing BA concentrations, while the fraction of [¹¹C]-photosynthates delivered to the roots under 0 mM and 0.5 mM BA treatments was lower than under 0.05 mM BA treatment, likely due to changes in root growth. Additionally, solid-phase extraction coupled with gamma counting, radio-fluorescence thin layer chromatography, and radio-fluorescence high-performance liquid chromatography techniques applied to tissue extracts provided insight into the effects of BA treatment on 'new' carbon (as ¹¹C) metabolism. Most notable was the strong influence reducing boron levels had on raising ¹¹C partitioning into glutamine, aspartic acid, and asparagine. Altogether, the growth of maize under different regimes of boron affected ¹¹CO₂ fixation, its metabolism and allocation belowground, and altered root growth. Finally, inductively coupled plasma mass spectrometry provided insight into the effects of BA treatment on plant uptake of other essential nutrients. Here, levels of boron and zinc systematically increased in foliar tissues with increasing BA concentration. However, levels of magnesium, potassium, calcium, manganese, and iron remained unaffected by treatment. The rise in foliar zinc levels with increased BA concentration may contribute to improved ¹¹CO₂ fixation under these conditions.

Citrus Physiological and Molecular Response to Boron Stresses

Since the essentiality of boron (B) to plant growth was reported nearly one century ago, the implication of B in physiological performance, productivity and quality of agricultural products, and the morphogenesis of apical meristem in plants has widely been studied. B stresses (B deficiency and toxicity), which lead to atrophy of canopy and deterioration of Citrus fruits, have long been discovered in citrus orchards. This paper reviews the research progress of B stresses on Citrus growth, photosynthesis, light use efficiency, nutrient absorption, organic acid metabolism, sugar metabolism and relocation, and antioxidant system. Moreover, the beneficial effects of B on plant stress tolerance and further research in this area were also discussed.

Induction of jasmonic acid biosynthetic genes inhibits Arabidopsis growth in response to low boron

The essential micronutrient boron (B) has key roles in cell wall integrity and B deficiency inhibits plant growth. The role of jasmonic acid (JA) in plant growth inhibition under B deficiency remains unclear. Here, we report that low B elevates JA biosynthesis in Arabidopsis thaliana by inducing the expression of JA biosynthesis genes. Treatment with JA inhibited plant growth and, a JA biosynthesis inhibitor enhanced plant growth, indicating that the JA induced by B deficiency affects plant growth. Furthermore, examination of the JA signaling mutants jasmonate resistant1, coronatine insensitive1-2, and myc2 showed that JA signaling negatively regulates plant growth under B deficiency. We identified a low-B responsive transcription factor, ERF018, and used yeast one-hybrid assays and transient activation assays in Nicotiana benthamiana leaf cells to demonstrate that ERF018 activates the expression of JA biosynthesis genes. ERF018 overexpression (OE) lines displayed stunted growth and up-regulation of JA biosynthesis genes under normal B conditions, compared to Col-0 and the difference between ERF018 OE lines and Col-0 diminished under low B. These results suggest that ERF018 enhances JA biosynthesis and thus negatively regulates plant growth. Taken together, our results highlight the importance of JA in the effect of low B on plant growth.

Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq

Citrus sinensis (L.) Osbeck seedlings were fertigated with nutrient solution containing 2 [magnesium (Mg)-sufficiency] or 0 mM (Mg-deficiency) Mg(NO3)2 for 16 weeks. Thereafter, RNA-Seq was used to investigate Mg-deficiency-responsive genes in the veins of upper and lower leaves in order to understand the molecular mechanisms for Mg-deficiency-induced vein lignification, enlargement and cracking, which appeared only in the lower leaves. In this study, 3065 upregulated and 1220 downregulated, and 1390 upregulated and 375 downregulated genes were identified in Mg-deficiency veins of lower leaves (MDVLL) vs Mg-sufficiency veins of lower leaves (MSVLL) and Mg-deficiency veins of upper leaves (MDVUL) vs Mg-sufficiency veins of upper leaves (MSVUL), respectively. There were 1473 common differentially expressed genes (DEGs) between MDVLL vs MSVLL and MDVUL vs MSVUL, 1463 of which displayed the same expression trend. Magnesium-deficiency-induced lignification, enlargement and cracking in veins of lower leaves might be related to the following factors: (i) numerous transciption factors and genes involved in lignin biosynthesis pathways, regulation of cell cycle and cell wall metabolism were upregulated; and (ii) reactive oxygen species, phytohormone and cell wall integrity signalings were activated. Conjoint analysis of proteome and transcriptome indicated that there were 287 and 56 common elements between DEGs and differentially abundant proteins (DAPs) identified in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, and that among these common elements, the abundances of 198 and 55 DAPs matched well with the transcript levels of the corresponding DEGs in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, indicating the existence of concordances between protein and transcript levels.

Interactive effects of pH and aluminum on the secretion of organic acid anions by roots and related metabolic factors in Citrus sinensis roots and leaves

Low pH and aluminum (Al)-toxicity often coexist in acidic soils. Citrus sinensis seedlings were treated with nutrient solution at a pH of 2.5, 3.0, 3.5 or 4.0 and an Al concentration of 0 or 1 mM for 18 weeks. Thereafter, malate, citrate, isocitrate, acid-metabolizing enzymes, and nonstructural carbohydrates in roots and leaves, and release of malate and citrate from roots were measured. Al concentration in roots and leaves increased under Al-toxicity, but it declined with elevating nutrient solution pH. Al-toxicity increased the levels of glucose, fructose, sucrose and total soluble sugars in leaves and roots at each given pH except for a similar sucrose level at pH 2.5-3.0, but it reduced or did not alter the levels of starch and total nonstructural carbohydrates (TNC) in leaves and roots with the exception that Al improved TNC level in roots at pH 4.0. Levels of nonstructural carbohydrates in roots and leaves rose with reducing pH with a few exceptions with or without Al-toxicity. A potential model for the possible role of root organic acid (OA) metabolism (anions) in C. sinensis Al-tolerance was proposed. With Al-toxicity, the elevated pH upregulated the OA metabolism, and increased the flow of carbon to OA metabolism, and the accumulation of malate and citrate in roots and subsequent release of them, thus reducing root and leaf Al and hence eliminating Al-toxicity. Without Al-toxicity, low pH stimulated the exudation of malate and citrate, an adaptive response of Citrus to low pH. The interactive effects of pH and pH on OA metabolism were different between roots and leaves.

How the cells were injured and the secondary metabolites in the shikimate pathway were changed by boron deficiency in trifoliate orange root

Boron (B) deficiency is frequently observed in citrus orchards as a major cause for loss of productivity and quality. The structural and morphological responses of roots to B deficiency have been reported in some plants. The study was conducted to get novel information about the B-deficient-induced cellular injuries and target secondary metabolites in the shikimate pathway. Fluorescent vital staining, paraffin section, transmission electron microscopy (TEM) and target metabolomics were to investigate the responses of the cell viability and structure, and target aromatic metabolites in the shikimate pathway in B-deficient trifoliate orange roots. Boron deprivation-induced ROS accumulation accelerated the membrane peroxidation, resulting in weakened cell vitality and cell rupture in roots. In addition, B deficiency increased phenylalanine (Phe), tyrosine (Try) in roots, thereby promoting the biosynthesis of salicylic acid, caffeic acid and ferulic acid. B-starvation up-regulated salicylic acid and lignin while reduced 3-indoleacetic acid (IAA) content. These adverse effects might be involved in the structural and morphological changes in B-deficient roots. What is more, the results provide a new insight into the mechanism of B deficiency-induced structural damage and elongation inhibition on roots.

Citrus Polyamines: Structure, Biosynthesis, and Physiological Functions

Polyamines (PAs) are ubiquitous biogenic amines found in all living organisms from bacteria to Archaea, and Eukaryotes including plants and animals. Since the first description of putrescine conjugate, feruloyl-putrescine (originally called subaphylline), from grapefruit leaves and juice, many research studies have highlighted the importance of PAs in growth, development, and other physiological processes in citrus plants. PAs appear to be involved in a wide range of physiological processes in citrus plants; however, their exact roles are not fully understood. Accordingly, in the present review, we discuss the biosynthesis of PAs in citrus plants, with an emphasis on the recent advances in identifying and characterizing PAs-biosynthetic genes and other upstream regulatory genes involved in transcriptional regulation of PAs metabolism. In addition, we will discuss the recent metabolic, genetic, and molecular evidence illustrating the roles of PAs metabolism in citrus physiology including somatic embryogenesis; root system formation, morphology, and architecture; plant growth and shoot system architecture; inflorescence, flowering, and flowering-associated events; fruit set, development, and quality; stomatal closure and gas-exchange; and chlorophyll fluorescence and photosynthesis. We believe that the molecular and biochemical understanding of PAs metabolism and their physiological roles in citrus plants will help citrus breeding programs to enhance tolerance to biotic and abiotic stresses and provide bases for further research into potential applications.

Boron Toxicity and Deficiency in Agricultural Plants

Boron is an essential plant micronutrient taken up via the roots mostly in the form of boric acid. Its important role in plant metabolism involves the stabilization of molecules with cis-diol groups. The element is involved in the cell wall and membrane structure and functioning; therefore, it participates in numerous ion, metabolite, and hormone transport reactions. Boron has an extremely narrow range between deficiency and toxicity, and inadequate boron supply exhibits a detrimental effect on the yield of agricultural plants. The deficiency problem can be solved by fertilization, whereas soil boron toxicity can be ameliorated using various procedures; however, these approaches are costly and time-consuming, and they often show temporary effects. Plant species, as well as the genotypes within the species, dramatically differ in terms of boron requirements; thus, the available soil boron which is deficient for one crop may exhibit toxic effects on another. The widely documented intraspecies genetic variability regarding boron utilization efficiency and toxicity tolerance, together with the knowledge of the physiology and genetics of boron, should result in the development of efficient and tolerant varieties that may represent a long-term sustainable solution for the problem of inadequate or excess boron supply.

Boron mitigates citrus root injuries by regulating intracellular pH and reactive oxygen species to resist H+-toxicity

Boron (B)-deficiency and H⁺-toxicity are important limiting factors for plants growth in acid soils. High B supply may reduce H⁺-toxicity-induced inhibition of growth in citrus. Trifoliate orange rootstock seedlings were irrigated with nutrient solution containing either 0 μM or 10 μM H₃BO₃ at two pH levels (pH4 (H⁺-toxicity) and pH6 (normal)). The results showed that H⁺-toxicity without B severely hampered main root elongation. Simultaneously, oxidative damage caused by H⁺-toxicity led to severe damage to the apical structure of root such as root crown abscission. However, B application promoted the root length, root cell viability and reduced cell wall (CW) thickness of root tips under H⁺-toxicity. Additionally, B application reduced the H⁺-toxicity-induced reactive oxygen species (ROS) accumulation in roots as characterized by lower fluorescence intensity of H₂O₂ and O₂^- staining. Moreover, ³¹P-NMR (³¹P nuclear magnetic resonance) spectra revealed B application regulated the pH of vacuoles and cytoplasm in root tips by reducing phosphoenolpyruvate carboxykinase (PEPCase) activity while enhancing NADP malic enzyme (NADP-ME) activity during H⁺-toxicity. Collectively, our results demonstrate that B supply alleviates H⁺-toxicity and promotes root growth by reducing ROS accumulation, attenuating intracellular acidic microenvironment to ensure normal chemical reactions in root tip cells.

Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.

Changes in secondary metabolites, organic acids and soluble sugars during the development of plum fruit cv. 'Furongli' (Prunus salicina Lindl)

BACKGROUND

Organic acids, sugars and pigments are key components that determine the taste and flavor of plum fruit. However, metabolism of organic acid and sugar is not fully understood during the development of plum fruit cv. 'Furongli'.

RESULTS

Mature fruit of 'Furongli' has the highest content of anthocyanins and the lowest content of total phenol compounds and flavonoids. Malate is the predominant organic acid anion in 'Furongli' fruit, followed by citrate and isocitrate. Glucose was the predominant sugar form, followed by fructose and sucrose. Correlation analysis indicated that malate content increased with increasing phosphoenolpyruvate carboxylase (PEPC) activity and decreasing nicotinamide adenine dinucleotide-malate dehydrogenase (NAD-MDH) activity. Citrate and isocitrate content increased with increasing PEPC and aconitase (ACO) activities, respectively. Both acid invertase and neutral invertase had higher activities at the early stage than later stage of fruit development. Fructose content decreased with increasing phosphoglucoisomerase (PGI) activity, whereas glucose content increased with decreasing hexokinase (HK) activity.

CONCLUSION

Dynamics in organic acid anions were not solely controlled by a single enzyme but regulated by the integrated activity of enzymes such as nicotinamide adenine dinucleotide phosphate-malic enzyme (NADP-ME), NAD-ME, PEPC, ACO and NADP-isocitrate dehydrogenase. Sugar metabolism enzymes such as PGI, invertase and HK may play vital roles in the regulation of individual sugar metabolic processes. © 2018 Society of Chemical Industry.

Aluminum effects on photosynthesis, reactive oxygen species and methylglyoxal detoxification in two Citrus species differing in aluminum tolerance

Citrus are mainly grown in low pH soils with high active aluminum (Al). 'Xuegan' (Citrus sinensis (L.) Osbeck) and 'Shatian pummelo' (Citrus grandis (L.) Osbeck) seedlings were fertilized for 18 weeks with nutrient solution containing either 0 mM (control) or 1 mM (Al toxicity) AlCl3·6H2O. Aluminum induced decreases of biomass, leaf photosynthesis, relative water content and total soluble protein levels, and increases of methylglyoxal levels only occurred in C. grandis roots and leaves. Besides, the Al-induced decreases of pigments and alterations of chlorophyll a fluorescence transients and fluorescence parameters were greater in C. grandis leaves than those in C. sinensis leaves. Aluminum-treated C. grandis had higher stem and leaf Al levels and similar root Al levels relative to Al-treated C. sinensis, but lower Al distribution in roots and Al uptake per plant. Aluminum toxicity decreased nitrogen, phosphorus, potassium, calcium, magnesium and sulfur uptake per plant in C. grandis and C. sinensis seedlings, with the exception of Al-treated C. sinensis seedlings exhibiting increased sulfur uptake per plant and unaltered magnesium uptake per plant. Under Al-stress, macroelement uptake per plant was higher in C. sinensis than that in C. grandis. Aluminum toxicity decreased the ratios of reduced glutathione/(reduced + oxidized glutathione) and of ascorbate/(ascorbate + dehydroascorbate) only in C. grandis roots and leaves. The activities of most antioxidant enzymes, sulfur metabolism-related enzymes and glyoxalases and the levels of S-containing compounds were higher in Al-treated C. sinensis roots and leaves than those in Al-treated C. grandis ones. Thus, C. sinensis displayed higher Al tolerance than C. grandis did. The higher Al tolerance of C. sinensis might involve: (i) more Al accumulation in roots and less transport of Al from roots to shoots; (ii) efficient maintenance of nutrient homeostasis; and (iii) efficient maintenance of redox homeostasis via detoxification systems of reactive oxygen species and methylglyoxal.

Enzymatic reactions involving the heteroatoms from organic substrates

Several enzymatic reactions of heteroatom-containing compounds have been explored as unnatural substrates. Considerable advances related to the search for efficient enzymatic systems able to support a broader substrate scope with high catalytic performance are described in the literature. These reports include mainly native and mutated enzymes and whole cells biocatalysis. Herein, we describe the historical background along with the progress of biocatalyzed reactions involving the heteroatom(S, Se, B, P and Si) from hetero-organic substrates.

Boron Deficiency in Trifoliate Orange Induces Changes in Pectin Composition and Architecture of Components in Root Cell Walls

Boron (B) is a micronutrient indispensable for citrus and B deficiency causes a considerable loss of productivity and quality in China. However, studies on pectin composition and architecture of cell wall components in trifoliate orange roots under B deficiency condition are not sufficient. In this study, we investigated the alteration in pectin characteristics and the architecture of cell wall components in trifoliate orange [Poncirus trifoliata (L.) Raf.] roots under B starvation. The results showed that B-deficient roots resulted in a significant enlargement of root tips and an obvious decrease in cell wall B and uronic acid content in Na₂CO₃-soluble pectin compared with B-adequate roots. Meanwhile, they showed a decrease of 2-keto-3-deoxyoctanoic acid in CDTA-soluble and Na₂CO₃-soluble pectin in cell walls, while the degree of methylation (DM) of CDTA-soluble pectin was significantly increased under B deficiency. Transmission electron microscope (TEM) micrographs of B deficient plants showed a distinct thickening of the cell walls, with the thickness 1.82 times greater than that of control plant roots. The results from Fourier-transform infrared spectroscopy (FTIR) showed that B deficiency changed the mode of hydrogen bonding between protein and carbohydrates (cellulose and hemicellulose). The FTIR spectra exhibited a destroyed protein structure and accumulation of wax and cellulose in the cell walls under B starvation. The ¹³C nuclear magnetic resonance (¹³C-NMR) spectra showed that B starvation changed the organic carbon structure of cell walls, and enhanced the contents of amino acid, cellulose, phenols, and lignin in the cell wall. The results reveal that the swelling and weakened structural integrity of cell walls, which induced by alteration on the network of pectin and cell wall components and structure in B-deficient roots, could be a major cause of occurrence of the rapid interruption of growth and significantly enlarged root tips in trifoliate orange roots under B-insufficient condition.

Long-term manganese-toxicity-induced alterations of physiology and leaf protein profiles in two Citrus species differing in manganese-tolerance

Manganese (Mn)-intolerant 'Sour pummelo' (Citrus grandis) and Mn-tolerant 'Xuegan' (Citrus sinensis) seedlings were irrigated for 17 weeks with 2 (control) or 600μM (Mn-toxicity or -excess) MnSO₄. C. sinensis had higher Mn-tolerance than C. grandis, as indicated by the higher photosynthesis rates in Mn-excess C. sinensis leaves. Under Mn-toxicity, Mn levels were similar between C. sinensis and C. grandis roots, but lower in C. sinensis leaves than in C. grandis leaves. This might be responsible for C. sinensis Mn-tolerance. Using two-dimensional electrophoresis, we identified more differentially abundant proteins (DAPs) in Mn-excess C. grandis than in Mn-excess C. sinensis leaves, which agrees with the higher Mn levels in Mn-excess C. grandis leaves. DAPs were mainly related to carbohydrate and energy metabolism, stress response, and protein and amino acid metabolism. DAPs involved in the cytoskeleton and signal transduction were found only in Mn-excess C. grandis leaves. We isolated more photosynthesis-related proteins with decreased abundances in Mn-excess C. grandis leaves than in Mn-excess C. sinensis leaves, which might account for the larger decrease in photosynthesis rates in C. grandis leaves. The abundances of proteins involved in reactive oxygen species (ROS) scavenging and photorespiration were increased in Mn-excess C. grandis leaves, while only proteins involved in ROS detoxification were increased in Mn-excess C. sinensis leaves. This agrees with the increased requirement for dissipating the excess absorbed light energy, which was higher in Mn-excess C. grandis leaves than Mn-excess C. sinensis leaves because Mn-toxicity inhibited photosynthesis to a greater degree in C. grandis leaves.

Magnesium-deficiency-induced alterations of gas exchange, major metabolites and key enzymes differ among roots, and lower and upper leaves of Citrus sinensis seedlings

Magnesium (Mg)-deficiency is a widespread problem adversely affecting the quality and yield of crops, including citrus. 'Xuegan' [Citrus sinensis (L.) Osbeck] seedlings were irrigated every other day with nutrient solution at an Mg concentration of 0 mM (Mg-deficiency) or 1 mM (Mg-sufficiency) for 16 weeks. Thereafter, biomass, leaf mass per area, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), pigments in the upper and lower leaves, Mg, gas exchange, organic acids, nonstructural carbohydrates, total soluble proteins, amino acids, phenolics and anthocyanins, and key enzymes related to organic acid, amino acid and phenolic metabolisms in the roots, and upper and lower leaves were assayed in order to test the hypothesis that Mg-deficiency-induced alterations of gas exchange, major metabolites and key enzymes may differ among the roots, and upper and lower leaves. Magnesium-deficiency affected the most measured parameters more in the lower than in the upper leaves except for the nonstructural carbohydrates, but the variation trends were similar between the two. Despite increased accumulation of nonstructural carbohydrates, the lower CO2 assimilation in the Mg-deficient leaves was not caused by the feedback inhibition mechanism via sugar accumulation. Both dark respiration and organic acid metabolism were elevated in the Mg-deficient lower leaves to 'consume' the excess carbohydrates, and inhibited in the Mg-deficient roots with less accumulation of nonstructural carbohydrates to keep the balance of net carbon. More total phenolics and fewer anthocyanins were accumulated in the Mg-deficient lower leaves, whereas the accumulation of both total phenolics and anthocyanins was reduced in the Mg-deficient roots. Interestingly, amino acid biosynthesis was repressed in the Mg-deficient roots and lower leaves, thus lowering the level of total free amino acids in these roots and leaves. To conclude, great differences existed in the Mg-deficiency-induced alterations of gas exchange, major metabolites and key enzymes among the roots, and upper and lower leaves.

Effect of boron deficiency on anatomical structure and chemical composition of petioles and photosynthesis of leaves in cotton (Gossypium hirsutum L.)

The main symptom of boron (B) deficiency in cotton is the formation of brown rings on leaf petioles. The objective of the present study was to determine the changes in the anatomical structure and chemical composition of petioles and photosynthesis of leaves in cotton under B deficiency. Compared to the control, B deficiency treatment resulted in large increases in the number of petioles with brown rings per plant (160.0%) and the number of rings on the petiole per functional leaf (711.1%) in cotton seedlings. The relative absorbance intensity in the fingerprint region of polysaccharide structure was decreased in petiole rings under B deficiency, while lignin contents were increased. Cotton plants mitigated the impairment of transport function in cotton petioles by increasing the areas of vascular bundles, phloem, xylem, and phloem fiber. Moreover, the stomatal conductance, photosynthetic rate, and transpiration rate in leaves were significantly decreased under B deficiency, thus impeding photosynthesis in cotton plants. Therefore, B deficiency reduces transport function in petioles and photosynthesis in leaves, and leads to the formation of noticeable brown rings on petioles of cotton seedlings.

Glycolysis Is Dynamic and Relates Closely to Respiration Rate in Stored Sugarbeet Roots

Although respiration is the principal cause of the loss of sucrose in postharvest sugarbeet (Beta vulgaris L.), the internal mechanisms that control root respiration rate are unknown. Available evidence, however, indicates that respiration rate is likely to be controlled by the availability of respiratory substrates, and glycolysis has a central role in generating these substrates. To determine glycolytic changes that occur in sugarbeet roots after harvest and to elucidate relationships between glycolysis and respiration, sugarbeet roots were stored for up to 60 days, during which activities of glycolytic enzymes and concentrations of glycolytic substrates, intermediates, cofactors, and products were determined. Respiration rate was also determined, and relationships between respiration rate and glycolytic enzymes and metabolites were evaluated. Glycolysis was highly variable during storage, with 10 of 14 glycolytic activities and 14 of 17 glycolytic metabolites significantly altered during storage. Changes in glycolytic enzyme activities and metabolites occurred throughout the 60 day storage period, but were greatest in the first 4 days after harvest. Positive relationships between changes in glycolytic enzyme activities and root respiration rate were abundant, with 10 of 14 enzyme activities elevated when root respiration was elevated and 9 glycolytic activities static during periods of unchanging respiration rate. Major roles for pyruvate kinase and phosphofructokinase in the regulation of postharvest sugarbeet root glycolysis were indicated based on changes in enzymatic activities and concentrations of their substrates and products. Additionally, a strong positive relationship between respiration rate and pyruvate kinase activity was found indicating that downstream TCA cycle enzymes were unlikely to regulate or restrict root respiration in a major way. Overall, these results establish that glycolysis is not static during sugarbeet root storage and that changes in glycolysis are closely related to changes in sugarbeet root respiration.

Different metabolite profile and metabolic pathway with leaves and roots in response to boron deficiency at the initial stage of citrus rootstock growth

Boron (B) is a microelement required for higher plants, and B deficiency has serious negative effect on metabolic processes. We concentrated on the changes in metabolite profiles of trifoliate orange leaves and roots as a consequence of B deficiency at the initial stage of growth by gas chromatography-mass spectrometry (GC-MS)-based metabolomics. Enlargement and browning of root tips were observed in B-deficient plants, while any obvious symptom was not recorded in the leaves after 30 days of B deprivation. The distinct patterns of alterations in metabolites observed in leaves and roots due to B deficiency suggest the presence of specific organ responses to B starvation. The accumulation of soluble sugars was occurred in leaves, which may be attributed to down-regulated pentose phosphate pathway (PPP) and amino acid biosynthesis under B deficiency, while the amount of most amino acids in roots was increased, indicating that the effects of B deficiency on amino acids metabolism in trifoliate orange may be a consequence of disruptions in root tissues and decreased protein biosynthesis. Several important products of shikimate pathway were also significantly affected by B deficiency, which may be related to abnormal growth of roots induced by B deficiency. Conclusively, our results revealed a global perspective of the discriminative metabolism responses appearing between B-deprived leaves and roots and provided new insight into the relationship between B deficiency symptom in roots and the altered amino acids profiling and shikimate pathway induced by B deficiency during seedling establishment.

Alterations of physiology and gene expression due to long-term magnesium-deficiency differ between leaves and roots of Citrus reticulata

Seedlings of Ponkan (Citrus reticulata) were irrigated with nutrient solution containing 0 (Mg-deficiency) or 1mM MgSO4 (control) every two day for 16 weeks. Thereafter, we examined magnesium (Mg)-deficiency-induced changes in leaf and root gas exchange, total soluble proteins and gene expression. Mg-deficiency lowered leaf CO2 assimilation, and increased leaf dark respiration. However, Mg-deficient roots had lower respiration. Total soluble protein level was not significantly altered by Mg-deficiency in roots, but was lower in Mg-deficient leaves than in controls. Using cDNA-AFLP, we obtained 70 and 71 differentially expressed genes from leaves and roots. These genes mainly functioned in signal transduction, stress response, carbohydrate and energy metabolism, cell transport, cell wall and cytoskeleton metabolism, nucleic acid, and protein metabolisms. Lipid metabolism (Ca(2+) signals)-related Mg-deficiency-responsive genes were isolated only from roots (leaves). Although little difference existed in the number of Mg-deficiency-responsive genes between them both, most of these genes only presented in Mg-deficient leaves or roots, and only four genes were shared by them both. Our data clearly demonstrated that Mg-deficiency-induced alterations of physiology and gene expression greatly differed between leaves and roots. In addition, we focused our discussion on the causes for photosynthetic decline in Mg-deficient leaves and the responses of roots to Mg-deficiency.

Expression of Arabidopsis Hexokinase in Citrus Guard Cells Controls Stomatal Aperture and Reduces Transpiration

Hexokinase (HXK) is a sugar-phosphorylating enzyme involved in sugar-sensing. It has recently been shown that HXK in guard cells mediates stomatal closure and coordinates photosynthesis with transpiration in the annual species tomato and Arabidopsis. To examine the role of HXK in the control of the stomatal movement of perennial plants, we generated citrus plants that express Arabidopsis HXK1 (AtHXK1) under KST1, a guard cell-specific promoter. The expression of KST1 in the guard cells of citrus plants has been verified using GFP as a reporter gene. The expression of AtHXK1 in the guard cells of citrus reduced stomatal conductance and transpiration with no negative effect on the rate of photosynthesis, leading to increased water-use efficiency. The effects of light intensity and humidity on stomatal behavior were examined in rooted leaves of the citrus plants. The optimal intensity of photosynthetically active radiation and lower humidity enhanced stomatal closure of AtHXK1-expressing leaves, supporting the role of sugar in the regulation of citrus stomata. These results suggest that HXK coordinates photosynthesis and transpiration and stimulates stomatal closure not only in annual species, but also in perennial species.

Boron-deficiency-responsive microRNAs and their targets in Citrus sinensis leaves

BACKGROUND

MicroRNAs play important roles in the adaptive responses of plants to nutrient deficiencies. Most research, however, has focused on nitrogen (N), phosphorus (P), sulfur (S), copper (Cu) and iron (Fe) deficiencies, limited data are available on the differential expression of miRNAs and their target genes in response to deficiencies of other nutrient elements. In this study, we identified the known and novel miRNAs as well as the boron (B)-deficiency-responsive miRNAs from citrus leaves in order to obtain the potential miRNAs related to the tolerance of citrus to B-deficiency.

METHODS

Seedlings of 'Xuegan' [Citrus sinensis (L.) Osbeck] were supplied every other day with B-deficient (0 μM H3BO3) or -sufficient (10 μM H3BO3) nutrient solution for 15 weeks. Thereafter, we sequenced two small RNA libraries from B-deficient and -sufficient (control) citrus leaves, respectively, using Illumina sequencing.

RESULTS

Ninety one (83 known and 8 novel) up- and 81 (75 known and 6 novel) down-regulated miRNAs were isolated from B-deficient leaves. The great alteration of miRNA expression might contribute to the tolerance of citrus to B-deficiency. The adaptive responses of miRNAs to B-deficiency might related to several aspects: (a) attenuation of plant growth and development by repressing auxin signaling due to decreased TIR1 level and ARF-mediated gene expression by altering the expression of miR393, miR160 and miR3946; (b) maintaining leaf phenotype and enhancing the stress tolerance by up-regulating NACs targeted by miR159, miR782, miR3946 and miR7539; (c) activation of the stress responses and antioxidant system through down-regulating the expression of miR164, miR6260, miR5929, miR6214, miR3946 and miR3446; (d) decreasing the expression of major facilitator superfamily protein genes targeted by miR5037, thus lowering B export from plants. Also, B-deficiency-induced down-regulation of miR408 might play a role in plant tolerance to B-deficiency by regulating Cu homeostasis and enhancing superoxide dismutase activity.

CONCLUSIONS

Our study reveals some novel responses of citrus to B-deficiency, which increase our understanding of the adaptive mechanisms of citrus to B-deficiency at the miRNA (post-transcriptional) level.

Boron deficiency in woody plants: various responses and tolerance mechanisms

Boron (B) is an essential microelement for higher plants, and its deficiency is widespread around the world and constrains the productivity of both agriculture and forestry. In the last two decades, numerous studies on model or herbaceous plants have contributed greatly to our understanding of the complex network of B-deficiency responses and mechanisms for tolerance. In woody plants, however, fewer studies have been conducted and they have not well been recently synthesized or related to the findings on model species on B transporters. Trees have a larger body size, longer lifespan and more B reserves than do herbaceous plants, indicating that woody species might undergo long-term or mild B deficiency more commonly and that regulation of B reserves helps trees cope with B deficiency. In addition, the highly heterozygous genetic background of tree species suggests that they may have more complex mechanisms of response and tolerance to B deficiency than do model plants. Boron-deficient trees usually exhibit two key visible symptoms: depression of growing points (root tip, bud, flower, and young leaf) and deformity of organs (root, shoot, leaf, and fruit). These symptoms may be ascribed to B functioning in the cell wall and membrane, and particularly to damage to vascular tissues and the suppression of both B and water transport. Boron deficiency also affects metabolic processes such as decreased leaf photosynthesis, and increased lignin and phenol content in trees. These negative effects will influence the quality and quantity of wood, fruit and other agricultural products. Boron efficiency probably originates from a combined effect of three processes: B uptake, B translocation and retranslocation, and B utilization. Root morphology and mycorrhiza can affect the B uptake efficiency of trees. During B translocation from the root to shoot, differences in B concentration between root cell sap and xylem exudate, as well as water use efficiency, may play key roles in tolerance to B deficiency. In addition, B retranslocation efficiency primarily depends on the extent of xylem-to-phloem transfer and the variety and amount of cis-diol moieties in the phloem. The B requirement for cell wall construction also contribute to the B use efficiency in trees. The present review will provide an update on the physiological and molecular responses and tolerance mechanisms to B deficiency in woody plants. Emphasis is placed on the roles of B reserves that are more important for tolerance to B deficiency in trees than in herbaceous plants and the possible physiological and molecular mechanisms of differential B efficiency in trees. We propose that B may be used to study the relationship between the cell wall and the membrane via the B-bridge. Transgenic B-efficient tree cultivars have considerable potential for forestry or fruit rootstock production on low B soils in the future.

An investigation of boron-toxicity in leaves of two citrus species differing in boron-tolerance using comparative proteomics

Limited data are available on boron (B)-toxicity-responsive proteins in plants. We first applied 2-dimensional electrophoresis (2-DE) to compare the effects of B-toxicity on leaf protein profiles in B-tolerant Citrus sinensis and B-intolerant Citrus grandis seedlings, and identified 27 (20) protein species with increased abundances and 23 (25) protein species with decreased abundances from the former (latter). Generally speaking, B-toxicity increased the abundances of protein species involved in antioxidation and detoxification, proteolysis, cell transport, and decreased the abundances of protein species involved in protein biosynthesis in the two citrus species. The higher B-tolerance of C. sinensis might include following several aspects: (a) protein species related to photosynthesis and energy metabolism in C. sinensis leaves were more adaptive to B-toxicity than in C. grandis ones, which was responsible for the higher photosynthesis and for the better maintenance of energy homeostasis in the former; and (b) the increased requirement for detoxification of reactive oxygen species and cytotoxic compounds due to decreased photosynthesis was less in B-toxic C. sinensis leaves than in B-toxic C. grandis ones. B-toxicity-responsive protein species involved in coenzyme biosynthesis differed between the two species, which might also contribute to the higher B-tolerance of C. sinensis.

BIOLOGICAL SIGNIFICANCE

B-toxicity occurs in many regions all over the world, especially in arid and semiarid regions due to the raising of B-rich water tables with high B accumulated in topsoil. In China, B-toxicity often occurs in some citrus orchards. However, the mechanisms of citrus B-tolerance are still not fully understood. Here, we first used 2-DE to identify some new B-toxicity-responsive-proteins involved in carbohydrate and energy metabolism, antioxidation and detoxification, signal transduction and nucleotide metabolism. Our results showed that proteins involved in photosynthesis and energy metabolism displayed more adaptive to B-toxicity in B-tolerant C. sinensis than in B-intolerant C. grandis, which might play a key role in citrus B-tolerance. Therefore, our results reveal some new mechanisms on plant B-response and tolerance.

Long-term boron-deficiency-responsive genes revealed by cDNA-AFLP differ between Citrus sinensis roots and leaves

Seedlings of Citrus sinensis (L.) Osbeck were supplied with boron (B)-deficient (without H3BO3) or -sufficient (10 μM H3BO3) nutrient solution for 15 weeks. We identified 54 (38) and 38 (45) up (down)-regulated cDNA-AFLP bands (transcript-derived fragments, TDFs) from B-deficient leaves and roots, respectively. These TDFs were mainly involved in protein and amino acid metabolism, carbohydrate and energy metabolism, nucleic acid metabolism, cell transport, signal transduction, and stress response and defense. The majority of the differentially expressed TDFs were isolated only from B-deficient roots or leaves, only seven TDFs with the same GenBank ID were isolated from the both. In addition, ATP biosynthesis-related TDFs were induced in B-deficient roots, but unaffected in B-deficient leaves. Most of the differentially expressed TDFs associated with signal transduction and stress defense were down-regulated in roots, but up-regulated in leaves. TDFs related to protein ubiquitination and proteolysis were induced in B-deficient leaves except for one TDF, while only two down-regulated TDFs associated with ubiquitination were detected in B-deficient roots. Thus, many differences existed in long-term B-deficiency-responsive genes between roots and leaves. In conclusion, our findings provided a global picture of the differential responses occurring in B-deficient roots and leaves and revealed new insight into the different adaptive mechanisms of C. sinensis roots and leaves to B-deficiency at the transcriptional level.