• 제목/요약/키워드: plant diseases detection

검색결과 90건 처리시간 0.024초

Single Nucleotide Polymorphisms (SNPs) for Advanced Genomic Research in Sericulture

  • Vijayan, Kunjupillai
    • International Journal of Industrial Entomology and Biomaterials
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    • 제19권1호
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    • pp.143-154
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    • 2009
  • Single nucleotide polymorphisms (SNPs) are the most frequent form of variation in the genome of any organism. Owing to their greater abundance, they are considered useful for identifying cultivars, construction of higher density linkage maps, and detection of genes (QTLs) associated with complex agronomic traits and diseases. Although, SNPs have been used recently for constructing a high density genetic map in silkworm and a set of 118 SNPs have been identified in tasar silkworms, not much progress has been made in sericulture to utilize the vast potential of SNPs. Thus, this review mainly focuses on some of the important methods of SNP discovery, validation and genotyping. Emphasis has also been given to the possible uses of SNP genotyping in the improvement of silkworms and their host plants.

스마트팜 피노믹스 시스템에서의 식물 질병 검출 알고리즘 (Plant Diseases Detection Algorithm in Smart Farm Phenomics System)

  • 박관익;심규동;백정현;이상화;박종일
    • 한국방송∙미디어공학회:학술대회논문집
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    • 한국방송∙미디어공학회 2022년도 하계학술대회
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    • pp.186-189
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    • 2022
  • 스마트팜 피노믹스 시스템은 재배하는 식물의 성장조건에 맞게 생육 환경을 일정하게 유지하고 관리하는 장치이지만, 그럼에도 불구하고 식물의 질병은 여러 가지 이유로 발생할 수 있다. 본 논문에서는 스마트팜 피노믹스 시스템에서 Mean Shift Segmentation 을 통한 식물의 질병을 자동으로 검출하는 식물 질병 검출 알고리즘을 제안한다. 식물의 질병 정도가 임의의 임계값을 넘을 경우, 해당 식물을 질병의 정도가 심한 식물로 판별하고, 적절한 수확시기를 결정하여 더 나은 상품성을 가진 식물을 재배할 수 있는 방법을 제시한다. 또한 식물의 질병이 급격하게 심해지는 기간을 확인하여 인간의 개입 없이 완전히 자동화된 시스템으로 더욱 세심하고 효율적인 식물 재배를 가능하게 함을 제시한다. 본 논문에서는 아이스버그(양상추)에 대한 재배 환경을 구축하여 생장 기간에 아이스버그에 발생하는 질병인 팁번 현상을 검출하는 실험을 진행하였다. 본 논문에서 제안한 방법은 다른 종류의 다양한 식물에서도 질병 검출이 가능하며, 스마트팜 피노믹스 시스템에서 질병 검출의 자동화를 위한 한 가지 방법으로 활용될 수 있을 것으로 기대된다.

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Comparative Genomic Analysis and Rapid Molecular Detection of Xanthomonas euvesicatoria Using Unique ATP-Dependent DNA Helicase recQ, hrpB1, and hrpB2 Genes Isolated from Physalis pubescens in China

  • Faisal Siddique;Yang Mingxiu;Xu Xiaofeng;Ni Zhe;Haseeb Younis;Peng Lili;Zhang Junhua
    • The Plant Pathology Journal
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    • 제39권2호
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    • pp.191-206
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    • 2023
  • Ground cherry (Physalis pubescens) is the most prominent species in the Solanaceae family due to its nutritional content, and prospective health advantages. It is grown all over the world, but notably in northern China. In 2019 firstly bacterial leaf spot (BLS) disease was identified on P. pubescens in China that caused by both BLS pathogens Xanthomonas euvesicatoria pv. euvesicatoria resulted in substantial monetary losses. Here, we compared whole genome sequences of X. euvesicatoria to other Xanthomonas species that caused BLS diseases for high similarities and dissimilarities in genomic sequences through average nucleotide identity (ANI) and BLAST comparison. Molecular techniques and phylogenetic trees were adopted to detect X. euvesicatoria on P. pubescens using recQ, hrpB1, and hrpB2 genes for efficient and precise identification. For rapid molecular detection of X. euvesicatoria, loop-mediated isothermal amplification, polymerase chain reaction (PCR), and real-time PCR techniques were used. Whole genome comparison results showed that the genome of X. euvesicatoria was more closely relative to X. perforans than X. vesicatoria, and X. gardneri with 98%, 84%, and 86% ANI, respectively. All infected leaves of P. pubescens found positive amplification, and negative controls did not show amplification. The findings of evolutionary history revealed that isolated strains XeC10RQ, XeH9RQ, XeA10RQ, and XeB10RQ that originated from China were closely relative and highly homologous to the X. euvesicatoria. This research provides information to researchers on genomic variation in BLS pathogens, and further molecular evolution and identification of X. euvesicatoria using the unique target recQ gene through advance molecular approaches.

밤나무 잉크병균, Phytophthora katsurae의 검출을 위한 Duplex PCR (A Duplex PCR for Detection of Phytophthora katsurae Causing Chestnut Ink Disease)

  • 이동현;이선근;김혜정;이상현;이상용;이종규
    • 식물병연구
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    • 제18권2호
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    • pp.73-79
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    • 2012
  • Phytophthora katsurae는 밤나무 잉크병의 원인이 되는 병원성 균류이다. P. katsurae를 검출하기 위하여 2개의 duplex PCR primer set을 제작하였다(SOPC 1F/1R+KatI 3F/5R, SOPC 1-1F/1-1R+KatI 3F/5R). SOPC 1F/1R과 SOPC 1-1F/1-1R primer pair는 sequence characteristic amplification regions(SCAR)를 이용하여 제작하였고, KatI 3F/5R primer pair는 internal transcribed spacer(ITS) 부위로부터 제작하였다. 추출한 genomic DNA를 1 mg/ml에서 1 ng/ml까지 10배씩 순차적으로 희석하여 균사량에 따른 Duplex PCR의 민감도를 확인한 결과, 2개의 primer set은 각각 1 ${\mu}g/ml$와 100 ng/ml까지 검출이 가능하였다. 유주포자를 $1{\times}10^6$부터 $1{\times}10^2$ cells/ml까지 10배씩 순차적으로 희석하고 genomic DNA를 추출하여 P. katsurae의 유주포자량에 의한 검출 한계를 확인한 결과, 2개의 primer set 모두 $1{\times}10^5$ cells/ml까지 검출할 수 있었다. 각각의 primer set은 PCR 검출을 실시하였을 때 P. katsurae 균주에서만 PCR 산물이 증폭된 반면에, Phytophthora 16종에서는 P. katsurae에 특이적인 PCR 증폭산물이 생성되지 않았다. 따라서, 2개의 primer set을 이용한 Duplex PCR은 P. katsurae의 신속하고 효과적인 검출에 유용하게 활용될 수 있을 것이다.

Occurrence and Distribution of Viruses Infecting Pepper in Korea

  • Choi, Gug-Seoun;Kim, Jae-Hyun;Lee, Dong-Hyuk;Kim, Jeong-Soo;Ryu, Ki-Hyun
    • The Plant Pathology Journal
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    • 제21권3호
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    • pp.258-261
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    • 2005
  • We conducted a survey on pepper virus diseases in 31 regions in Korea from November 2001 to December 2004. Using electron microscopy, test plant reaction, rapid immuno-filter paper assay (RIPA), reverse transcription-polymerase chain reaction (RT-PCR) and/or analysis of viral nucleotide sequences, we found a number of viruses from 1,056 samples that we collected. These included Cucumber mosaic virus (CMV), Pepper mottle virus (PepMoV), Pepper mild mottle virus (PMMoV), Broad bean wilt virus 2 (BBWV2), Tobacco mild green mosaic virus (TMGMV), and Tomato spotted wilt virus (TSWV). Of the samples analyzed, $343(32.5\%)$ were infected with CMV, $209(19.8\%)$ with PepMoV, $141(13.4\%)$ with PMMoV, $12(1.1\%)$ with BBWV2, $40(3.8\%)$ with TMGMV, $5(0.5\%)$ with TSWV, $153(14.5\%)$ with CMV and PepMoV, $54 (5.1\%)$ with CMV and PMMoV, $31(2.9\%)$ with PepMoV and PMMoV, $3(0.3\%)$ with CMV and BBWV2, $1(0.1\%)$ with CMV, PepMoV and BBWV2, $8(0.8\%)$ with CMV, PepMoV and PMMoV, and $30 (2.8\%)$ samples were infected with viruses which were not identified. CMV was the most predominant virus in all inspected fields and the number of the samples infected with PMMoV was relatively low as compared PepMoV infection level in pepper. TMGMV was only found in the southern part of Korea, while TSWV was isolated in Anyang and Yesan. However, we did not encounter in this survey the Alfalfa mosaic virus (AMV), Potato virus Y (PVY), Tobacco mosaic virus (TMV), and Pepper vein chlorosis virus (PVCV).

The development of herbicide-resistant maize: stable Agrobacterium-mediated transformation of maize using explants of type II embryogenic calli

  • Kim, Hyun A.;Utomo, Setyo Dwi;Kwon, Suk Yoon;Min, Sung Ran;Kim, Jin Seog;Yoo, Han Sang;Choi, Pil Son
    • Plant Biotechnology Reports
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    • 제3권4호
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    • pp.277-283
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    • 2009
  • One of the limitations to conducting maize Agrobacterium-mediated transformation using explants of immature zygotic embryos routinely is the availability of the explants. To produce immature embryos routinely and continuously requires a well-equipped greenhouse and laborious artificial pollination. To overcome this limitation, an Agrobacterium-mediated transformation system using explants of type II embryogenic calli was developed. Once the type II embryogenic calli are produced, they can be subcultured and/or proliferated conveniently. The objectives of this study were to demonstrate a stable Agrobacterium-mediated transformation of maize using explants of type II embryonic calli and to evaluate the efficiency of the protocol in order to develop herbicide-resistant maize. The type II embryogenic calli were inoculated with Agrobacterium tumefaciens strain C58C1 carrying binary vector pTF102, and then were subsequently cultured on the following media: co-cultivation medium for 1 day, delay medium for 7 days, selection medium for $4{\times}14$ days, regeneration medium, and finally on germination medium. The T-DNA of the vector carried two cassettes (Ubi promoter-EPSPs ORF-nos and 35S promoter-bar ORF-nos). The EPSPs conferred resistance to glyphosate and bar conferred resistance to phosphinothricin. The confirmation of stable transformation and the efficiency of transformation was based on the resistance to phosphinothricin indicated by the growth of putative transgenic calli on selection medium amended with $4mg\;1^{-1}$ phosphinothricin, northern blot analysis of bar gene, and leaf painting assay for detection of bar gene-based herbicide resistance. Northern blot analysis and leaf painting assay confirmed the expression of bar transgenes in the $R_1$ generation. The average transformation efficiency was 0.60%. Based on northern blot analysis and leaf painting assay, line 31 was selected as an elite line of maize resistant to herbicide.

Development qRT-PCR Protocol to Predict Strawberry Fusarium Wilt Occurrence

  • Hong, Sung Won;Kim, Da-Ran;Kim, Ji Su;Cho, Gyeongjun;Jeon, Chang Wook;Kwak, Youn-Sig
    • The Plant Pathology Journal
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    • 제34권3호
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    • pp.163-170
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    • 2018
  • Strawberry Fusarium wilt disease, caused by Fusarium oxysporum f. sp. fragariae, is the most devastating disease in strawberry production. The pathogen produces chlamydospores which tolerate against harsh environment, fungicide and survive for decades in soil. Development of detection and quantification techniques are regarded significantly in many soilborne pathogens to prevent damage from diseases. In this study, we improved specific-quantitative primers for F. oxysporum f. sp. fragariae to reveal correlation between the pathogen density and the disease severity. Standard curve $r^2$ value of the specific-quantitative primers for qRT-PCR and meting curve were over 0.99 and $80.5^{\circ}C$, respectively. Over pathogen $10^5cfu/g$ of soil was required to cause the disease in both lab and field conditions. With the minimum density to develop the wilt disease, the pathogen affected near 60% in nursery plantation. A biological control microbe agent and soil solarization reduced the pathogen population 2-fold and 1.5-fold in soil, respectively. The developed F. oxysporum f. sp. fragariae specific qRT-PCR protocol may contribute to evaluating soil healthiness and appropriate decision making to control the disease.

The Use of qNMR for Quality Control of Coumarin-based Pharmaceuticals and Plant Medicines

  • Crocoli, Luana C.;Molon, Vinicius B.;Moura, Sidnei
    • Natural Product Sciences
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    • 제27권2호
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    • pp.128-133
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    • 2021
  • The Coumarin (1,2-benzopyrone) is the main secondary metabolite of Mikania laevigata Sch. Beep ex Baker and Mikania glomerata Spreng., which are popularly known as guaco. These plants have been used mainly in traditional medicine in the treatment of respiratory diseases because their bronchodilator effect. However, there are around 200 species of Mikania, which are quite similar in appearance. From these, only M. leavigata and M. glomerata have high concentrations of coumarins. In this line, the falsification of products Mikania based has been frequent. In this sense, this work demonstrated the application of the easy, fast, e not destructive method based in Nuclear Magnetic Resonance in quantitative mode (qNMR) for the determination of coumarin in both commercial and homemade guaco products. Thus, in the first step the compounds were extract from guaco leaves and syrups using chloroform (CHCl3), with or without ultrasound. About the method, was linear with a R2 = 0.9947 for 1,2-benzopyrone, with detection and quantification limits with were 0.11 and 0.36 mg mL-1 respectively. In the same line, the method was safe with RSD <0.3% and with recovery ranging from 93-101%. To confirm the applicability of the method, in the last step was applied to 10 real samples (6 from leaves and 4 from syrups). The content of the coumarin in the leaf extract ranged from 0.62 to 1.30 mg mL-1. For syrups I, II and IV, the content of coumarin was in accordance with the manufacturers. However, for de Syrup III, the concentration was 155% higher. In summary, the qNMR is a rapid method with minimal sample preparation that can be used to quantify coumarin in home-made plant extracts as well as in commercial samples as syrup for instance. This method is applicable for quality control of different plants-based products.

A New Approach Using the SYBR Green-Based Real-Time PCR Method for Detection of Soft Rot Pectobacterium odoriferum Associated with Kimchi Cabbage

  • Yong Ju, Jin;Dawon, Jo;Soon-Wo, Kwon;Samnyu, Jee;Jeong-Seon, Kim;Jegadeesh, Raman;Soo-Jin, Kim
    • The Plant Pathology Journal
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    • 제38권6호
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    • pp.656-664
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    • 2022
  • Pectobacterium odoriferum is the primary causative agent in Kimchi cabbage soft-rot diseases. The pathogenic bacteria Pectobacterium genera are responsible for significant yield losses in crops. However, P. odoriferum shares a vast range of hosts with P. carotovorum, P. versatile, and P. brasiliense, and has similar biochemical, phenotypic, and genetic characteristics to these species. Therefore, it is essential to develop a P. odoriferumspecific diagnostic method for soft-rot disease because of the complicated diagnostic process and management as described above. Therefore, in this study, to select P. odoriferum-specific genes, species-specific genes were selected using the data of the P. odoriferum JK2.1 whole genome and similar bacterial species registered with NCBI. Thereafter, the specificity of the selected gene was tested through blast analysis. We identified novel species-specific genes to detect and quantify targeted P. odoriferum and designed specific primer sets targeting HAD family hydrolases. It was confirmed that the selected primer set formed a specific amplicon of 360 bp only in the DNA of P. odoriferum using 29 Pectobacterium species and related species. Furthermore, the population density of P. odoriferum can be estimated without genomic DNA extraction through SYBR Green-based real-time quantitative PCR using a primer set in plants. As a result, the newly developed diagnostic method enables rapid and accurate diagnosis and continuous monitoring of soft-rot disease in Kimchi cabbage without additional procedures from the plant tissue.

전남지역의 호박에 발생하는 바이러스 병 발생 실태 (Virus Diseases Occurred on Squash in Jeonnam Province)

  • 고숙주;이용환;차광홍;이수헌;최홍수
    • 식물병연구
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    • 제13권1호
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    • pp.71-73
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    • 2007
  • 전라남도 호박 주산단지의 2000년 바이러스병 발생포장율은 노지재배 76.1%,억제재배 55%,반촉성재배는 발생이 없었으며, 포장별 이병주율은 반촉성재배 3.6%, 노지재배 100%이었다. 포장에서 채집된 시료에 대한 RT-PCR 검정결과 노지재배는 40점 시료 중 WMV 16점, ZYMV 10점, PRSV 2점이 각각 검출되었으며, WMV, ZYMV, PRSV의 2개 또는 3개 바이러스에 중복감염된 시료도 7점이었다. 억제재배는 21점 시료중 WMV 7점, ZYMV 6점, PRSV 6점, WMV와 PRSV의 2개 바이러스에 중복감염된 시료가 1점이었으며, CMV는 검출되지 않았다.