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    Micromonospora endophytica sp. nov., an endophytic actinobacteria of Thai upland rice (Oryza sativa)
    An actinobacterial strain, DCWR9-8-2 T, was isolated from a leaf of Thai upland rice (Oryza sativa) collected in Chumporn province, Thailand. Strain DCWR9-8-2 T is Gram-stain-positive aerobic bacteria that produce single spores directly on the vegetative hypha. Cell wall peptidoglycan of this strain exhibits meso-diaminopimelic acid and glycine, the reducing sugars of whole-cell hydrolysate are arabinose, glucose, ribose, xylose and small amount of mannose. The phospholipid profiles in the membrane are comprised of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides. The major menaquinones are MK-9(H 4) and MK-10(H 6). The diagnostic cellular fatty acids are iso-C 16:0 and iso-C 15:0. The G+C content of the genomic DNA is 72.5 mol%. The result of 16S rRNA sequence analysis of the strain revealed that this strain was closely related to Micromonospora auratinigra TT1-11 T (99.25%). On the other hand, the result of gyrB gene sequence analysis revealed that this strain was closed to M. eburnea JCM 12345 T (96.30%). In addition, a combination of DNA-DNA hybridization results and some phenotypic properties supported that this strain should be judged as a novel species of the genus Micromonospora, for which the name M. endophytica sp. nov. is proposed. The type strain is DCWR9-8-2 T (=BCC 67267 T =NBRC 110008 T).
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    Development of novel InDel markers by whole-genome sequence comparison and genetic diversity assessment of Thailand rice blast fungus populations
    (2025-12-01)
    Thamkirati, Napassorn
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    Suktrakul, Worrawit
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    Ngernmuen, Athipat
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    Toojinda, Theerayut
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    Katengam, Sureeporn
    InDel markers are commonly used to assess genetic relationships among populations. In this study, we employed a whole-genome sequence comparison method to identify and develop InDel markers for the rice blast fungus Pyricularia oryzae. We analyzed 152 whole-genome sequences of P. oryzae isolates from diverse global regions, including Brazil, Burundi, China, Colombia, Côte d'Ivoire, France, Ghana, Hungary, India, Japan, Korea, Laos, Madagascar, Mali, Morocco, Nepal, the Philippines, Portugal, Spain, Suriname, Thailand, the UK, the USA, and Zambia. Our analysis identified a total of 233,595 InDel loci distributed across the seven chromosomes of P. oryzae. From these, 82 loci were selected based on their high polymorphism across the 152 genome sequences. The effectiveness of these 82 loci was assessed by analyzing the genetic diversity of 47 Thai rice blast isolates alongside two reference isolates, GUY11 (France) and KJ201 (Korea). Of the 82 InDel loci, 33 exhibited polymorphisms, with 2–4 alleles per locus and polymorphic information content (PIC) scores ranging from 0.04 to 0.67. Principal coordinate and structure analyses revealed two genetic subgroups among the Thai rice blast isolates, categorized according to host specificity. Genetic relationships highlighted disparities among rice blast populations based on their respective hosts: rice and grassy weeds. This finding suggests a correlation between genetic relatedness and the plant hosts susceptible to rice blast disease. The newly developed InDel markers provide a valuable resource for future research in this field.
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    Isolation and expression analysis of the Flavanone 3-Hydroxylase genes in Lotus (Nelumbo nucifera gaertn.), Waterlily (Nymphaea sp.) and transient silencing in Waterlily
    (2017-04-01)
    Chaipanya, Chaivarakun
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    Arunyanart, Sumay
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    Flavanone 3-hydroxylase (F3H) converts flavanones from dihydroflavonols, which leads to production of flavonoid compounds via the anthocyanin biosynthesis pathway in plants. In this study, the F3H gene was isolated from lotus (Nelumbo nucifera Gaertn.) cv. Buntharik (white petal lotus), cv. Satabankacha (pink petal lotus), and waterlily (Nymphaea sp.) var. St. Louis Gold by reverse transcription PCR (RT-PCR). The open reading frames (ORF) of three cultivars’ genes were 1,134 bp in length, encoding a predicted protein of 377 amino acids. Their nucleotide sequences were identical, and the amino acid sequence shared high homology to F3H from different plant species. Expression of F3H was specifically regulated in petals and stamens, while less expression was found in leaf tissue of waterlily variety St. Louis Gold. The correlation of F3H expression according to specific colouration was performed in waterlily. The F3H gene was more highly expressed in decreasing order of red, purplish blue, and yellow petals when compared using semi quantitative PCR (sqPCR). Gene regulation according to flowering stage and pigmentation was determined in lotus. The F3H expression was slightly diminished in petals of cultivar Satabankacha at the fully-opening stage, whereas it was detected in the cultivar Buntharik only when white petals were tinted with pink. An RNAi gene-silencing vector, pJA8F3H, encoding a hairpin F3H RNA, was introduced to waterlily petals using the Agrobacterium infiltration method, and the F3H expression was analysed at 1 and 3 days post infiltration (dpi) by sqPCR. The results showed that the F3H expression was down-regulated at 3 dpi in flowers tested of the red petal variety and purplish blue petal variety compared to controls. The results confirmed that pJA8F3H is efficient and could be used as a transformation vector to transiently suppress F3H expression in waterlily or lotus.
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    Tissue culture and transformation of the antisense DFR gene into lotus (Nelumbo nucifera Gaertn.) through particle bombardment
    (2013-09-24)
    Buathong, Raveevatoo
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    Phansiri, Salak
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    Arunyanart, Sumay
    The effects of explant and plant growth regulators on callus induction and plant regeneration and particle bombardment-induced transformation were examined in lotus (Nelumbo nucifera Gaertn.) cv. Buntharik. The apical buds from embryos (~3. mm) formed an embryogenic callus when cultured on MS medium supplemented with 40. μM 1-napthaleneactic acid (NAA) and 0.5. μM 1-phenyl-3-(1,2,3-thiadiazol-5-yl)-urea (TDZ) for 8 weeks. All of the embryogenic calluses were transferred to MS medium supplemented with 0, 40, 50 and 60. μM 6-benzyladenine (BA) and the highest number of shoots was achieved in the medium supplemented with 50. μM BA after 8 weeks of culture. The transformation of lotus using a particle bombardment device was examined with the shoot clusters from embryogenic apices. The pCAMBIA2301anti-DFR plasmid contained β. -glucuronidase (GUS) as a reporter gene, neomycin phosphotransferase (NPTII) as a selectable marker, and antisense dihydroflavonol 4-reductase (anti-. DFR) as the gene of interest. The particle bombardment procedure with a helium gas pressure of 1100. psi and a target distance of 6. cm yielded the highest number of blue spots (4.8 spots/shoot cluster). However, stable transformations, as confirmed by polymerase chain reaction and reverse transcription polymerase chain reaction analysis, were only achieved using a helium gas pressure of 1100. psi and a target distance of 9. cm. Our work illustrates that the stable transformation of lotus is possible, and we suggest that this methodology can be used to target and modify specific charactics of this plant. © 2013 Elsevier B.V.
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    Analysis of secondary metabolites and genes related to the pathogenicity of the rice blast fungus Pyricularia oryzae
    (2022-09-01)
    Pradapphai, P.
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    Kumlung, T.
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    Pyricularia oryzae causes rice blast disease and is one of the most significant plant pathogens worldwide. The rice blast fungus can produce a variety of phytotoxic secondary metabolites and has been found to be essential for host invasion. Two isolates, virulent isolate RBR55003 and non-virulent isolate CCO56003 were selected which based on their abilities to cause blast symptoms on rice leaves. Pyriculol and picolinic acid were detected in culture filtrate of both isolates during the exponential growth phase. Expression of genes involved in fungal pathogenicity and plant defense were analyzed. The expression of MoPks19 gene in isolate RBR55003 was higher than avirulent isolate CCO56003, indicating that MoPks19 may play a role in the pathogenesis of RBR55003. The expression of the OsWRKY30 gene that plays an important role in the regulation of a defense-related gene in rice was higher in CCO56003 inoculated than in RBR55003 inoculated rice sample, indicating the increased resistance of rice plants occurring in rice after non-virulent isolate infection, while the expression of the OsCPS4 gene involved in phytoalexin synthesis in rice was not different after isolate infections. Gene expression analysis revealed different responses according to plant-pathogen relationships.
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    Morphological and Molecular Identification of Pythium spp. from Hydroponically-Grown Lettuce
    (2022-01-01)
    Talubnak, Chulalak
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    Schoonbeek, Henk Jan
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    Jaenaksorn, Tanimnun
    Herein, hydroponic Pythium communities in Thailand were investigated. The 38 Pythium isolates from asymptomatic and symptomatic lettuce roots were identified using morphological and molecular features. The data indicated that P. aphanidermatum and P. myriotylum were the predominant species. Regarding the rDNA-ITS study, all isolates were identified as P. aphanidermatum, P. myriotylum, P. deliense, or an unidentified Pythium species. The reconfirmation of the three unidentified Pythium isolates using the cytochrome oxidase subunit I (COI) gene in comparison to the representative isolates was achieved using P. aphanidermatum and P. myriotylum. The COI phylogenetic trees were similar to that of the ITS tree. Additionally, pathogenicity of the Pythium representative isolates to plant seeds was evaluated in a laboratory assay. The seedlings suffered serious symptoms from P. myriotylum SR31 infection, with 90-100% disease severity. The other isolates presented disease severity of less than 20% when compared with uninoculated control. This study provides a comprehensive identification of Pythium root rot in lettuce grown on hydroponics in Thailand and provides information on beneficial microorganisms and a resistance inducer in lettuce root rot.
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    Mating type and genetic diversity analysis of Pyricularia oryzae collected from Thai rice varieties
    (2018-12-01)
    Tansian, P.
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    Rice blast disease caused by Pyricularia oryzae, is one of the most damaged of rice production worldwide. The fungi are a great diversity on both genotype and pathotype. The genetic relationship of P. oryzae collected in Thailand during year 2016 and 2017 was analyzed. Rice plants appeared blast symptom were collected from epidemic areas and was isolated by single spore. All isolates were identified for mating type using MAT1-1 and MAT1-2 primer sets. In this result, the mating type MAT1-2 was mostly found in Thailand and only about 7.7 % of MAT1-1 was found in the population. In this observation, both MAT1-1 and MAT1-2 were found from isolates collected from the same location in Phetchabun province. Therefore, the genetic analysis of 14 Magnaporthe grisea using microsatellite (MGM) markers was cluster-analyzed using UPGMA method of the SHAN program. The result showed cluster analysis was separated the population into 11 groups. Group 1 to 7 showed the percentage of the population with 3.8, 5.8, 36.5, 13.5, 3.8, 25.1 and 3.8, respectively. For group 8-11, the rice blast pathogen from North and South of Thailand were separated into single isolate group. Group 6 was the highest diversity of province numbers which obtained from diverse rice varieties that showed similar genotype but difference in pathogenicity. The difference isolates of fungi could infect the same rice variety. Genetic diversity and determination of mating type of rice blast populations in Thailand are needed to study and useful for predicting an epidemic of rice blast disease and selecting the appropriate isolates for blast breeding programs.
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    Blast resistance evaluation and genetic inheritance of gene controlling leaf blast resistance in Dawk Pa-yawm Rai variety (GS23774)
    (2020-01-01)
    Janthasri, S.
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    The landrace rice Dawk Pa-yawm Rai variety was highly resistant to 18 blast isolates, moderately resistant to 5 and susceptible to 2 blast isolates. Therefore, Dawk Pa-yawm Rai variety was broad-spectrum resistance to many blast isolates and can be used as genetic resource in breeding programs for blast disease resistance. The genetic inheritance of blast resistance in F<inf>2</inf> population was identified. Seven hundred and thirty F<inf>2</inf> plants from a cross between KDML105 (recipient) and Dawk Pa-yawm Rai (donor) were generated. The disease assessment revealed 524 F<inf>2</inf> plants were resistant and 206 F<inf>2</inf> plants were susceptible. The segregation of resistance and susceptible phenotypes showed a goodness of fit to the ratio 3:1 (R:S). The result found is important factor and useful in mapping of blast resistant gene in Dawk Pa-yawm Rai variety.
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    Micromonospora oryzae sp. Nov., isolated from roots of upland rice
    An actinomycete strain, designated CP2R9-1<sup>T</sup>, was isolated from root internal tissues of upland rice (Oryza sativa). Based on a polyphasic approach, strain CP2R9-1<sup>T</sup> was characterized as a member of the genus Micromonospora. meso- Diaminopimelic acid and 3-OH-diaminopimelic acid were present in the cell-wall peptidoglycan. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unidentified phospholipids and four unidentified polar lipids. Predominant menaquinones were MK-9(H<inf>4</inf>), MK-9(H<inf>6</inf>) and MK-10(H<inf>4</inf>). Whole-cell sugars consisted of ribose, xylose, arabinose and glucose. Phylogenetic analysis of the nearly complete 16S rRNA gene sequence suggested that strain CP2R9-1<sup>T</sup> was closely related to Micromonospora haikouensis 232617<sup>T</sup> (99.32% similarity), Micromonospora carbonacea DSM 43168<sup>T</sup> (99.18%) and Micromonospora krabiensis MA-2<sup>T</sup> (99.16%). Strain CP2R9-1<sup>T</sup> was distinct from its closest relatives based on low levels of DNA–DNA relatedness (21.3¡0.1– 41.7¡0.7%) and phenotypic differences. The results presented in this study showed that strain CP2R9-1<sup>T</sup> represents a novel species of the genus Micromonospora, for which the name Micromonospora oryzae sp. nov. is proposed. The type strain is CP2R9-1<sup>T</sup> (5BCC 67266T5NBRC 110007<sup>T</sup>).
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    Phytoalexin production of lettuce (Lactuca sativa L.) grown in hydroponics and its in vitro inhibitory effect on plant pathogenic fungi
    (2017-09-01)
    Talubnak, Chulalak
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    Jaenaksorn, Tanimnun
    A series of experiments were conducted to investigate phytoalexin production from five varieties of lettuce in hydroponics using abiotic (2.5, 5% CuSO<inf>4</inf>; 0.5, 1% AgNO<inf>3</inf>) and biotic elicitors (non-pathogenic Pythium sp.) at different plant ages. It showed that phytoalexin was successfully induced in tested lettuce grown in hydroponics after elicitation with abiotic elicitors throughout the trial. Phytoalexin showed yellow fluorescent spot under 365 nm UV light with R<inf>f</inf> 0.45-0.48 and clear inhibition zone where Aspergillus niger failed to develop on TLC plate. For biotic elicitors, no yellow fluorescent spot on TLC plate was observed from tested lettuce varieties however inhibition zone at R<inf>f</inf> 0.9 was detected at 8-9 weeks from red oak, green oak, and red coral. Moreover, crude extract of lettuce elicited with abiotic elicitors possessed in vitro antifungal activity against C. gloeosporioides, C. lunata, F. oxysporum, and P. aphanidermatum probably due to phytoalexin (lettucenin A) in the extract.