Genomics-based Sensitive and Specific Novel Primers for Simultaneous Detection of Burkholderia glumae and Burkholderia gladioli in Rice Seeds

Lee, Chaeyeong; Lee, Hyun‐Hee; Mannaa, Mohamed; Kim, Namgyu; Park, Jung–Wook; Kim, Juyun; Seo, Young-Su

doi:10.5423/ppj.oa.07.2018.0136

Cited by 10 publications

(6 citation statements)

References 37 publications

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“…The BG1 primers are likely not suitable for detection of all B. gladioli panicle blight pathogens. Duplex qPCR and dPCR assays using both the B. glumae-specific Bglu3 primers and the B. gladioli-specific Bgla9 primers [24] to distinguish B. glumae from B. gladioli and detect all panicle blight pathogens are better approaches for future use.…”

Section: Discussionmentioning

confidence: 99%

“…Specificity of two sets of previous B. glumae-specific primers BG1F/BG1R [23] and Bglu3F/Bglu3R [24] (Table 2) were validated by BLASTN, BLASTP, and alignment of the primer sequences against their target sequences in WGS and colony PCR against test strains (Table 1). DNA sequences were aligned using the MUSCLE program integrated in the MEGA5 software [41] and displayed using the BioEdit Sequence Alignment Editor version 7.2.5 [42].…”

Section: Evaluation Of Previously Designed B Glumae-specific Primersmentioning

confidence: 99%

“…The primers targeting the 16S-23S ribosomal RNA gene intergenic transcribed spacer sequence [5] generated non-specific amplification from Burkholderia and Pseudomonas [23]. Lee et al also designed B. glumae-specific and B. gladioli-specific primers for qPCR [24]. This study aimed to develop droplet dPCR assays on the bacterial panicle blight pathogens B. glumae and B. gladioli.…”

Section: Introductionmentioning

confidence: 99%

“…This study aimed to develop droplet dPCR assays on the bacterial panicle blight pathogens B. glumae and B. gladioli. We tested two sets of B. glumae-specific primers BG1F/BG1R [23] and Bglu3F/Bglu3R [24] and found the BG1F/BG1R primers are specific to the tested B. glumae and B. gladioli strains. We thus developed an EvaGreen droplet dPCR assay on detection of seed-borne B. glumae and B. gladioli using BG1F/BG1R primers and analyzed the evolutionary divergence of B. gladioli based on genome sequences.…”

Section: Introductionmentioning

confidence: 99%

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Development of Droplet Digital PCR Assay for Detection of Seed-Borne Burkholderia glumae and B. gladioli Causing Bacterial Panicle Blight Disease of Rice

Zhang

Luo²,

Chen³

et al. 2022

Microorganisms

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Bacterial panicle blight of rice or bacterial grain rot of rice is a worldwide rice disease. Burkholderia glumae and B. gladioli are the causal agents. The early and accurate detection of seed-borne B. glumae and B. gladioli is critical for domestic and international quarantine and effective control of the disease. Here, genomic analyses revealed that B. gladioli contains five phylogroups and the BG1 primer pair designed to target the 3’-end sequence of a gene encoding a Rhs family protein is specific to B. glumae and two phylogroups within B. gladioli. Using the BG1 primer pair, a 138-bp DNA fragment was amplified only from the tested panicle blight pathogens B. glumae and B. gladioli. An EvaGreen droplet digital PCR (dPCR) assay on detection and quantification of the two pathogens was developed from a SYBR Green real-time quantitative PCR (qPCR). The detection limits of the EvaGreen droplet dPCR on the two pathogens were identical at 2 × 103 colony forming units (CFU)∙mL−1 from bacterial suspensions and 2 × 102 CFU∙seed−1 from rice seeds. The EvaGreen droplet dPCR assay showed 10-fold detection sensitivity of the SYBR Green qPCR and could detect a single copy of the target gene in a 20-μL assay. Together, the SYBR Green qPCR assay allows for routine high-throughput detection of the panicle blight pathogens and the EvaGreen droplet dPCR assay provides a high-sensitive and high-accurate diagnostic method for quarantine of the pathogens.

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Section: Discussionmentioning

confidence: 99%

Section: Evaluation Of Previously Designed B Glumae-specific Primersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Development of Droplet Digital PCR Assay for Detection of Seed-Borne Burkholderia glumae and B. gladioli Causing Bacterial Panicle Blight Disease of Rice

Zhang

Luo²,

Chen³

et al. 2022

Microorganisms

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“…Disease severity was evaluated by measuring shoot length and pathogen propagation in the inoculated plants. In these, the B. glumae biomass in the inoculated plants was quantified using qPCR based on procedures described in previous reports [ 17 , 18 , 19 ]. qPCR was performed using the SYBR Premix Ex Taq II (Takara Bio, Shiga, Japan) with a TAKARA PCR Thermal Cycler Dice (Takara Bio) according to the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

A Seed-Borne Bacterium of Rice, Pantoea dispersa BB1, Protects Rice from the Seedling Rot Caused by the Bacterial Pathogen Burkholderia glumae

Kouzai

Akimoto-Tomiyama

2022

Life

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Seedling rot, caused by the bacterial pathogen Burkholderia glumae, is a major disease of rice. It originates from pathogen-contaminated seeds and is thus mainly controlled by pesticide treatments of seeds. We previously demonstrated that the seed-borne bacteria of rice may be a useful and sustainable alternative to pesticides to manage seedling rot, but they are limited in terms of variety. Here, we report that another seed-borne bacterium, Pantoea dispersa BB1, protects rice from B. glumae. We screened 72 bacterial isolates from rice seeds of three genetically different cultivars inoculated or non-inoculated with B. glumae. 16S rRNA gene sequencing revealed that pathogen inoculation affected the composition of culturable seed-borne bacterial communities and increased the presence of Pantoea and Paenibacillus species. Among three Pantoea and Paenibacillus isolates that exhibit tolerance to toxoflavin, a virulence factor of B. glumae, P. dispersa BB1 significantly mitigated the symptoms of rice seedling rot. The culture filtrate of BB1 inhibited the growth of B. glumae in vitro, suggesting that this isolate secretes antibacterial compounds. Seed treatment with BB1 suppressed pathogen propagation in plants, although seed treatment with the culture filtrate did not. Because BB1 did not show pathogenicity in rice, our findings demonstrate that BB1 is a promising biocontrol agent against seedling rot.

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Recent Strategies in the Management of Bacterial Diseases for Cereals

Benchlih,

Benaissa,

Dehbi

et al. 2024

Interdisciplinary Biotechnological Advances

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Genomics-based Sensitive and Specific Novel Primers for Simultaneous Detection of Burkholderia glumae and Burkholderia gladioli in Rice Seeds

Cited by 10 publications

References 37 publications

Development of Droplet Digital PCR Assay for Detection of Seed-Borne Burkholderia glumae and B. gladioli Causing Bacterial Panicle Blight Disease of Rice

Development of Droplet Digital PCR Assay for Detection of Seed-Borne Burkholderia glumae and B. gladioli Causing Bacterial Panicle Blight Disease of Rice

A Seed-Borne Bacterium of Rice, Pantoea dispersa BB1, Protects Rice from the Seedling Rot Caused by the Bacterial Pathogen Burkholderia glumae

Recent Strategies in the Management of Bacterial Diseases for Cereals

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