Multi-omics analyses reveal stone cell distribution pattern in pear fruit

Stone cells are the brachysclereid cells in pear (Pyrus) fruit, consisting almost entirely of lignified secondary cell walls. They are distributed mainly near the fruit core and spread radially in the whole fruit. However, the development of stone cells has not been comprehensively characterized, and little is known about the regulation of stone cell formation at the transcriptomic, proteomic, and metabolomic levels. In the present study, we performed phenomic analysis on the stone cells and their associated vascular bundles distributed near the fruit cores. Transcriptomic, proteomic, and metabolomic analyses revealed a significant positive regulation of biological processes which contribute to the lignification and lignin deposition in stone cells near the fruit core, including sucrose metabolism and phenylalanine, tyrosine, tryptophan, and phenylalanine biosynthesis. We found many metabolites generated from the phenylpropanoid pathway contributing to the cell wall formation of stone cells near the fruit core. Furthermore, we identified a key transcription factor, PbbZIP48, which was highly expressed near the fruit core and was shown to regulate lignin biosynthesis in stone cells. In conclusion, the present study provides insight into the mechanism of lignified stone cell formation near the pear fruit core at multiple levels.

Transcriptome analysis provides new ideas for studying the regulation of glucose-induced lignin biosynthesis in pear calli

BACKGROUND

Glucose can be involved in metabolic activities as a structural substance or signaling molecule and plays an important regulatory role in fruit development. Glucose metabolism is closely related to the phenylpropanoid pathway, but the specific role of glucose in regulating lignin biosynthesis in pear fruit is still unclear. The transcriptome of pear calli generated from fruit and treated with glucose was analyzed to investigate the role of glucose in lignin biosynthesis.

RESULTS

The treatment of exogenous glucose significantly enhanced the accumulation of lignin in pear calli. A total of 6566 differentially expressed genes were obtained by transcriptome sequencing. Glycolysis was found to be the pathway with significant changes. Many differentially expressed genes were enriched in secondary metabolic pathways, especially the phenylpropanoid pathway. Expression of structural genes (PbPAL, PbHCT, PbCOMT, PbPRX) in lignin biosynthesis was up-regulated after glucose treatment. In addition, glucose might regulate lignin biosynthesis through interactions with ABA, GA, and SA signaling. Several candidate MYB transcription factors involved in glucose-induced lignin biosynthesis have also been revealed. The qRT-PCR analyses showed that the expression pattern of PbPFP at early developmental stage in 'Dangshansuli' fruits was consistent with the trend of lignin content. Transient expression of PbPFP resulted in a significant increase of lignin content in 'Dangshansuli' fruits at 35 days after full bloom (DAB) and tobacco leaves, indicating that PbPFP (Pbr015118.1) might be associated with the enhancement of lignin biosynthesis in response to glucose treatment.

CONCLUSIONS

PbPFP plays a positive role in regulating lignin biosynthesis in response to glucose treatment. This study may reveal the regulatory pathway related to lignin accumulation in pear calli induced by glucose.

CAD Genes: Genome-Wide Identification, Evolution, and Their Contribution to Lignin Biosynthesis in Pear (Pyrus bretschneideri)

The synthetic enzyme cinnamyl alcohol dehydrogenase (CAD) is involved in responses to various stresses during plant growth. It regulates the monolignol biosynthesis and catalyzes hydroxyl cinnamaldehyde reduction to the corresponding alcohols. Although the CAD gene families have been explored in some species, little known is in Rosaceae. In this study, we identified 149 genes in Pyrus bretschneideri (PbrCAD), Malus domestica (MDPCAD), Prunus mume (PmCAD) and Fragaria vesca (mrnaCAD). They were phylogenetically clustered into six subgroups. All CAD genes contained ADH-N and ADH-zinc-N domains and were distributed on chromosomes unevenly. Dispersed and WGD/segmental duplications accounted the highest number of evolutionary events. Eight collinear gene pairs were identified among the four Rosaceae species, and the highest number was recorded in pear as five pairs. The five PbrCAD gene pairs had undergone purifying selection under Ka/Ks analysis. Furthermore, nine genes were identified based on transcriptomic and stone cell content in pear fruit. In qRT-PCR, the expression patterns of PbrCAD1, PbrCAD20, PbrCAD27, and PbrCAD31 were consistent with variation in stone cell content during pear fruit development. These results will provide valuable information for understanding the relationship between gene expressions and stone cell number in fruit.

PbMC1a/1b regulates lignification during stone cell development in pear (Pyrus bretschneideri) fruit

Programmed cell death (PCD) and secondary cell wall (SCW) thickening in pear fruit are accompanied by the deposition of cellulose and lignin to form stone cells. Metacaspase is an important protease for development, tissue renewal and PCD. The understanding of the molecular mechanism whereby pear (Pyrus) metacaspase promotes PCD and cell wall lignification is still limited. In this study, the Metacaspases gene family (PbMCs) from P. bretschneideri was identified. PbMC1a/1b was associated with lignin deposition and stone cell formation by physiological data, semiquantitative real-time polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR). Relative to wild-type (WT) Arabidopsis, the overexpression of PbMC1a/1b increased lignin deposition and delayed growth, thickened the cell walls of vessels, xylary fibers and interfascicular fibers, and increased the expression of lignin biosynthetic genes. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and GST pull-down assays indicated that the PbMC1a/1b protein physically interacted with PbRD21. Simultaneously, the transient expression of PbMC1a/1b and PbRD21 led to significant changes in the expression of genes and lignin contents in pear fruits and flesh calli. These results indicate that PbMC1a/1b plays an important role in cell wall lignification, possibly by interacting with PbRD21 to increase the mRNA levels of some lignin synthesis-associated genes and promote the formation of stone cells in pear fruit.

Comparison of Three Methods for Calculating Protein Content in Developing Apple Flower Buds

Three methods (Kjeldahl, sulfuric acid-hydrogen peroxide, and summation of amino acid content) for determining and calculating the protein content of apple flower buds were compared. Quantitation of protein content based on summation of amino acids appears to be the most accurate method. A new nitrogen:protein conversion factor (5.51) was calculated based on total amino acid analysis. This new conversion factor could replace the conventional 6.25 factor for estimating total protein content of apple flower bud by the Kjeldahl method. However, Kjeldahl is not an accurate method for estimating protein content in apple flower bud tissue, regardless of the conversion factor, and probably would not be a good method for estimation of protein in other plant species.

Correction to: Identification and mapping of expressed genes associated with the 2DL QTL for fusarium head blight resistance in the wheat line Wuhan 1

Following publication of the original article [1], we have been notified that some important information was omitted by the authors in the Copyright note. The Copyright note should read as below.

Identification and mapping of expressed genes associated with the 2DL QTL for fusarium head blight resistance in the wheat line Wuhan 1

Background

Fusarium head blight (FHB) is a problem of great concern in small grain cereals, especially wheat. A quantitative trait locus (QTL) for FHB resistance (FHB_SFI) located on the long arm of chromosome 2D in the spring wheat genotype Wuhan 1 is a resistance locus which has potential to improve the FHB resistance of bread wheat since it confers effective resistance to wheat breeding lines. Recently, differentially expressed genes (DEG) have been identified by comparing near isogenic lines (NIL) carrying the susceptible and resistant alleles for the 2DL QTL, using RNA-Seq. In the present study, we aimed to identify candidate genes located within the genetic interval for the 2DL QTL for FHB resistance, as assessed by single floret inoculation (FHB_SFI), and possibly contributing to it.

Results

Combining previous and additional bioinformatics analyses, 26 DEG that were located on chromosome arm 2DL were selected for further characterization of their expression profile by RT-qPCR. Seven of those DEG showed a consistent differential expression profile between either three pairs of near isogenic lines or other genotypes carrying the R and S alleles for the 2DL QTL for FHB resistance. UN25696, which was identified in previous expression work using microarray was also confirmed to have a differential expression pattern. Those eight candidate genes were further characterized in 85 lines of a double haploid mapping population derived from the cross Wuhan 1/Nyubai, the population where the 2DL QTL was originally identified. The expression QTL for gene Traes_2DL_179570792 overlapped completely with the mapping interval for the 2DL QTL for FHB_SFI while the expression QTL for UN25696 mapped near the QTL, but did not overlap with it. None of the other genes had a significant eQTL on chromosome 2DL. Higher expression of Traes_2DL_179570792 and UN25696 was associated with the resistant allele at that locus.

Conclusions

Of the 26 DEG from the 2DL chromosome further characterized in this study, only two had an expression QTL located in or near the interval for the 2DL QTL. Traes_2DL_179570792 is the first expression marker identified as associated with the 2DL QTL.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0748-6) contains supplementary material, which is available to authorized users.

Effects of Selected Plant Growth Regulators on Bread Wheat Spike Development

Although the grain yield of wheat is finally determined after anthesis, the yield potential is largely dependent on early growth and development. At the specific stage from double ridge to terminal spikelet, spikelet initiation occurs and can affect the number of grains per spike and the grain yield. A factorial experiment using a randomized complete blocks design with six replicates was used to study the effect of three growth regulators (3‑indoleacetic acid [IAA], gibberellic acid [GA3], and 6‑benzylaminopurine [6‑BAP]) on two bread wheat (Triticum aestivum L.) cultivars (Rijaw and Azar‑2), at the Campus of Agriculture and Natural Resources of Razi University, in Kermanshah, Iran, during the 2013–2014 and 2014–2015 cropping seasons. The effect of the hormones was not significant for spikelet initiation number or spikelet initiation rate based on days and growing degree days (GDDs), but apical meristem length and rate of elongation of the apical meristem were affected by exogenous application of hormones in both years. The Rijaw genotype was better than Azar‑2 with respect to apical meristem traits. As well, biplot diagrams showed that the treatment combination 6‑BAP × Rijaw was the best in terms of shoot apex length and rate of shoot apex elongation and that the treatment combination GA3×Rijaw was the best in terms of spikelet number and rate of spikelet initiation. It is concluded that each hormone can improve specific apical meristem characteristics and that the rate of each hormone’s effect depends on the plant’s genetic feature and on the environmental conditions.

The possible role of NS3 protease activity of hepatitis C virus on fibrogenesis and miR-122 expression in hepatic stellate cells

The various roles of hepatitis C virus (HCV) NS3 protein in viral pathogenesis are emphasized, especially in the progression of fibrosis and tumors. The levels of miR-122 have been widely accepted as a critical factor in viral pathogenesis and disease progression. However, the possible correlation between miR-122 levels and fibrosis state has been less investigated. Therefore, in this study, plasmids expressing protease competent and protease mutated non-structural proteins 3 (NS3) were transfected into LX-2 cell line. Subsequently, the total RNA was extracted and real-time PCR was performed to measure the expression level of miR-122, collagen type 1 alpha 1 (COL1A1), alpha smooth muscle actin (α-SMA), and tissue inhibitor of metaloproteinase 1 (TIMP-1). Moreover, the transforming growth factor beta (TGF-β) levels in the supernatants of transfected cells were evaluated by ELISA. The gene expression analysis of fibrotic genes and TGF-β cytokine in LX-2 cells showed that protease competent NS3 had a significant fibrogenic impact when compared to protease defective NS3 or GFP control plasmids (P <0.001). The results also demonstrated that the expression of miR-122 was downregulated in both versions of the cells transfected with NS3 plasmids (P <0.01) irrespective of protease function. These results suggested that the protease function of NS3 protein is a crucial factor for the induction of hepatic fibrosis but it doesn't play a complete role in the expression of miR-122.

Preharvest ultraviolet-C irradiation: Influence on physicochemical parameters associated with strawberry fruit quality

Postharvest ultraviolet-C (UV-C) hormesis has been shown effective for the treatment of the edible part of several horticultural crops such as strawberry fruit; however, there is a lack of information on its potential preharvest impact. In the present study three strawberry cultivars (Fragaria × ananassa Duch. 'Albion', 'Charlotte' and 'Seascape') were exposed to UV-C during two growth seasons for a period of three weeks. Treatment begins when the first flowers were wide open and fruits at commercial maturity were harvested within one week after UV treatment. The physicochemical quality parameters of the fruits harvested from the treated plants were compared to those of the fruits of the untreated control plants. Preharvest UV-C treatment tended to increase fruit firmness in all cultivars with significant differences declared only for 'Albion' and 'Seascape' in season 2. Fruits from treated plants were generally redder but a significant difference was observed only for cultivar 'Charlotte' in the second growing season. Other color attributes were not affected by UV-C, neither were organic acids, simple sugars, soluble solids content (SSC), titratable acidity (TA) and pH, although in most cases slight decreases were noticed. Cultivar and growing season were the factors that mostly influenced on the parameters under study. The present study show that cumulative preharvest UV-C treatment of 3.6 kJ m^-2 did not adversely affected important strawberry quality parameters.

Effect of Inoculation with Arbuscular Mycorrhizal Fungi on Selected Spring Wheat Lines

<p class="sar-body"><span lang="EN-US">An experiment was performed in a completely randomized split-plot design using five lines of spring wheat (<em>Triticum aestivum </em>L.) (AW-774, AC Carberry, HY-162, Major and AAC Scotia) and two arbuscular mycorrhizal fungi (AMF) strains (<em>Rhizoglomus irregulare </em>and <em>Glomus cubense</em>). Two different inoculant forms (solid and liquid) for the <em>G. cubense</em> strain were evaluated. The main plot was AMF, and the subplot was spring wheat lines. Data on heading date, plant height, fresh, and dry biomass, yield, grain quality (chemical composition of the seeds, gluten, and sugar), root structure, and colonization by AMF were collected. The results show a positive effect of inoculation in comparison with the control treatment. The liquid and solid <em>G. cubense</em> inoculants provided better results than inoculation with <em>R.</em> <em>irregulare</em>. Fungus indicators were in agreement with root morphological parameters because of the effect induced by AMF activity. Yield increased significantly in the mycorrhizal treatments.</span></p>

Effects of preharvest ultraviolet-C irradiation on fruit phytochemical profiles and antioxidant capacity in three strawberry (Fragaria × ananassa Duch.) cultivars

BACKGROUND

Ultraviolet-C (UV-C) has proven effective in extending shelf-life, reducing disease incidence and increasing the levels of health-promoting compounds in several crops. While most studies were conducted at the postharvest stage, our study examined the effect of preharvest UV-C application in three strawberry cultivars (Fragaria × ananassa Duch. 'Albion', 'Charlotte' and 'Seascape'). UV-C treatment was applied from the onset of flowering until the fruits reached commercial maturity on plants grown for two consecutive seasons under greenhouse conditions. The phytochemical profiles and antioxidant capacity of the fruits were assessed at harvest.

RESULTS

The ellagic acid and kaempferol-3-glucuronide contents were significantly increased only in fruits of the cultivar 'Albion' collected from UV-C-treated plants in season 1. UV-C did not consistently affect the other phenolic compounds that were measured. Based on the results of the ferric-reducing antioxidant power, oxygen radical absorbance capacity and total phenolic content assays, the antioxidant capacity of the three strawberry cultivars was not affected by UV-C. Season and cultivar had a decisive impact on these parameters.

CONCLUSION

The effect of preharvest UV-C on the levels of bioactive compounds in strawberry fruits appears to be cultivar- dependent, with season or growing conditions having a significant impact.

Antifungal Studies of Selected Essential Oils and a Commercial Formulation against Botrytis Cinerea

<p>Growing concerns about food safety and environmental protection have created a need for new and safe plant disease control strategies. The aim of this study was to find an alternative to synthetic fungicides currently used in the control of the devastating fungal pathogen <em>Botrytis cinerea</em> Pers., the causal agent of grey mould disease of strawberry (<em>Fragariaananassa </em>Duch). The antifungal activity of the essential oils of <em>Origanumvulgare</em> L., <em>Monardadidyma</em> L. and of a commercial formulation of thyme oil (Gloves Off®) was investigated against <em>B. cinerea</em> and compared with controls. Contact phase effects of different concentrations of the essential oils and commercial formulation were found to inhibit the growth of <em>B. cinerea</em> in a dose dependent manner. Complete growth inhibition of the pathogen was recorded at 200 µg/ml of ‘Gloves Off®’. The mycelial growth of the pathogen was significantly reduced at the highest concentration of the essential oils of <em>O. vulgare</em><em> </em>and<em> M.</em><em> didyma</em> tested, which was 51.2 µg/ml. Spore germination and germ tube elongation were also inhibited by the essential oils and Gloves Off®. Light microscopic observations revealed that the essential oils caused morphological degenerations, such as cytoplasmic coagulation, hyphal shrivelling and protoplast leakage of the fungal hyphae. The essential oils of <em>O.</em><em> vulgare</em> L. and <em>M.</em><em> didyma</em> L. are promising, antifungal agents against <em>B. cinerea</em>similar to the commercial formulation ‘Gloves Off®’.</p>

Superoxide dismutase responses of strawberry cultivars to infection by Mycosphaerella fragariae

In controlled conditions, the effect of leaf infection by Mycosphaerella fragariae on total superoxide dismutase (SOD, EC 1.15.1.1) activity and induction of SOD isozymes was studied in three different strawberry cultivars, i.e. "Joliette" (resistant), "Honeoye" (partially resistant) and "Kent" (susceptible). Infection of the strawberry leaves with M. fragariae resulted in increase in SOD activities in all three cv. Total SOD increased 1d after inoculation in Joliette and Kent, and 2d after inoculation in Honeoye and reached the highest level in all three cv, at the 2nd day after inoculation, then slowly declined afterward. Total SODs in Joliette and Honeoye at the 2nd day after inoculation were 4516 and 4947Ug(-1) FW, respectively, which were significantly higher than that of Kent (3255Ug(-1)FW). Banding pattern of SOD isozymes in all three cv was also affected by infection. Electrophoresis profile of infected cv revealed two newly synthesized isozymes in Joliette and Honeoye, in which one band, i.e. R(f) = 0.53 was observed exclusively in inoculated Joliette and Honeoye. Therefore, it is considered to be associated with leaf spot resistance.

Antioxidant Capacity and Phenolic Content of Selected Strawberry Genotypes

Eighteen strawberry genotypes were evaluated for their phenolic content and antioxidant capacity using several methods. High antioxidant capacity was found for `Harmonie', `Saint-Jean d'Orléans', and `Saint-Laurent d'Orléans', which were reported to have better shelf life than `Kent'. `Harmonie', `Saint-Jean d'Orléans', `Orléans', and some advanced selections had higher hydroxycinnamic acids, benzoic acids, and flavonols than `Kent'. The significant variation in antioxidant capacity and total phenolic compounds clearly shows the potential value of certain new cultivars and advanced lines as parents in a breeding program. The future plan is to examine individual antioxidant and their role in disease resistance and extension of shelf life and to use selected genotypes as parents to developed new lines.

Which polyphenolic compounds contribute to the total antioxidant activities of apple?

The antioxidant activities of eight apple cultivars were studied by using the ferric reducing/antioxidant power (FRAP), the beta-carotene-linoleic acid model system (beta-CLAMS), and the photochemiluminescent (PCL) assays. The antioxidant activity of apples is highly correlated to the total phenolic content (TPC) measured by the Folin-Ciocalteu method and the total polyphenolic index (TPI) obtained by HPLC. Extracts of the peel and flesh were analyzed and assayed separately. The FRAP activities of both peel and flesh extracts correlate well with the TPC (r = 0.95 and 0.99, respectively) and the TPI (r = 0.82 and 0.99, respectively). Similar results were found in the beta-CLAMS activities, showing correlation coefficients of r = 0.90 and 0.91 with the TPC for the peel and flesh extracts and of r = 0.90 and 0.84 with the TPI for the peel and flesh extracts, respectively. The antioxidant activity measured by the PCL assay was not correlated with TPC or TPI due to the lack of integratable lag phase in this method with the flavan-3-ols/procyanidins. Among the five major polyphenolic groups, flavan-3-ols/procyanidins had the highest positive correlation with the FRAP and beta-CLAMS activities: r = 0.84 and 0.88 for the peel extracts, respectively; and r = 0.98 and 0.87 for the flesh extracts, respectively. At individual compound level, epicatechin and procyanidin B2 were the major contributors to the antioxidant activity of apple. Hydroxycinnamic acids may have a significant role in the flesh.

Understory light and root ginsenosides in forest-grown Panax quinquefolius

The objective of this study was to determine the relationship between light levels in the understory of a broadleaf forest and the content of six ginsenosides (Rg(1), Re, Rb(1), Rc, Rb(2,) and Rd) in 1- and 2-year-old American ginseng (Panax quinquefolius L.) roots. Our results revealed that ginsenoside contents in 1- and 2 year-old roots collected in September were significantly related to direct and total light levels, and duration of sunflecks. At this time, the effect of light levels accounted for up to 48 and 62% of the variation in ginsenoside contents of 1- and 2-year-old American ginseng roots. Also, red (R) and far red (FR) light, and the R:FR ratio significantly affected Rd, Rc, and Rg(1) contents in 2-year-old roots, accounting for up to 40% of the variation in ginsenoside contents.

Assessment of the protein quality of 15 new northern adapted cultivars of quality protein maize using amino acid analysis

Amino acid determinations were carried out on 15 new northern adapted cultivars of quality protein maize (QPM) containing opaque-2 modifier genes to ascertain whether their amino acid scoring patterns could be used to select high-lysine QPM genotypes and to assess their protein quality. Total protein in these cultivars ranged from 8.0 to 10.2% compared to two commercial maize varieties, Dekalb DK435 (7.9%) and Pioneer 3925 (10.3%). Four of these QPM genotypes, QPM-C26, QPM-C21, QPM-C79, and QPM-C59, contained high levels of lysine (4.43-4.58 g of lysine/100 g of protein), whereas the remaining varied from 3.43 to 4.21 g of lysine/100 g of protein, compared to Dekalb DK435 and Pioneer 3925, which contained 2.9 and 3. 1 g of lysine/100 g of protein, respectively. Although lysine is the first limiting amino acid in QPM inbreds, the high-lysine QPM genotypes may supply approximately 70.2-72.6% of human protein requirements, compared to 46.2% for Dekalb DK435 and 50.1% for Pioneer 3925, 55-63% for oats, and 59-60.3% for barley. Northern adapted QPM genotypes may have the potential to increase their lysine content even further, either by an increase in specific high-lysine-containing nonzein proteins, such as the synthesis of factor EF-1a, or by a further reduction in the 19 and 22 kDa alpha-zein in the endosperm or both. This knowledge could assist maize breeders in the selection of new high-performance QPM genotypes with improved protein quality and quantity.

Antibiotic activity of the pyrenocines

Pyrenocine A, a phytotoxin produced by Pyrenochaeta terrestris (Hansen) Gorenz, Walker and Larson, possesses general antibiotic activity against plants, fungi, and bacteria. Effective doses for 50% inhibition (ED50s) are 4 micrograms/mL for onion seedling elongation; 14, 20, 20, and 25 micrograms/mL for the germination of asexual spores of Fusarium oxysporum f. sp. cepae, Fusarium solani f. sp. pisi, Mucor hiemalis, and Rhizopus stolonifer, respectively. Pyrenocine A also inhibits the linear mycelial growth of both P. terrestris and F. oxysporum with ED50s calculated as 77 and 54 micrograms/mL, respectively. Gram-positive bacteria are more susceptible to pyrenocine A than Gram-negative bacteria. ED50s are estimated as 30, 45, and 200 micrograms/mL for the inhibition of growth of Bacillus subtilis, Staphylococcus aureus, and Escherichia coli, respectively, with Pseudomonas aeruginosa resistant to those concentrations tested. Pyrenocine A acts primarily as a biostatic rather than a biocidal agent with all organisms tested showing some degree of recovery when released from pyrenocine A. Pyrenocines B and C show little antibiotic activity in the bioassays performed.