Displaying publications 1 - 20 of 109 in total

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  1. Fluorescence-based immunoassay for the detection of Xanthomonas oryzae pv. oryzae in rice leaf
    Awaludin N, Abdullah J, Salam F, Ramachandran K, Yusof NA, Wasoh H
    Anal Biochem, 2020 12 01;610:113876.
    PMID: 32750357 DOI: 10.1016/j.ab.2020.113876
    The identification of rice bacterial leaf blight disease requires a simple, rapid, highly sensitive, and quantitative approach that can be applied as an early detection monitoring tool in rice health. This paper highlights the development of a turn-off fluorescence-based immunoassay for the early detection of Xanthomonas oryzae pv. oryzae (Xoo), a gram-negative bacterium that causes rice bacterial leaf blight disease. Antibodies against Xoo bacterial cells were produced as specific bio-recognition molecules and the conjugation of these antibodies with graphene quantum dots and gold nanoparticles was performed and characterized, respectively. The combination of both these bio-probes as a fluorescent donor and metal quencher led to changes in the fluorescence signal. The immunoreaction between AntiXoo-GQDs, Xoo cells, and AntiXoo-AuNPs in the immuno-aggregation complex led to the energy transfer in the turn-off fluorescence-based quenching system. The change in fluorescence intensity was proportional to the logarithm of Xoo cells in the range of 100-105 CFU mL-1. The limit of detection was achieved at 22 CFU mL-1 and the specificity test against other plant disease pathogens showed high specificity towards Xoo. The detection of Xoo in real plant samples was also performed in this study and demonstrated satisfactory results.
    Matched MeSH terms: Plant Diseases/microbiology
  2. Expression of rice thaumatin-like protein gene in transgenic banana plants enhances resistance to fusarium wilt
    Mahdavi F, Sariah M, Maziah M
    Appl Biochem Biotechnol, 2012 Feb;166(4):1008-19.
    PMID: 22183565 DOI: 10.1007/s12010-011-9489-3
    The possibility of controlling Fusarium wilt--caused by Fusarium oxysporum sp. cubensec (race 4)--was investigated by genetic engineering of banana plants for constitutive expression of rice thaumatin-like protein (tlp) gene. Transgene was introduced to cauliflower-like bodies' cluster, induced from meristemic parts of male inflorescences, using particle bombardment with plasmid carrying a rice tlp gene driving by the CaMV 35S promoter. Hygromycin B was used as the selection reagent. The presence and integration of rice tlp gene in genomic DNA confirmed by PCR and Southern blot analyses. RT-PCR revealed the expression of transgene in leaf and root tissues in transformants. Bioassay of transgenic banana plants challenged with Fusarium wilt pathogen showed that expression of TLP enhanced resistance to F. oxysporum sp. cubensec (race 4) compared to control plants.
    Matched MeSH terms: Plant Diseases/microbiology
  3. Fulltext Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development
    Passos MA, de Cruz VO, Emediato FL, de Teixeira CC, Azevedo VC, Brasileiro AC, et al.
    BMC Genomics, 2013 Feb 05;14:78.
    PMID: 23379821 DOI: 10.1186/1471-2164-14-78
    BACKGROUND: Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen conidiospores.

    RESULTS: The study generated 846,762 high quality sequence reads, with an average length of 334 bp and totalling 283 Mbp. De novo assembly generated 36,384 and 35,269 unigene sequences for M. acuminata Calcutta 4 and Cavendish Grande Naine, respectively. A total of 64.4% of the unigenes were annotated through Basic Local Alignment Search Tool (BLAST) similarity analyses against public databases.Assembled sequences were functionally mapped to Gene Ontology (GO) terms, with unigene functions covering a diverse range of molecular functions, biological processes and cellular components. Genes from a number of defense-related pathways were observed in transcripts from each cDNA library. Over 99% of contig unigenes mapped to exon regions in the reference M. acuminata DH Pahang whole genome sequence. A total of 4068 genic-SSR loci were identified in Calcutta 4 and 4095 in Cavendish Grande Naine. A subset of 95 potential defense-related gene-derived simple sequence repeat (SSR) loci were validated for specific amplification and polymorphism across M. acuminata accessions. Fourteen loci were polymorphic, with alleles per polymorphic locus ranging from 3 to 8 and polymorphism information content ranging from 0.34 to 0.82.

    CONCLUSIONS: A large set of unigenes were characterized in this study for both M. acuminata Calcutta 4 and Cavendish Grande Naine, increasing the number of public domain Musa ESTs. This transcriptome is an invaluable resource for furthering our understanding of biological processes elicited during biotic stresses in Musa. Gene-based markers will facilitate molecular breeding strategies, forming the basis of genetic linkage mapping and analysis of quantitative trait loci.

    Matched MeSH terms: Plant Diseases/microbiology
  4. Fulltext Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani
    Khayi S, Blin P, Pédron J, Chong TM, Chan KG, Moumni M, et al.
    BMC Genomics, 2015;16:788.
    PMID: 26467299 DOI: 10.1186/s12864-015-1997-z
    Dickeya solani is an emerging pathogen that causes soft rot and blackleg diseases in several crops including Solanum tuberosum, but little is known about its genomic diversity and evolution.
    Matched MeSH terms: Plant Diseases/microbiology
  5. Fulltext EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense
    Sakeh NM, Abdullah SNA, Bahari MNA, Azzeme AM, Shaharuddin NA, Idris AS
    BMC Plant Biol, 2021 Jan 22;21(1):59.
    PMID: 33482731 DOI: 10.1186/s12870-020-02812-7
    BACKGROUND: Hemibiotrophic pathogen such as the fungal pathogen Ganoderma boninense that is destructive to oil palm, manipulates host defense mechanism by strategically switching from biotrophic to necrotrophic phase. Our previous study revealed two distinguishable expression profiles of oil palm genes that formed the basis in deducing biotrophic phase at early interaction which switched to necrotrophic phase at a later stage of infection.

    RESULTS: The present report is a continuing study from our previous published transcriptomic profiling of oil palm seedlings against G. boninense. We focused on identifying differentially expressed genes (DEGs) encoding transcription factors (TFs) from the same RNA-seq data; resulting in 106 upregulated and 108 downregulated TFs being identified. The DEGs are involved in four established defense-related pathways responsible for cell wall modification, reactive oxygen species (ROS)-mediated signaling, programmed cell death (PCD) and plant innate immunity. We discovered upregulation of JUNGBRUNNEN 1 (EgJUB1) during the fungal biotrophic phase while Ethylene Responsive Factor 113 (EgERF113) demonstrated prominent upregulation when the palm switches to defense against necrotrophic phase. EgJUB1 was shown to have a binding activity to a 19 bp palindromic SNBE1 element, WNNYBTNNNNNNNAMGNHW found in the promoter region of co-expressing EgHSFC-2b. Further in silico analysis of promoter regions revealed co-expression of EgJUB1 with TFs containing SNBE1 element with single nucleotide change at either the 5th or 18th position. Meanwhile, EgERF113 binds to both GCC and DRE/CRT elements promoting plasticity in upregulating the downstream defense-related genes. Both TFs were proven to be nuclear-localized based on subcellular localization experiment using onion epidermal cells.

    CONCLUSION: Our findings demonstrated unprecedented transcriptional reprogramming of specific TFs potentially to enable regulation of a specific set of genes during different infection phases of this hemibiotrophic fungal pathogen. The results propose the intricacy of oil palm defense response in orchestrating EgJUB1 during biotrophic and EgERF113 during the subsequent transition to the necrotrophic phase. Binding of EgJUB1 to SNBE motif instead of NACBS while EgERF113 to GCC-box and DRE/CRT motifs is unconventional and not normally associated with pathogen infection. Identification of these phase-specific oil palm TFs is important in designing strategies to tackle or attenuate the progress of infection.

    Matched MeSH terms: Plant Diseases/microbiology
  6. Fulltext RNA-seq data of Ganoderma boninense at axenic culture condition and under in planta pathogen-oil palm (Elaeis guineensis Jacq.) interaction
    Wong MY, Govender NT, Ong CS
    BMC Res Notes, 2019 Sep 24;12(1):631.
    PMID: 31551084 DOI: 10.1186/s13104-019-4652-y
    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.

    Matched MeSH terms: Plant Diseases/microbiology
  7. Fulltext GanoCare® Improves Oil Palm Growth and Resistance against Ganoderma Basal Stem Rot Disease in Nursery and Field Trials
    Rebitanim NA, Hanafi MM, Idris AS, Abdullah SNA, Mohidin H, Rebitanim NZ
    Biomed Res Int, 2020;2020:3063710.
    PMID: 32420335 DOI: 10.1155/2020/3063710
    Basal stem rot (BSR) caused by Ganoderma boninense is a major threat to sustainable oil palm production especially in Southeast Asia and has brought economic losses to the oil palm industry around the world. With no definitive cure at present, this study introduces a new fertilizer technology called GanoCare®, as an effort to suppress BSR incidence in oil palm. Experiments were carried out to evaluate the effect of GanoCare® on growth, physiology, and BSR disease suppression using sitting technique in the oil palm nursery stage. A follow-up using similar treatments was carried out in the field to test on severity of Ganoderma using baiting technique under natural condition. Treatments tested were 10 g/month and 30 g/three months given as pretreatment only or continuous treatment. Results showed that GanoCare® increased the height, bulb diameter, leaf area, chlorophyll content, photosynthesis rate, and fresh and dry weight of the leaf, bole, and root of oil palm seedlings in the nursery trial. Seedlings treated with GanoCare® exhibited reduced percentage of disease severity, incidence, and dead seedlings, compared to the control. In nursery and field, lowest percentage of dead seedlings due to Ganoderma was found in seedlings given combination of pretreatment and continuous treatment of 30 g/three months (T4) with 5.56 and 6.67%, while control seedlings significantly marked the maximum percentage of 94.45 and 93.33%. The most successful treatment in both nursery and field was T4 with disease reductions of 77.78 and 82.36%, respectively, proving that nutrients contained in GanoCare® are essential in allowing better development of a strong defense system in the seedlings.
    Matched MeSH terms: Plant Diseases/microbiology*
  8. Fulltext Antioxidant Enzyme Activities and Secondary Metabolite Profiling of Oil Palm Seedlings Treated with Combination of NPK Fertilizers Infected with Ganoderma boninense
    Sahebi M, Hanafi MM, Mohidin H, Rafii MY, Azizi P, Idris AS, et al.
    Biomed Res Int, 2018;2018:1494157.
    PMID: 29721500 DOI: 10.1155/2018/1494157
    Oil palm (Elaeis guineensis Jacq) is one of the major sources of edible oil. Reducing the effect of Ganoderma, main cause of basal stem rot (BSR) on oil palm, is the main propose of this study. Understanding the oil palm defense mechanism against Ganoderma infection through monitoring changes in the secondary metabolite compounds levels before/after infection by Ganoderma under different fertilizing treatment is required. Oil palm requires macro- and microelements for growth and yield. Manipulating the nutrient for oil palm is a method to control the disease. The 3-4-month-old oil palm seedlings were given different macronutrient treatments to evaluate induction of defense related enzymes and production of secondary metabolite compounds in response to G. boninense inoculation. The observed trend of changes in the infected and uninfected seedlings was a slightly higher activity for β-1,3-glucanases, chitinase, peroxidase, and phenylalanine ammonia-lyase during the process of pathogenesis. It was found that PR proteins gave positive response to the interaction between oil palm seedlings and Ganoderma infection. Although the responses were activated systematically, they were short-lasting as the changes in enzymes activities appeared before the occurrence of visible symptoms. Effect of different nutrients doses was obviously observed among the results of the secondary metabolite compounds. Many identified/unidentified metabolite compounds were presented, of which some were involved in plant cell defense mechanism against pathogens, mostly belonging to alkaloids with bitter-tasting nitrogenous-compounds, and some had the potential to be used as new markers to detect basal stem rot at the initial step of disease.
    Matched MeSH terms: Plant Diseases/microbiology*
  9. Fulltext Molecular characterization and screening for sheath blight resistance using Malaysian isolates of Rhizoctonia solani
    Nadarajah K, Omar NS, Rosli MM, Shin Tze O
    Biomed Res Int, 2014;2014:434257.
    PMID: 25258710 DOI: 10.1155/2014/434257
    Two field isolates of Rhizoctonia solani were isolated from infected paddy plants in Malaysia. These isolates were verified via ITS-rDNA analysis that yielded ~720 bp products of the ITS1-5.8S-ITS4 region, respectively. The sequenced products showed insertion and substitution incidences which may result in strain diversity and possible variation in disease severity. These strains showed some regional and host-specific relatedness via Maximum Likelihood and further phylogenetic analysis via Maximum Parsimony showed that these strains were closely related to R. solani AG1-1A (with 99-100% identity). Subsequent to strain verification and analysis, these isolates were used in the screening of twenty rice varieties for tolerance or resistance to sheath blight via mycelial plug method where both isolates (1801 and 1802) showed resistance or moderate resistance to Teqing, TETEP, and Jasmine 85. Isolate 1802 was more virulent based on the disease severity index values. This study also showed that the mycelial plug techniques were efficient in providing uniform inoculum and humidity for screening. In addition this study shows that the disease severity index is a better mode of scoring for resistance compared to lesion length. These findings will provide a solid basis for our future breeding and screening activities at the institution.
    Matched MeSH terms: Plant Diseases/microbiology*
  10. Cgl-SLT2 is required for appressorium formation, sporulation and pathogenicity in Colletotrichum gloeosporioides
    Yong HY, Bakar FD, Illias RM, Mahadi NM, Murad AM
    Braz J Microbiol, 2013 Dec;44(4):1241-50.
    PMID: 24688518
    The mitogen-activated protein (MAP) kinase pathways has been implicated in the pathogenicity of various pathogenic fungi and plays important roles in regulating pathogenicity-related morphogenesis. This work describes the isolation and characterization of MAP kinase gene, Cgl-SLT2, from Colletotrichum gloeosporioides. A DNA sequence, including 1,633 bp of Cgl-SLT2 open-reading frame and its promoter and terminator regions, was isolated via DNA walking and cloned. To analyze gene function, a gene disruption cassette containing hygromycin-resistant gene was constructed, and Cgl-SLT2 was inactivated via gene deletion. Analysis on Cgl-slt2 mutant revealed a defect in vegetative growth and sporulation as compared to the wild-type strain. When grown under nutrient-limiting conditions, hyperbranched hyphal morphology was observed in the mutant. Conidia induction for germination on rubber wax-coated hard surfaces revealed no differences in the percentage of conidial germination between the wild-type and Cgl-slt2 mutant. However, the percentage of appressorium formation in the mutant was greatly reduced. Bipolar germination in the mutant was higher than in the wild-type at 8-h post-induction. A pathogenicity assay revealed that the mutant was unable to infect either wounded or unwounded mangoes. These results suggest that the Cgl-SLT2 MAP kinase is required for C. gloeosporioides conidiation, polarized growth, appressorium formation and pathogenicity.
    Matched MeSH terms: Plant Diseases/microbiology
  11. Morphological and molecular characterization of Fusarium. solani and F. oxysporum associated with crown disease of oil palm
    Hafizi R, Salleh B, Latiffah Z
    Braz J Microbiol, 2013;44(3):959-68.
    PMID: 24516465
    Crown disease (CD) is infecting oil palm in the early stages of the crop development. Previous studies showed that Fusarium species were commonly associated with CD. However, the identity of the species has not been resolved. This study was carried out to identify and characterize through morphological approaches and to determine the genetic diversity of the Fusarium species. 51 isolates (39%) of Fusarium solani and 40 isolates (31%) of Fusarium oxysporum were recovered from oil palm with typical CD symptoms collected from nine states in Malaysia, together with samples from Padang and Medan, Indonesia. Based on morphological characteristics, isolates in both Fusarium species were classified into two distinct morphotypes; Morphotypes I and II. Molecular characterization based on IGS-RFLP analysis produced 27 haplotypes among the F. solani isolates and 33 haplotypes for F. oxysporum isolates, which indicated high levels of intraspecific variations. From UPGMA cluster analysis, the isolates in both Fusarium species were divided into two main clusters with the percentage of similarity from 87% to 100% for F. solani, and 89% to 100% for F. oxysporum isolates, which was in accordance with the Morphotypes I and II. The results of the present study indicated that F. solani and F. oxysporum associated with CD of oil palm in Malaysia and Indonesia were highly variable.
    Matched MeSH terms: Plant Diseases/microbiology*
  12. Fulltext Phytopathogenic organisms and mycotoxigenic fungi: Why do we control one and neglect the other? A biological control perspective in Malaysia
    Yazid SNE, Jinap S, Ismail SI, Magan N, Samsudin NIP
    Compr Rev Food Sci Food Saf, 2020 03;19(2):643-669.
    PMID: 33325175 DOI: 10.1111/1541-4337.12541
    In this review, we present the current information on development and applications of biological control against phytopathogenic organisms as well as mycotoxigenic fungi in Malaysia as part of the integrated pest management (IPM) programs in a collective effort to achieve food security. Although the biological control of phytopathogenic organisms of economically important crops is well established and widely practiced in Malaysia with considerable success, the same cannot be said for mycotoxigenic fungi. This is surprising because the year round hot and humid Malaysian tropical climate is very conducive for the colonization of mycotoxigenic fungi and the potential contamination with mycotoxins. This suggests that less focus has been made on the control of mycotoxigenic species in the genera Aspergillus, Fusarium, and Penicillium in Malaysia, despite the food security and health implications of exposure to the mycotoxins produced by these species. At present, there is limited research in Malaysia related to biological control of the key mycotoxins, especially aflatoxins, Fusarium-related mycotoxins, and ochratoxin A, in key food and feed chains. The expected threats of climate change, its impacts on both plant physiology and the proliferation of mycotoxigenic fungi, and the contamination of food and feed commodities with mycotoxins, including the discovery of masked mycotoxins, will pose significant new global challenges that will impact on mycotoxin management strategies in food and feed crops worldwide. Future research, especially in Malaysia, should urgently focus on these challenges to develop IPM strategies that include biological control for minimizing mycotoxins in economically important food and feed chains for the benefit of ensuring food safety and food security under climate change scenarios.
    Matched MeSH terms: Plant Diseases/microbiology*
  13. Phenotypic screening and molecular analysis of blast resistance in fragrant rice for marker assisted selection
    Khan MA, Sen PP, Bhuiyan R, Kabir E, Chowdhury AK, Fukuta Y, et al.
    C. R. Biol., 2014 May;337(5):318-24.
    PMID: 24841958 DOI: 10.1016/j.crvi.2014.02.007
    Experiments were conducted to identify blast-resistant fragrant genotypes for the development of a durable blast-resistant rice variety during years 2012-2013. The results indicate that out of 140 test materials including 114 fragrant germplasms, 25 differential varieties (DVs) harbouring 23 blast-resistant genes, only 16 fragrant rice germplasms showed comparatively better performance against a virulent isolate of blast disease. The reaction pattern of single-spore isolate of Magnaporthe oryzae to differential varieties showed that Pish, Pi9, Pita-2 and Pita are the effective blast-resistant genes against the tested blast isolates in Bangladesh. The DNA markers profiles of selected 16 rice germplasms indicated that genotype Chinigura contained Pish, Pi9 and Pita genes; on the other hand, both BRRI dhan50 and Bawaibhog contained Pish and Pita genes in their genetic background. Genotypes Jirakatari, BR5, and Gopalbhog possessed Pish gene, while Uknimodhu, Deshikatari, Radhunipagol, Kalijira (3), Chinikanai each contained the Pita gene only. There are some materials that did not contain any target gene(s) in their genetic background, but proved resistant in pathogenicity tests. This information provided valuable genetic information for breeders to develop durable blast-resistant fragrant or aromatic rice varieties in Bangladesh.
    Matched MeSH terms: Plant Diseases/microbiology*
  14. Microsatellite and minisatellite markers based DNA fingerprinting and genetic diversity of blast and ufra resistant genotypes
    Latif MA, Rafii Yusop M, Motiur Rahman M, Bashar Talukdar MR
    C. R. Biol., 2011 Apr;334(4):282-9.
    PMID: 21513897 DOI: 10.1016/j.crvi.2011.02.003
    A total of 78 alleles and 29 loci were detected from nine microsatellite and three minisatellite markers, respectively across 26 blast and ufra disease resistant genotypes. For blast resistant genotypes, the Polymorphic Information Content (PIC) values ranged from 0.280 to 0.726 and RM21 was considered as the best marker. PIC values ranged from 0.5953 to 0.8296 for ufra resistant genotypes and RM23 was the best marker for characterization of ufra resistant genotypes. The genetic similarity analysis using UPGMA clustering generated nine clusters with coefficient of 0.66 for blast resistant genotypes while five genetic clusters with similarity coefficient of 0.42 for ufra resistant genotypes. In order to develop resistant varieties of two major diseases of rice, hybridisation should be made using the parents, BR29 and NJ70507, BR36 and NJ70507 for blast, while BR11 and Aokazi, BR3 and Aokazi, Rayda and BR3 and Rayda and BR11 for ufra.
    Matched MeSH terms: Plant Diseases/microbiology
  15. Current advance methods for the identification of blast resistance genes in rice
    Tanweer FA, Rafii MY, Sijam K, Rahim HA, Ahmed F, Latif MA
    C. R. Biol., 2015 May;338(5):321-34.
    PMID: 25843222 DOI: 10.1016/j.crvi.2015.03.001
    Rice blast caused by Magnaporthe oryzae is one of the most devastating diseases of rice around the world and crop losses due to blast are considerably high. Many blast resistant rice varieties have been developed by classical plant breeding and adopted by farmers in various rice-growing countries. However, the variability in the pathogenicity of the blast fungus according to environment made blast disease a major concern for farmers, which remains a threat to the rice industry. With the utilization of molecular techniques, plant breeders have improved rice production systems and minimized yield losses. In this article, we have summarized the current advanced molecular techniques used for controlling blast disease. With the advent of new technologies like marker-assisted selection, molecular mapping, map-based cloning, marker-assisted backcrossing and allele mining, breeders have identified more than 100 Pi loci and 350 QTL in rice genome responsible for blast disease. These Pi genes and QTLs can be introgressed into a blast-susceptible cultivar through marker-assisted backcross breeding. These molecular techniques provide timesaving, environment friendly and labour-cost-saving ways to control blast disease. The knowledge of host-plant interactions in the frame of blast disease will lead to develop resistant varieties in the future.
    Matched MeSH terms: Plant Diseases/microbiology*
  16. Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativa L.)
    Ashkani S, Yusop MR, Shabanimofrad M, Azady A, Ghasemzadeh A, Azizi P, et al.
    Curr Issues Mol Biol, 2015;17:57-73.
    PMID: 25706446
    Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.
    Matched MeSH terms: Plant Diseases/microbiology*
  17. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses
    Mohd-Assaad N, McDonald BA, Croll D
    Environ Microbiol, 2019 08;21(8):2677-2695.
    PMID: 30838748 DOI: 10.1111/1462-2920.14583
    Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.
    Matched MeSH terms: Plant Diseases/microbiology
  18. Genome sequence of Kosakonia radicincitans UMEnt01/12, a bacterium associated with bacterial wilt diseased banana plant
    Suhaimi NS, Yap KP, Ajam N, Thong KL
    FEMS Microbiol Lett, 2014 Sep;358(1):11-3.
    PMID: 25047976
    Kosakonia radicincitans (formerly known as Enterobacter radicincitans), an endophytic bacterium was isolated from the symptomatic tissues of bacterial wilt diseased banana (Musa spp.) plant in Malaysia. The total genome size of K. radicincitans UMEnt01/12 is 5 783 769 bp with 5463 coding sequences (CDS), 75 tRNAs, and 9 rRNAs. The annotated draft genome of the K. radicincitans UMEnt01/12 strain might shed light on its role as a bacterial wilt-associated bacterium.
    Matched MeSH terms: Plant Diseases/microbiology
  19. Epinecidin-1, a marine antifungal peptide, inhibits Botrytis cinerea and delays gray mold in postharvest peaches
    Fan L, Wei Y, Chen Y, Jiang S, Xu F, Zhang C, et al.
    Food Chem, 2023 Mar 01;403:134419.
    PMID: 36191421 DOI: 10.1016/j.foodchem.2022.134419
    This study investigatedthe mechanism of epinecidin-1 against Botrytis cinerea, in vitro, and its effectiveness at inhibiting gray mold on postharvest peach fruit. We found that in vitro, epinecidin-1 had significantly greater antifungal activity against B. cinerea than either clavanin-A or mytimycin, two other marine derived antimicrobial peptides that we tested. Its antifungal activity was heat-resistant (15 min at 40-100 °C) and tolerant to lower concentrations of cations (<100 mM Na+, K+; <10 mM Ca2+). Epinecidin-1 interacted directly with B. cinerea genomic DNA, and that in mycelia, epinecidin-1 exposure induced accumulation of intracellular ROS and increased the permeability of cell membranes resulting in leakage of nucleic acids and aberrant cell morphology. Meanwhile, 200 μM of epinecidin-1 had a significant inhibitory effect on gray mold injected into peach fruit. These results suggested that epinecidin-1 showed promise as a potential method for controlling postharvest gray mold in peaches.
    Matched MeSH terms: Plant Diseases/microbiology
  20. Molecular phylogeny of Rigidoporus microporus isolates associated with white rot disease of rubber trees (Hevea brasiliensis)
    Oghenekaro AO, Miettinen O, Omorusi VI, Evueh GA, Farid MA, Gazis R, et al.
    Fungal Biol, 2014 May-Jun;118(5-6):495-506.
    PMID: 24863478 DOI: 10.1016/j.funbio.2014.04.001
    Rigidoporus microporus (Polyporales, Basidiomycota) syn. Rigidoporus lignosus is the most destructive root pathogen of rubber plantations distributed in tropical and sub-tropical regions. Our primary objective was to characterize Nigerian isolates from rubber tree and compare them with other West African, Southeast Asian and American isolates. To characterize the 20 isolates from Nigeria, we used sequence data of the nuclear ribosomal DNA ITS and LSU, β-tubulin and translation elongation factor 1-α (tef1) gene sequences. Altogether, 40 isolates of R. microporus were included in the analyses. Isolates from Africa, Asia and South/Central America formed three distinctive clades corresponding to at least three species. No phylogeographic pattern was detected among R. microporus collected from West and Central African rubber plantations suggesting continuous gene flow among these populations. Our molecular phylogenetic analysis suggests the presence of two distinctive species associated with the white rot disease. Phylogenetic analyses placed R. microporus in the Hymenochaetales in the vicinity of Oxyporus. This is the first study to characterize R. microporus isolates from Nigeria through molecular phylogenetic techniques, and also the first to compare isolates from rubber plantations in Africa and Asia.
    Matched MeSH terms: Plant Diseases/microbiology*
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