Transcriptome analysis of pear leaves in response to calcium treatment during Botryosphaeria dothidea infection

2021 ◽  
Author(s):  
Xun Sun ◽  
Yun Wang ◽  
Bisheng Pan ◽  
Wenyu Xu ◽  
Shaoling Zhang
Keyword(s):  
Gene Annotation ◽  
Fruit Trees ◽  
Pathogen Resistance ◽  
Post Inoculation ◽  
Botryosphaeria Dothidea ◽  
Calcium Treatment ◽  
Significant Differential Expression ◽  
Phenylpropanoid Biosynthesis ◽  
Exogenous Calcium ◽  
Rot Disease

Pear (Pyrus bretschneideri Rehd.), one of the most widely planted fruit trees in the world, is infected by pear ring rot disease, which is triggered by Botryosphaeria dothidea (B. dothidea) fungus. Previous research has shown that exogenous calcium enhanced pear resistance to B. dothidea. To explore the molecular mechanism of calcium in pear pathogen resistance, we searched the differentially expressed genes (DEGs) between calcium and H2O treatment with B. dothidea inoculation in pear by using RNA-seq data. On the basis of the standard of a proportion of calcium/H2O fold change > 2, and the false discovery rate (FDR) < 0.05, 2812 and 572 genes with significant differential expression were identified between the H2O and calcium treatments under B. dothidea inoculation at 2 days post inoculation (dpi) (D2) and 8 dpi (D8), respectively, indicating that significantly more genes in D2 responded to calcium treatment. Results of the gene annotation showed that DEGs were focused on plant-pathogen interactions, hormone signal transduction and phenylpropanoid biosynthesis in D2. Moreover, transient silencing of PbrCML30 (Pear CalModulin-Like proteins 30), which had significantly higher expression in response to calcium than H2O treatments, conferred compromised resistance to B. dothidea. Exogenous calcium treatment slightly alleviated the symptoms of TRV2-PbrCML30 leaves compared with TRV2 leaves under inoculation, supporting its key role in pear resistance to B. dothidea. Overall, the information obtained in this study provides a possible mechanism of calcium in regulating pear resistance to B. dothidea.

scholarly journals RcTGA1 and glucosinolate biosynthesis pathway involvement in the defence of rose against the necrotrophic fungus Botrytis cinerea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Penghua Gao ◽  
Hao Zhang ◽  
Huijun Yan ◽  
Qigang Wang ◽  
Bo Yan ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Gene Annotation ◽  
Infected Plant ◽  
Grey Mould ◽  
Cascade Reactions ◽  
Postharvest Quality ◽  
Rna Seq ◽  
Protein Activity ◽  
Phenylpropanoid Biosynthesis ◽  
And Cluster Analysis

Abstract Background Rose is an important economic crop in horticulture. However, its field growth and postharvest quality are negatively affected by grey mould disease caused by Botrytis c. However, it is unclear how rose plants defend themselves against this fungal pathogen. Here, we used transcriptomic, metabolomic and VIGS analyses to explore the mechanism of resistance to Botrytis c. Result In this study, a protein activity analysis revealed a significant increase in defence enzyme activities in infected plants. RNA-Seq of plants infected for 0 h, 36 h, 60 h and 72 h produced a total of 54 GB of clean reads. Among these reads, 3990, 5995 and 8683 differentially expressed genes (DEGs) were found in CK vs. T36, CK vs. T60 and CK vs. T72, respectively. Gene annotation and cluster analysis of the DEGs revealed a variety of defence responses to Botrytis c. infection, including resistance (R) proteins, MAPK cascade reactions, plant hormone signal transduction pathways, plant-pathogen interaction pathways, Ca2+ and disease resistance-related genes. qPCR verification showed the reliability of the transcriptome data. The PTRV2-RcTGA1-infected plant material showed improved susceptibility of rose to Botrytis c. A total of 635 metabolites were detected in all samples, which could be divided into 29 groups. Metabonomic data showed that a total of 59, 78 and 74 DEMs were obtained for T36, T60 and T72 (T36: Botrytis c. inoculated rose flowers at 36 h; T60: Botrytis c. inoculated rose flowers at 60 h; T72: Botrytis c. inoculated rose flowers at 72 h) compared to CK, respectively. A variety of secondary metabolites are related to biological disease resistance, including tannins, amino acids and derivatives, and alkaloids, among others; they were significantly increased and enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways. This study provides a theoretical basis for breeding new cultivars that are resistant to Botrytis c. Conclusion Fifty-four GB of clean reads were generated through RNA-Seq. R proteins, ROS signalling, Ca2+ signalling, MAPK signalling, and SA signalling were activated in the Old Blush response to Botrytis c. RcTGA1 positively regulates rose resistance to Botrytis c. A total of 635 metabolites were detected in all samples. DEMs were enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways.

scholarly journals Bioinformatic-Based Approaches for Disease-Resistance Gene Discovery in Plants

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2259
Author(s):  
Andrea Fernandez-Gutierrez ◽  
Juan J. Gutierrez-Gonzalez
Keyword(s):  
Disease Resistance ◽  
Resistance Genes ◽  
Gene Annotation ◽  
Pathogen Resistance ◽  
Limiting Factors ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Nucleotide Binding Sites ◽  
Bioinformatic Tools ◽  
Computer Based

Pathogens are among the most limiting factors for crop success and expansion. Thus, finding the underlying genetic cause of pathogen resistance is the main goal for plant geneticists. The activation of a plant’s immune system is mediated by the presence of specific receptors known as disease-resistance genes (R genes). Typical R genes encode functional immune receptors with nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) domains, making the NBS-LRRs the largest family of plant resistance genes. Establishing host resistance is crucial for plant growth and crop yield but also for reducing pesticide use. In this regard, pyramiding R genes is thought to be the most ecologically friendly way to enhance the durability of resistance. To accomplish this, researchers must first identify the related genes, or linked markers, within the genomes. However, the duplicated nature, with the presence of frequent paralogues, and clustered characteristic of NLRs make them difficult to predict with the classic automatic gene annotation pipelines. In the last several years, efforts have been made to develop new methods leading to a proliferation of reports on cloned genes. Herein, we review the bioinformatic tools to assist the discovery of R genes in plants, focusing on well-established pipelines with an important computer-based component.

scholarly journals First Report of Diaporthe hongkongensis Causing Fruit rot on Peach (Prunus persica) in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Zhou Zhang ◽  
Zheng Bing Zhang ◽  
Yuan Tai Huang ◽  
FeiXiang Wang ◽  
Wei Hua Hu ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Fruit Rot ◽  
Hunan Province ◽  
Post Inoculation ◽  
Distilled Water ◽  
Conidial Suspension ◽  
Internal Transcribed Spacer Region ◽  
First Report ◽  
Representative Isolate ◽  
Rot Disease

Peach [Prunus persica (L.) Batsch] is an important deciduous fruit tree in the family Rosaceae and is a widely grown fruit in China (Verde et al., 2013). In July and August 2018, a fruit rot disease was observed in a few peach orchards in Zhuzhou city, the Hunan Province of China. Approximately 30% of the fruit in more than 400 trees was affected. Symptoms displayed were brown necrotic spots that expanded, coalesced, and lead to fruit being rotten. Symptomatic tissues excised from the margins of lesions were surface sterilized in 70% ethanol for 10 s, 0.1% HgCl2 for 2 min, rinsed with sterile distilled water three times, and incubated on potato dextrose agar (PDA) at 26°C in the dark. Fungal colonies with similar morphology developed, and eight fungal colonies were isolated for further identification. Colonies grown on PDA were grayish-white with white aerial mycelium. After an incubation period of approximately 3 weeks, pycnidia developed and produced α-conidia and β-conidia. The α-conidia were one-celled, hyaline, fusiform, and ranged in size from 6.0 to 8.4 × 2.1 to 3.1 μm, whereas the β-conidia were filiform, hamate, and 15.0 to 27.0 × 0.8 to 1.6 μm. For molecular identification, total genomic DNA was extracted from the mycelium of a representative isolate HT-1 and the internal transcribed spacer region (ITS), β-tubulin gene (TUB), translation elongation factor 1-α gene (TEF1), calmodulin (CAL), and histone H3 gene (HIS) were amplified and sequenced (Meng et al. 2018). The ITS, TUB, TEF1, CAL and HIS sequences (GenBank accession nos. MT740484, MT749776, MT749778, MT749777, and MT749779, respectively) were obtained and in analysis by BLAST against sequences in NCBI GenBank, showed 99.37 to 100% identity with D. hongkongensis or D. lithocarpus (the synonym of D. hongkongensis) (Gao et al., 2016) (GenBank accession nos. MG832540.1 for ITS, LT601561.1 for TUB, KJ490551.1 for HIS, KY433566.1 for TEF1, and MK442962.1 for CAL). Pathogenicity tests were performed on peach fruits by inoculation of mycelial plugs and conidial suspensions. In one set, 0.5 mm diameter mycelial discs, which were obtained from an actively growing representative isolate of the fungus on PDA, were placed individually on the surface of each fruit. Sterile agar plugs were used as controls. In another set, each of the fruits was inoculated by application of 1 ml conidial suspension (105 conidia/ml) by a spray bottle. Control assays were carried out with sterile distilled water. All treatments were maintained in humid chambers at 26°C with a 12-h photoperiod. The inoculation tests were conducted twice, with each one having three fruits as replications. Six days post-inoculation, symptoms of fruit rot were observed on inoculated fruits, whereas no symptoms developed on fruits treated with agar plugs and sterile water. The fungus was re-isolated and identified to be D. hongkongensis by morphological and molecular methods, thus fulfilling Koch’s Postulates. This fungus has been reported to cause fruit rot on kiwifruit (Li et al. 2016) and is also known to cause peach tree dieback in China (Dissanayake et al. 2017). However, to our knowledge, this is the first report of D. hongkongensis causing peach fruit rot disease in China. The identification of the pathogen will provide important information for growers to manage this disease.

scholarly journals Transcriptome Analysis of Rice Roots in Response to Root-Knot Nematode Infection

2020 ◽  
Vol 21 (3) ◽  
pp. 848
Author(s):  
Yuan Zhou ◽  
Di Zhao ◽  
Li Shuang ◽  
Dongxue Xiao ◽  
Yuanhu Xuan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Gene Annotation ◽  
Oryza Sativa L ◽  
Development Stage ◽  
Post Inoculation ◽  
Rna Seq ◽  
Wild Type ◽  
Root Knot Nematode ◽  
Rice Roots ◽  
Invasion Stage

Meloidogyne incognita and Meloidogyne graminicola are root-knot nematodes (RKNs) infecting rice (Oryza sativa L.) roots and severely decreasing yield, whose mechanisms of action remain unclear. We investigated RKN invasion and development in rice roots through RNA-seq transcriptome analysis. The results showed that 952 and 647 genes were differently expressed after 6 (invasion stage) and 18 (development stage) days post inoculation, respectively. Gene annotation showed that the differentially expressed genes were classified into diverse metabolic and stress response categories. Furthermore, phytohormone, transcription factor, redox signaling, and defense response pathways were enriched upon RKN infection. RNA-seq validation using qRT-PCR confirmed that CBL-interacting protein kinase (CIPK) genes (CIPK5, 8, 9, 11, 14, 23, 24, and 31) as well as brassinosteroid (BR)-related genes (OsBAK1, OsBRI1, D2, and D11) were altered by RKN infection. Analysis of the CIPK9 mutant and overexpressor indicated that the RKN populations were smaller in cipk9 and larger in CIPK9 OX, while more galls were produced in CIPK9 OX plant roots than the in wild-type roots. Significantly fewer numbers of second-stage infective juveniles (J2s) were observed in the plants expressing the BR biosynthesis gene D2 mutant and the BR receptor BRI1 activation-tagged mutant (bri1-D), and fewer galls were observed in bri1-D roots than in wild-type roots. The roots of plants expressing the regulator of ethylene signaling ERS1 (ethylene response sensor 1) mutant contained higher numbers of J2s and developed more galls compared with wild-type roots, suggesting that these signals function in RKN invasion or development. Our findings broaden our understanding of rice responses to RKN invasion and provide useful information for further research on RKN defense mechanisms.

scholarly journals FOLIAR PREHARVEST CALCIUM TREATMENT INFLUENCE ON YIELD AND QUALITY ATTRIBUTES OF STRAWBERRY

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 666d-666
Author(s):  
Joseph A. Fiola ◽  
Donald W. Schaffner
Keyword(s):  
Fruit Size ◽  
Limiting Factors ◽  
Calcium Treatment ◽  
Major Objective ◽  
Yield And Quality ◽  
Fruit Samples ◽  
Treatment Interaction ◽  
Exogenous Calcium ◽  
Spray Treatment

The major limiting factors for commercial marketability of strawberries grown in the Northeast is firmness and shelf-life. The major objective of the research is to study basic and applied aspects of exogenous calcium treatments on yield and quality of New Jersey grown berries. In 1990, 8328-1 and 8237-1 (NJUS advanced selections), and `Earliglow' and `Raritan' standards, were treated with 4 foliar Ca sprays (Nutrical) at 10 day intervals from bloom through harvest. In 1991, sprays (3) were applied at bloom, bloom+15 days, and pre-harvest. An `Earliglow' plot was utilized to test timing: bloom, mid-spray, or pre-harvest. Leaf and fruit samples were taken from treated and untreated plots prior to each application. Instron texture tests were performed to quantify firmness; a taste panel evaluated quality (color, texture, flavor, and overall quality). With multiple sprays, there were no significant differences in yield, fruit size, and Brix%, between treatments; however there were significant differences between genotypes and a genotype-by-treatment interaction. The lone bloom spray treatment reduced fruit size. Ethylene was reduced with calcium treatment, respiration was unaffected. Differences in flavor attributes were genotype specific.

scholarly journals RNA-seq data of Ganoderma boninense at axenic culture condition and under in planta pathogen-oil palm (Elaeis guineensis Jacq.) interaction

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Mui Yun Wong ◽  
Nisha T. Govender ◽  
Chia Sui Ong
Keyword(s):  
Oil Palm ◽  
Molecular Mechanisms ◽  
Elaeis Guineensis ◽  
Early Stage ◽  
Axenic Culture ◽  
Economic Losses ◽  
Post Inoculation ◽  
Ganoderma Boninense ◽  
In Planta ◽  
Rot Disease

Abstract Objective Basal stem rot disease causes severe economic losses to oil palm production in South-east Asia and little is known on the pathogenicity of the pathogen, the basidiomyceteous Ganoderma boninense. Our data presented here aims to identify both the house-keeping and pathogenicity genes of G. boninense using Illumina sequencing reads. Description The hemibiotroph G. boninense establishes via root contact during early stage of colonization and subsequently kills the host tissue as the disease progresses. Information on the pathogenicity factors/genes that causes BSR remain poorly understood. In addition, the molecular expressions corresponding to G. boninense growth and pathogenicity are not reported. Here, six transcriptome datasets of G. boninense from two contrasting conditions (three biological replicates per condition) are presented. The first datasets, collected from a 7-day-old axenic condition provide an insight onto genes responsible for sustenance, growth and development of G. boninense while datasets of the infecting G. boninense collected from oil palm-G. boninense pathosystem (in planta condition) at 1 month post-inoculation offer a comprehensive avenue to understand G. boninense pathogenesis and infection especially in regard to molecular mechanisms and pathways. Raw sequences deposited in Sequence Read Archive (SRA) are available at NCBI SRA portal with PRJNA514399, bioproject ID.

Influence of Temperature on the Pathogenesis and Gene Expression of Rhizoctonia solani Causing Web Blight/Wet Root Rot Disease in Mungbean

2020 ◽  
Author(s):  
Bishnu Maya Bashyal ◽  
Bhupendra Singh Kharayat ◽  
Pooja Parmar ◽  
Ashish Kumar Gupta ◽  
S. C. Dubey ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Rhizoctonia Solani ◽  
Root Rot ◽  
Time Interval ◽  
Post Inoculation ◽  
Root Rot Disease ◽  
Different Temperatures ◽  
Rot Disease ◽  
Blight Disease ◽  
Web Blight

Background: Mungbean (Vigna radiata L. Wilzeck) is one of the most important pulse crops and grown in almost all parts of the India. Web blight/wet root rot disease of mungbean is caused by Rhizoctonia solani Kühn. Crop environmental factors plays a vital role in the development of web blight disease caused by R. solani. An understanding of the role of environmental factors on the infection and survival of the pathogen is necessary to develop disease management practices. Methods: The effect of different temperatures (4oC, 20oC, 25oC, 30oC and 35oC) on mycelial growth of seven different R. solani isolates belonging to different anastomosis group were evaluated under in vitro conditions. Effect of different temperatures on the development of root rot/web blight disease of mungbean was also evaluated under phytotron conditions at various temperatures with constant relative humidity (85%) and illumination (alternate dark and light period of 12 h). Effect of temperatures on the expression of selected pathogenicity related genes was evaluated through real time PCR. Result: Maximum radial growth in R. solani isolates was observed at 25 and 30oC after 48 hrs of incubation. Maximum disease incidence was observed with R. solani isolate RUPU-18 (73.11%) followed by R-17 (68.75%), RDLM-1 (63.45%) at 25oC on mungbean genotype Pusa Vishal. Expression of genes like ABC transporter was observed only at 35oC, while other genes like 1, 3 glucan hydrolase expressed maximum at 25oC after 24, 48 and 72 hrs post inoculation. Present study suggested that the expression of pathogenicity related genes in mungbean-R. solani system is dependent on the temperature and time interval post pathogen inoculation.

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