Analysis of <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i> Population in Mali and Burkina Faso Reveals a High Level of Genetic and Pathogenic Diversity

Wonni, Issa; Cottyn, Bart; Detemmerman, Liselot; Dao, Sounkalo; Ouédraogo, Léonard; Sarra, S.; Tekete, C.; Poussier, Stéphane; Corral, Rene; Triplett, Lindsay R.; Koïta, Ousmane; Koebnik, Ralf; Leach, Jan E.; Szurek, Boris; Maes, Martine

doi:10.1094/phyto-07-13-0213-r

Cited by 43 publications

(52 citation statements)

References 47 publications

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“…Finally, MLST and RFLP analyses focusing on a large collection of X. oryzae pv. oryzicola strains revealed a high level of genetic diversity among African strains (35).…”

mentioning

confidence: 99%

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

Poulin

Grygiel

Magne

et al. 2015

Appl Environ Microbiol

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dMultilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales. M olecular typing of pathogen populations is essential to gain insight into their genetic diversity and population dynamics in order to elaborate efficient strategies for disease control (1, 2). In agricultural systems, pests are ideally controlled by integrated approaches, including eradication or treatment of diseased organisms and planting of resistant varieties. However, the durability of resistance can be challenged if pathogen diversity is significant. Importantly, gene flow between pathogen populations can facilitate the breakdown of resistance in crop plants (3). Hence, efficient and precise molecular-typing tools for identifying strains and differentiating among related bacterial isolates are essential for microevolutionary reconstruction as a population genetics approach for integrated plant protection.Rice, one of the major crops worldwide, is affected by two bacterial diseases that are caused by strains of Xanthomonas oryzae, bacterial leaf blight (BLB), caused by X. oryzae pv. oryzae, and bacterial leaf streak (BLS), caused by X. oryzae pv. oryzicola. Collectively, these two diseases cause significant yield losses in tropical and temperate rice-growing areas. X. oryzae pv. oryzae colonizes xylem vessels upon entry into the vascular system. X. oryzae pv. oryzicola infects the plant via natural openings and colonizes the mesophyll (4). Genomes of members of both pathovars have been sequenced; however, the determinants of tissue specificity are still largely unknown (5, 6). While X. oryzae pv. oryzicola has been shown to be seedborne and seed transmitted (7,8), the evidenc...

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“…Finally, MLST and RFLP analyses focusing on a large collection of X. oryzae pv. oryzicola strains revealed a high level of genetic diversity among African strains (35).…”

mentioning

confidence: 99%

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

Poulin

Grygiel

Magne

et al. 2015

Appl Environ Microbiol

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“…Seed-borne dissemination of X. oryzae pv. oryzicola is a problem in parts of Asia and, presumably, in Africa (4). While clean seed and quarantine programs are prevalent in Asia, these have not yet been developed in Africa.…”

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confidence: 99%

“…oryzae and X. oryzae pv. oryzicola from field-collected leaf samples (4) and from seed samples (International Rice Research Institute Seed Health Unit, personal communication). However, the adoption of these primers for field-level surveys or for routine screens of seed samples by quarantine officials has been limited largely due to the high costs and requirements for sophisticated laboratories to perform the available diagnostic assays.…”

mentioning

confidence: 99%

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

Lang

Langlois

Nguyen

et al. 2014

Appl Environ Microbiol

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dMolecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 10 4 to 10 5 CFU ml ؊1 , while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens.

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“…oryzae) isolated from rice plants with BLB in 2003 by Gonzalez et al (2007) and BAI105 (X. oryzae pv. oryzicola) isolated from BLS symptoms in 2012 by Wonni et al (2014). These strains belong to major group representing the genetic diversity in West Africa (Poulin et al, 2015).…”

Section: Bacterial Culturesmentioning

confidence: 99%

“…BLS was first reported in Burkina Faso in 2009 by Wonni et al (2011). The disease is present in all major rice production areas and it is becoming a threat to rice production (Wonni et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Antibacterial activity of extracts of three aromatic plants from Burkina Faso against rice pathogen, Xanthomanas oryzae

Wonni¹,

Ouédraogo²,

Ouédraogo³

et al. 2016

Afr. J. Microbiol. Res.

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Plant extracts can have powerful antibacterial activity and may be used as biological control against important plant pathogens. This study assessed effect of extracts of Cymbopogon citratus, Eucalyptus camaldulensis and Mentha piperita against two pathovars of Xanthomonas oryzae attacking rice. Both in vitro and in vivo approaches were used for different strains of X. oryzae originating from Burkina Faso. The three essential oils (EOs) have antibacterial activity in vitro test (agar diffusion method), but, EO from C. citratus at 1:5 dilution (v/v) resulted in the highest inhibition (over 30 mm of inhibition zone) against X. oryzae pv. oryzae and X. oryzae pv. oryzicola. However, they reduced significantly rice seed germination and induced herbicide effects on rice leaves. On the other hand, aqueous extracts from C. citratus stimulated bacterial growth, while extracts from E. camaldulensis had an inhibitory effect (28 mm of inhibition zone at 3:10 dilution, w/v). Therefore, the characterization of active compounds will determine one or more compound(s) involved in the antibacterial activity.

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Analysis of Xanthomonas oryzae pv. oryzicola Population in Mali and Burkina Faso Reveals a High Level of Genetic and Pathogenic Diversity

Cited by 43 publications

References 47 publications

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

Antibacterial activity of extracts of three aromatic plants from Burkina Faso against rice pathogen, Xanthomanas oryzae

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